user manual

Typhoon
User’s Guide v3.0
for Microsoft Windows

um 375-635
Amplify, Cy, Ettan, ECF, ECL Plus, FluorSep, ImageQuant, Typhoon, Vistra Green,
and Wonder Wedge are trademarks of Amersham Biosciences Limited.
Amersham and Amersham Biosciences are trademarks of Amersham plc.
BODIPY, NanoOrange, PicoGreen, RiboGreen, SYBR, SYPRO, Texas Red, and
TOTO are trademarks of Molecular Probes, Inc.
Coomassie is a trademark of Imperial Chemical Industries, Ltd.
Ethernet is a trademark of Xerox Corporation.
Kapton and Mylar are trademarks of DuPont Corporation.
Kodak is a trademark of Eastman Kodak Company.
Microsoft and Windows are trademarks of Microsoft Corporation.
SeaKem is a trademark of FMC Corporation.
Tween is a trademark of ICI Americas Inc.
Whatman is a trademark of Whatman International Ltd.

The Typhoon instrument is covered by one or more of the following US patents:

5,528,050; 5,459,325; and foreign equivalents.
The Typhoon system is for research purposes only. It is not intended or approved
for diagnosis of disease in humans or animals.
All goods and services are sold subject to the terms and conditions of sale of the
company within the Amersham Biosciences group that supplies them. A copy of
these terms and conditions is available on request.

Amersham Biosciences UK Limited Amersham Place Little Chalfont

Buckinghamshire England HP7 9NA
Amersham Biosciences AB SE-751 84 Uppsala Sweden
Amersham Biosciences Corp 800 Centennial Avenue PO Box 1327 Piscataway
NJ 08855 USA
Amersham Biosciences Europe GmbH Munzinger Strasse 9 D-79111 Freiburg
Germany
Amersham Biosciences (SV) Corp 928 East Arques Avenue Sunnyvale
CA 94085-4520 USA

© Amersham Biosciences 2002—All rights reserved

May 2002
Table of contents

Preface
About this guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Related publications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiii
Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Special safety text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Trained operator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Assumptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Safety standards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xiv
Site requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Electrical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Environmental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv
Blue laser module (Typhoon 9400 and 9410 only) . . . . . . . . . . xv
Assistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xvi

Part one Introduction

Chapter 1 Introduction to the Typhoon system
1.1 Typhoon system hardware components . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.2 Models of the Typhoon instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
1.3 Optional accessories for the Typhoon system . . . . . . . . . . . . . . . . . . . 1-3
1.4 Software components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
1.5 How the Typhoon system works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
1.6 Typhoon scan acquisition modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
1.7 Before you begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7

Chapter 2 Safety
2.1 General safety precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2 Typhoon system serial numbers and safety labels . . . . . . . . . . . . . . . . 2-2
2.3 Electrical safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.3.1 Electrical connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6

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2.3.2 Operating voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7

2.3.3 Fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.3.4 High-voltage hazard and precautions . . . . . . . . . . . . . . . . . . 2-8
2.4 Laser light safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.4.1 Laser-light warning labels . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.4.2 Instrument safety precautions . . . . . . . . . . . . . . . . . . . . . . . 2-12
2.4.3 Blue laser module safety precautions
(Typhoon 9400 and 9410 only) . . . . . . . . . . . . . . . . . . . . . . 2-13
2.5 Pinching and general warnings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
2.6 Hazardous materials precautions . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14

Chapter 3 Getting started

3.1 Turning on and warming up the Typhoon instrument . . . . . . . . . . . . . 3-1
3.2 Turning on the computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.3 Starting the Scanner Control software . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.4 About the Typhoon instrument states . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.5 Workflows for scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.5.1 Workflow for storage phosphor scanning . . . . . . . . . . . . . . . . 3-5
3.5.2 Workflow for fluorescence scanning . . . . . . . . . . . . . . . . . . . . 3-7
3.5.3 Workflow for chemiluminescence scanning . . . . . . . . . . . . . . 3-8
3.6 Customizing the scan area for multiple samples . . . . . . . . . . . . . . . 3-10
3.6.1 Creating a new tray definition . . . . . . . . . . . . . . . . . . . . . . . 3-11
3.6.2 Copying a tray definition . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13
3.6.3 Deleting a tray definition . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15
3.7 Saving the scan parameters as a template . . . . . . . . . . . . . . . . . . . . 3-15
3.7.1 Creating a new template . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-15
3.7.2 Selecting a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
3.7.3 Modifying a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-18
3.7.4 Selecting a template to use as a default . . . . . . . . . . . . . . . . 3-19
3.7.5 Deleting a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-19
3.8 Closing the Scanner Control software . . . . . . . . . . . . . . . . . . . . . . . 3-20
3.9 Turning off the Typhoon instrument . . . . . . . . . . . . . . . . . . . . . . . . . 3-20
3.10 Turning off the computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-21

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Part two Scanning in the storage phosphor mode

Chapter 4 About storage phosphor screen autoradiography
4.1 How the Typhoon instrument generates an image . . . . . . . . . . . . . . . . 4-1
4.1.1 Storing the image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.1.2 Releasing the stored information . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.2 Advantages of storage phosphor screen autoradiography . . . . . . . . . . 4-2
4.3 Types of storage phosphor screens . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
4.3.1 General-purpose storage phosphor screen . . . . . . . . . . . . . . . 4-4
4.3.2 Low-energy storage phosphor screen . . . . . . . . . . . . . . . . . . . 4-4
4.3.3 Tritium storage phosphor screen . . . . . . . . . . . . . . . . . . . . . . 4-4

Chapter 5 Preparing for storage phosphor screen autoradiography

5.1 Guidelines for preparing the samples . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.1.1 General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.1.2 Using wet gels with the storage phosphor screen . . . . . . . . . . 5-2
5.1.3 Using radioactive standards . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
5.2 Preparing the storage phosphor screen for exposure. . . . . . . . . . . . . . 5-3
5.2.1 Protecting the storage phosphor screen . . . . . . . . . . . . . . . . . 5-3
5.2.2 Verifying that the storage phosphor screen is clean . . . . . . . . . 5-4
5.2.3 Cleaning the storage phosphor screen. . . . . . . . . . . . . . . . . . . 5-4
5.2.4 Erasing the storage phosphor screen . . . . . . . . . . . . . . . . . . . 5-4
5.3 Guidelines for exposing the storage phosphor screen . . . . . . . . . . . . . 5-6
5.4 Guidelines for placing the sample in the exposure cassette . . . . . . . . 5-7
5.5 Placing the sample in the exposure cassette. . . . . . . . . . . . . . . . . . . . 5-8
5.6 Placing the screen in the exposure cassette . . . . . . . . . . . . . . . . . . . . 5-9
5.6.1 Positioning a mounted screen . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
5.6.2 Positioning an unmounted screen . . . . . . . . . . . . . . . . . . . . 5-11
5.7 Exposing the storage phosphor screen . . . . . . . . . . . . . . . . . . . . . . . 5-12

Chapter 6 Scanning a storage phosphor screen

6.1 Verifying the Typhoon instrument is clean . . . . . . . . . . . . . . . . . . . . . . 6-1
6.1.1 Checking for radioactive contamination . . . . . . . . . . . . . . . . . 6-1
6.1.2 Cleaning the glass platen . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.1.3 Cleaning the sample lid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3

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6.2 Removing the exposed screen from the exposure cassette . . . . . . . . . 6-4
6.3 Loading the storage phosphor screen into the instrument. . . . . . . . . . 6-5
6.4 Checking the instrument state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
6.5 Selecting the scan parameters in the Scanner Control window . . . . . . 6-7
6.5.1 Selecting a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
6.5.2 Selecting the storage phosphor scan acquisition mode . . . . . 6-8
6.5.3 Selecting the scan area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
6.5.4 Selecting the sample orientation . . . . . . . . . . . . . . . . . . . . . 6-10
6.5.5 Selecting how to scan the sample. . . . . . . . . . . . . . . . . . . . . 6-13
6.5.6 Selecting the pixel size . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-13
6.5.7 Selecting the image analysis software . . . . . . . . . . . . . . . . . 6-14
6.5.8 Entering user comments (optional). . . . . . . . . . . . . . . . . . . . 6-15
6.6 Starting a scan and checking the progress . . . . . . . . . . . . . . . . . . . 6-15
6.6.1 Starting a scan of a single sample or scan area . . . . . . . . . . 6-15
6.6.2 Starting a scan of multiple samples and scan areas . . . . . . . 6-16
6.6.3 The initialization process . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-18
6.6.4 Canceling the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-18
6.6.5 Monitoring the scan progress . . . . . . . . . . . . . . . . . . . . . . . . 6-19
6.6.6 Viewing the preview image for saturated data . . . . . . . . . . . 6-20
6.6.7 Completing the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-20
6.7 Cleaning up after the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-21
6.8 Storing the storage phosphor screen . . . . . . . . . . . . . . . . . . . . . . . . 6-21
6.9 Analyzing or preprocessing the scanned image . . . . . . . . . . . . . . . . 6-22

Part three Scanning in the fluorescence mode

Chapter 7 About fluorescence scanning
7.1 How fluorescence works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.2 Advantages of direct fluorescence . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.3 Emission filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
7.4 Beamsplitters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.5 Linking fluorescent scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.6 Multilabel (multichannel) experiments . . . . . . . . . . . . . . . . . . . . . . . 7-6
7.7 Common fluorochromes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6

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Chapter 8 Setting up for fluorescence scanning

8.1 Preparing the sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.1.1 General guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.1.2 Label guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2
8.1.3 Low-fluorescence sample support guidelines . . . . . . . . . . . . . 8-3
8.2 Cleaning the glass platen and sample lid . . . . . . . . . . . . . . . . . . . . . . 8-5
8.2.1 Cleaning the glass platen . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
8.2.2 Cleaning the sample lid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-7
8.3 Determining how to position the sample . . . . . . . . . . . . . . . . . . . . . . . 8-7
8.3.1 Determining the sample orientation. . . . . . . . . . . . . . . . . . . . . 8-7
8.3.2 Determining the sample placement. . . . . . . . . . . . . . . . . . . . . 8-8
8.4 Placing a gel or membrane on the glass platen . . . . . . . . . . . . . . . . . 8-9
8.5 Placing a sandwich gel on the glass platen . . . . . . . . . . . . . . . . . . . 8-10
8.6 Placing the slide holder and microarray slides on the glass platen
(Typhoon 8610, 9210, and 9410 only) . . . . . . . . . . . . . . . . . . . . . . 8-13
8.7 Placing the gel alignment guide and multiple sandwich gels
on the glass platen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-17
8.7.1 Loading one or two large sandwich gels . . . . . . . . . . . . . . . . 8-17
8.7.2 Loading one through four small sandwich gels . . . . . . . . . . . 8-19

Chapter 9 Scanning a fluorescent sample

9.1 Checking the instrument state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1
9.2 Selecting the scan parameters in the Scanner Control window . . . . . . 9-2
9.2.1 Selecting a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-2
9.2.2 Selecting the fluorescence scan acquisition mode . . . . . . . . . 9-3
9.2.3 Selecting the scan area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.2.4 Selecting the sample orientation . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.2.5 Selecting the Press Sample parameter . . . . . . . . . . . . . . . . . . 9-6
9.2.6 Selecting the pixel size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6
9.2.7 Selecting the focal plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-8
9.2.8 Selecting the image analysis software . . . . . . . . . . . . . . . . . . . 9-8
9.2.9 Entering user comments (optional) . . . . . . . . . . . . . . . . . . . . . 9-8
9.3 Using the Setup window to select the fluorescence parameters. . . . . . 9-9
9.3.1 Displaying the Fluorescence Setup window . . . . . . . . . . . . . . . 9-9
9.3.2 Selecting the number of scans . . . . . . . . . . . . . . . . . . . . . . . . 9-9

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9.3.3 Selecting the emission filter . . . . . . . . . . . . . . . . . . . . . . . . . 9-10

9.3.4 Setting the PMT voltage . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-10
9.3.5 Selecting the laser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-11
9.3.6 Selecting the sensitivity (limit of detection) . . . . . . . . . . . . . . 9-12
9.3.7 Linking scans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-12
9.3.8 Closing the Fluorescence Setup window . . . . . . . . . . . . . . . 9-17
9.4 Starting a scan and checking the progress . . . . . . . . . . . . . . . . . . . 9-17
9.4.1 Starting a single-channel scan of
a single sample or single scan area . . . . . . . . . . . . . . . . . . . 9-18
9.4.2 Starting a multichannel (non-DIGE) scan of
multiple samples and multiple scan areas . . . . . . . . . . . . . . 9-19
9.4.3 Starting a multichannel (DIGE) scan of
multiple samples and multiple scan areas . . . . . . . . . . . . . . 9-21
9.4.4 The initialization process . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-24
9.4.5 Canceling the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-24
9.4.6 Monitoring the scan progress . . . . . . . . . . . . . . . . . . . . . . . . 9-24
9.4.7 Viewing the preview image for saturated data . . . . . . . . . . . 9-26
9.4.8 Completing the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-26
9.5 Removing the sample from the Typhoon instrument. . . . . . . . . . . . . 9-27
9.6 Cleaning the glass platen and sample lid . . . . . . . . . . . . . . . . . . . . . 9-27
9.7 Analyzing or preprocessing the scanned image . . . . . . . . . . . . . . . . 9-27

Part four Scanning in the chemiluminescence mode

Chapter 10 About chemiluminescence scanning
10.1 How chemiluminescence works. . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.2 Advantages of chemiluminescence . . . . . . . . . . . . . . . . . . . . . . . . . 10-1
10.3 How to optimize the chemiluminescent experiment . . . . . . . . . . . . . 10-2
10.4 Beamsplitters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3

Chapter 11 Setting up for chemiluminescence scanning

11.1 Preparing the sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1
11.2 Cleaning the glass platen and sample lid . . . . . . . . . . . . . . . . . . . . . 11-1
11.2.1 Cleaning the glass platen . . . . . . . . . . . . . . . . . . . . . . . . . . 11-1
11.2.2 Cleaning the sample lid . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-3

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11.3 Loading the sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11-3

11.3.1 Determining the sample orientation . . . . . . . . . . . . . . . . . . . 11-3
11.3.2 Determining the sample placement . . . . . . . . . . . . . . . . . . . 11-4
11.3.3 Placing a sample on the glass platen . . . . . . . . . . . . . . . . . . 11-5

Chapter 12 Scanning a chemiluminescent sample

12.1 Checking the instrument state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-1
12.2 Selecting the scan parameters in the Scanner Control window . . . . . 12-2
12.2.1 Selecting a template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-2
12.2.2 Selecting the chemiluminescence scan acquisition mode . . 12-3
12.2.3 Selecting the scan area . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-3
12.2.4 Selecting the sample orientation . . . . . . . . . . . . . . . . . . . . . 12-4
12.2.5 Selecting the Press Sample parameter . . . . . . . . . . . . . . . . 12-6
12.2.6 Selecting the pixel size . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-6
12.2.7 Selecting the focal plane . . . . . . . . . . . . . . . . . . . . . . . . . . 12-7
12.2.8 Selecting the image analysis software . . . . . . . . . . . . . . . . . 12-8
12.2.9 Entering user comments (optional) . . . . . . . . . . . . . . . . . . . 12-8
12.3 Using the Setup window to select the chemiluminescence
parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-8
12.3.1 Displaying the Chemiluminescence Setup window . . . . . . . . 12-9
12.3.2 Selecting the sensitivity (limit of detection) . . . . . . . . . . . . . 12-9
12.3.3 Selecting a beamsplitter for a multichannel scan . . . . . . . . 12-9
12.3.4 Setting the PMT voltage . . . . . . . . . . . . . . . . . . . . . . . . . . 12-10
12.3.5 Closing the Chemiluminescence Setup window . . . . . . . . . 12-11
12.4 Starting a scan and checking the progress . . . . . . . . . . . . . . . . . . . 12-11
12.4.1 Starting a single-channel scan of a single sample or
scan area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-12
12.4.2 Starting a multichannel (non-DIGE) scan of
multiple samples and scan areas. . . . . . . . . . . . . . . . . . . . 12-13
12.4.3 Starting a multichannel (DIGE) scan of
multiple samples and multiple scan areas . . . . . . . . . . . . . 12-15
12.4.4 The initialization process . . . . . . . . . . . . . . . . . . . . . . . . . 12-17
12.4.5 Canceling the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-17
12.4.6 Monitoring the scan progress . . . . . . . . . . . . . . . . . . . . . . 12-18
12.4.7 Viewing the preview image for saturated data . . . . . . . . . . 12-19
12.4.8 Completing the scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12-20

Typhoon User’s Guide ● ix

Table of contents

12.5 Removing the sample from the Typhoon instrument. . . . . . . . . . . . 12-20

12.6 Cleaning the glass platen and sample lid . . . . . . . . . . . . . . . . . . . . 12-20
12.7 Analyzing or preprocessing the scanned image . . . . . . . . . . . . . . . 12-20

Part five Maintaining the Typhoon system hardware

Chapter 13 Maintaining the Typhoon instrument
13.1 Starting the Typhoon Direct Instrument Access software. . . . . . . . . . 13-1
13.2 Selecting a laser shut-off time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-3
13.3 Changing the TCP/IP address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-4
13.4 Installing an optical filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-6
13.4.1 Moving the filter changer to the access door . . . . . . . . . . . 13-7
13.4.2 Accessing the filter changer . . . . . . . . . . . . . . . . . . . . . . . . 13-8
13.4.3 Inserting a new optical filter . . . . . . . . . . . . . . . . . . . . . . . 13-10
13.4.4 Closing the doors and replacing the front cover . . . . . . . . 13-12
13.4.5 Registering a new optical filter in Scanner Control . . . . . . 13-12
13.5 Removing an optical filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-13
13.6 Changing the definition of an optical filter . . . . . . . . . . . . . . . . . . . 13-16
13.7 Changing the fuses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13-17
13.8 Moving the Typhoon instrument . . . . . . . . . . . . . . . . . . . . . . . . . . 13-19
13.8.1 Determining a new location for the instrument . . . . . . . . . 13-19
13.8.2 Preparing to move the Typhoon instrument . . . . . . . . . . . 13-20
13.8.3 Completing the installation after the move . . . . . . . . . . . . 13-21

Chapter 14 Maintaining the Typhoon system accessories

14.1 Cleaning the Image Eraser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14-1
14.2 Changing the bulbs in the Image Eraser. . . . . . . . . . . . . . . . . . . . . . 14-2
14.3 Changing the fuses in the Image Eraser . . . . . . . . . . . . . . . . . . . . . 14-3
14.4 Cleaning and protecting the exposure cassettes . . . . . . . . . . . . . . . . 14-5
14.5 Cleaning and protecting the microarray slide holder
(Typhoon 8610, 9210, and 9410 only) . . . . . . . . . . . . . . . . . . . . . . 14-6
14.6 Cleaning and protecting the gel alignment guides . . . . . . . . . . . . . . 14-6

x ● Typhoon User’s Guide

 Table of contents

Part six Appendixes

Appendix A Troubleshooting
A.1 Power and communication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1
A.2 Scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
A.3 Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-5

Appendix B Quick reference for menus and windows

B.1 Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1
B.2 Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2

Appendix C Literature references

Glossary

Typhoon User’s Guide ● xi

Preface

About this guide

The Typhoon User’s Guide provides information on how to use the
Typhoon™ system to scan fluorescent samples, chemiluminescent samples,
and storage phosphor screens that have been exposed to radioactive
samples.

• Part one: Introduction—Describes the Typhoon instrument, the safety

information, and basic instructions for using the instrument and the
Scanner Control software.

• Part two: Scanning in the storage phosphor mode—Describes how to

use the Typhoon system to scan a storage phosphor screen.

• Part three: Scanning in the fluorescence mode—Describes how to use

the Typhoon system to scan a fluorescent sample.

• Part four: Scanning in the chemiluminescence mode—Describes how

to use the Typhoon system to scan a chemiluminescent sample.

• Part five: Maintaining the Typhoon system hardware—Describes how

to maintain the Typhoon instrument, Image Eraser, exposure cassettes,
microarray slide holder, and gel alignment guides.

• Part six: Appendixes—Provides troubleshooting and reference

information.

Related publications
In addition to the Typhoon User’s Guide and Typhoon Installation
Instructions, you should be familiar with the ImageQuant™ image analysis
software documentation.

Typhoon User’s Guide ● xiii

Preface

Safety
Chapter 2 in this guide provides important safety information that should be
used when operating the Typhoon system. Before using the Typhoon system,
read and understand the safety information thoroughly.

Special safety text

Make sure you follow the precautionary statements presented in this guide.

Warning Indicates a possibility of serious or fatal injury to the user or other persons if the
precautions or instructions are not observed.

Caution Indicates that damage to the instrument, loss of data, or invalid data could occur
if the user fails to comply with the advice given.

Important Highlights information that is critical for optimal performance of the system.

Note: Identifies items of general interest.

Trained operator
Warning The operator of the Typhoon system is assumed to be trained in the correct
operation of the system and the safety issues. Throughout the Typhoon User’s
Guide, the word “you” refers to this trained operator.

Assumptions
The software-related instructions in this user’s guide assume you have basic
computer skills. You should be familiar with the Microsoft™ Windows™
graphical user interface. You should also know how to use a mouse. If you
do not have these skills, refer to the Windows documentation or Help.

Safety standards
The Typhoon instrument complies with CE and other applicable standards.
For the latest CE conformity information, contact Technical Support. See
Assistance for contact information.

xiv ● Typhoon User’s Guide

 Site requirements

Site requirements
This section lists a summary of the site requirements for the Typhoon system.
For more information on site requirements, see section 13.8.1.

Electrical
The electrical currents listed below refer to the minimum required circuit
breaker size.

Instrument: 15 A 100–120 V~
10 A 220–240 V~
Blue laser module: 20 A 100–120 V~ (dedicated circuit)
13 A 220–240 V~ (dedicated circuit)
Line frequency: 50–60 Hz

Environmental
Temperature: 15–30 °C (59–86 ˚F)
Humidity: Noncondensing 10%–80% relative humidity

Instrument
Weight: 160 kg (350 lb)
Height: 48.26 cm (19 in)
Width: 118.11 cm (46.5 in)
Depth: 77.47 cm (30.5 in)

Blue laser module (Typhoon 9400 and 9410 only)

Weight: 29.5 kg (65 lb)
Height: 48.0 cm (18.9 in)
Width: 30 cm (11.8 in)
Depth: 78 cm (30.4 in)

A fan is built into the blue laser module. The fan exhausts the heat from
the blue laser module into the instrument room. The blue laser module
can dissipate over 2 kW (6 800 BTU/hr) of heat. To reduce heat buildup
in the instrument room, you can vent the exhaust into the ceiling space or
outside the building if local safety and building codes permit. For additional
information on attaching an exhaust hose, contact Technical Support. See
Assistance for contact information.

If you vent the exhaust into the ceiling space, make sure that your building
ventilation system can handle the heat energy that is vented. You should also
take into account that the Typhoon instrument, computer, and monitor can
dissipate approximately 900 W (3 000 BTU/hr) of heat energy.

Typhoon User’s Guide ● xv

Preface

Assistance
When calling for assistance, be prepared to supply the serial number of your
instrument. The serial number is located in the Scanner Information area
of the Scanner Control window and on the lower right side of the instrument
near the plug (figure 2-2). For contact by phone or fax, use one of the
telephone numbers below.

Asia Pacific Latin America

Tel: +852 2811 8693 Tel: +55 11 3667 5700
Fax: +852 2811 5251 Fax: +55 11 3667 87 99
Australasia Middle East and Africa
Tel: +61 2 9899 0999 Tel: +30 (1) 96 00 687
Fax: +61 2 9899 7511 Fax: +30 (1) 96 00 693
Austria Netherlands
Tel: 01 576 0616 22 Tel: 0165 580 410
Fax: 01 576 0616 27 Fax: 0165 580 401
Belgium Norway
Tel: 0800 73 888 Tel: 2318 5800
Fax: 03 272 1637 Fax: 2318 6800
Canada Portugal
Tel: +1 800 463 5800 Tel: 21 417 70 35
Fax: +1 800 567 1008 Fax: 21 417 31 84
Central, East, and Southeast Europe Russia & other C.I.S. & N.I.S.
Tel: +43 1 982 3826 Tel: +7 (095) 232 0250, 956 1137
Fax: +43 1 985 8327 Fax: +7 (095) 230 6377
Denmark Southeast Asia
Tel: 45 16 2400 Tel: +60 3 8024 2080
Fax: 45 16 2424 Fax: +60 3 8024 2090
Finland & Baltics Spain
Tel: +358 (0)9 512 39 40 Tel: 93 594 49 50
Fax: +358 (0)9 512 17 10 Fax: 93 594 49 55
France Sweden
Tel: 01 69 35 67 00 Tel: 018 612 1900
Fax: 01 69 41 96 77 Fax: 018 612 1910
Germany Switzerland
Tel: 0761 4903 291 Tel: 01 802 81 50
Fax: 0761 4903 405 Fax: 01 802 81 51
Italy UK
Tel: 02 27322 1 Tel: 0800 616928
Fax: 02 27302 212 Fax: 0800 616927
Japan USA
Tel: +81 3 5331 9336 Tel: +1 800 526 3593
Fax: +81 3 5331 9370 Fax: +1 877 295 8102

Web site
[Link]

xvi ● Typhoon User’s Guide

Part one

Introduction
Chapter 1 Introduction to the
Typhoon system

The Typhoon instrument is a variable-mode imager that produces digital

images of radioactive, fluorescent, or chemiluminescent samples. The
Typhoon system consists of an instrument, instrument control software,
and a variety of accessories. Several models of the Typhoon instrument are
available. This chapter introduces you to the Typhoon system and contains
the following topics:

• Typhoon system hardware components (section 1.1)

• Models of the Typhoon instrument (section 1.2)
• Optional accessories for the Typhoon system (section 1.3)
• Software components (section 1.4)
• How the Typhoon system works (section 1.5)
• Typhoon scan acquisition modes (section 1.6)
• Before you begin (section 1.7)

1.1 Typhoon system hardware components

The Typhoon system includes the following hardware components (figure 1-1):

• Typhoon instrument—Scans exposed storage phosphor screens, fluorescent

samples, and chemiluminescent samples.

• (Typhoon 9400 and 9410 only) Blue laser module—Contains the blue laser
and the power supply for the laser.

In addition, the Typhoon system includes Ethernet™ cables, power cords,

and tools.

Typhoon User’s Guide ● p1-1

Part one Introduction

(a) Typhoon instrument

(b) Blue laser module

(Typhoon 9400 and 9410 only)

Figure 1-1. Components of the Typhoon system: (a) the Typhoon instrument and
(b) the blue laser module (Typhoon 9400 and 9410 only).

p1-2 ● Typhoon User’s Guide

 Chapter 1 Introduction to the Typhoon system

1.2 Models of the Typhoon instrument

Table 1-1 describes the various models of the Typhoon instrument.

Table 1-1. Available models of the Typhoon instrument

Model name Description

Typhoon 9200 Basic instrument model that contains a red and green laser.

Typhoon 9210 Typhoon 9200 with the added capability of scanning using
a 10-µm pixel size.

Typhoon 9400 Typhoon 9200 with an external blue laser.

Typhoon 9410 Typhoon 9400 with the added capability of scanning using
a 10-µm pixel size.

Typhoon 8610 A Typhoon 8600 instrument that has been updated with the
new Scanner Control v2.0 or higher software and has the same
features as a Typhoon 9210.

1.3 Optional accessories for the Typhoon system

The following are the optional accessories (figure 1-2) that can be used with
the Typhoon system:

• Image Eraser—Erases storage phosphor screens for reuse.

• Storage phosphor screen—Collects and temporarily stores an image from

a radioactive sample. Several types and sizes of storage phosphor screens
are available (section 4.3).

• Exposure cassette—Holds the storage phosphor screen in a light-tight

environment. Several types and sizes of exposure cassettes are available
(section 4.3).

• (Typhoon 8610, 9210, and 9410 only) Microarray slide holder—Allows

you to scan one or two microarray slides (section 8.6).

• Gel alignment guides—Allows you to scan gels created using difference gel
electrophoresis (DIGE). You can place two large gels (Ettan™ DALT) or
four smaller gels (DIGE SE600) so that they can be read in the same scan
(section 8.7).

Typhoon User’s Guide ● p1-3

Part one Introduction

(a) Optional accessories for storage phosphor scanning

1 1

A B C D E F G H I J K L M N O P Q R
2 2

3 3

4 4

5 5

6 6

7 7

8 8

Image Eraser 9 9

10 10

11 11

12 12

13 13

14 14

15 15

16 16

17 17

18 Exposure Cassette 18

19 19

20 20

21 21
A B C D E F G H I J K L M N O P Q R

22 22

Exposure cassette for mounted screens Mounted storage phosphor screen

1
A B C D E F G H I J
2

6
Time Erase

10 Exposure Cassette

Image Eraser 11

12

13

Exposure cassette for unmounted screens Unmounted storage phosphor screen

(b) Optional accessories for fluorescence scanning

Gripper
(4 included in kit)

Microarray slide holder

SE 600 gel alignment guide

Slide restraint Ettan DALT gel alignment guide

Figure 1-2. Optional accessories for the Typhoon system: (a) storage phosphor accessories and
(b) fluorescence accessories.

p1-4 ● Typhoon User’s Guide

 Chapter 1 Introduction to the Typhoon system

1.4 Software components

You install the Scanner Control software on a computer running the Microsoft
Windows operating system. The computer connects to the Typhoon instrument
using an Ethernet connection.

In addition, you must install the Internet Explorer browser software to

use the Typhoon Direct Instrument Access software. You use the Typhoon
Direct Instrument Access software to perform several maintenance procedures,
which are described in chapter 13.

1.5 How the Typhoon system works

The Typhoon instrument scans and processes samples in the following
sequence:

1. You place an exposed storage phosphor screen, a fluorescent sample,

or a chemiluminescent sample onto the glass platen of the instrument.

2. You use the Scanner Control software to select parameters that are
appropriate for the type of sample you are scanning and to start
the scan.

3. The screen or sample emits light in the following ways:

• When the red (633 nm) laser illuminates each one-pixel section of
an exposed storage phosphor screen, the phosphor emits blue light.

• When the green laser (532 nm) or the red laser (633 nm) illuminates
each one-pixel section of a fluorescent sample, the fluorochrome
emits light with a characteristic spectrum.

• (Typhoon 9400 and 9410 only) When the blue laser (457 nm or
488 nm) illuminates each one-pixel section of a fluorescent sample,
the fluorochrome emits light with a characteristic spectrum.

• The chemiluminescent sample emits light with a characteristic

spectrum.

4. The optical system collects the emitted light. If you select one or more
emission filters, the optical system directs the light through the selected
emission filter(s). Each filter allows only the emitted light within the filter’s
bandwidth to pass through to the designated photomultiplier tube (PMT).

5. The PMT converts the light to an electric current, which varies with the
intensity of the light collected by the PMT. The analog signal from the
PMT is then converted into digital information, and the digital information
is stored on the hard disk of the computer.

Typhoon User’s Guide ● p1-5

Part one Introduction

After the scan, you use the ImageQuant (or equivalent) software to map
the digital information to the appropriate pixel location on the monitor
and produce an accurate image of the original sample. You can use
ImageQuant to quantitate the variations in the signal. The level of
signal is proportional to the amount of radioactivity, fluorescence,
or chemiluminescence present in the sample.

1.6 Typhoon scan acquisition modes

The Typhoon instrument scans samples using the following scan
acquisition modes:

• Storage phosphor mode—Creates images from samples labeled with

radioisotopes using storage phosphor technology. Part two of this
guide describes how to use the Typhoon system to scan in the storage
phosphor mode.

• Fluorescence mode—Creates images from samples labeled with fluorescent

dyes. The available excitation modes are—

- Red-excited mode—Creates an image from a sample labeled or

stained with a fluorescent dye that is excited at 633 nm.

- Green-excited mode—Creates an image from a sample labeled or

stained with a fluorescent dye that is excited at 532 nm.

- (Typhoon 9400 and 9410 only) Blue-excited mode—Creates an image

from a sample labeled or stained with a fluorescent dye that is excited
at either 457 nm or 488 nm. You select the desired wavelength.

- Multilabel-excited mode—Creates an image from a sample labeled with

up to four fluorescent dyes. The dyes can be excited by one or more
of the four laser wavelengths.

Part three of this guide describes how to use the Typhoon system to scan
using each of the fluorescence modes.

• Chemiluminescence mode—Creates images from chemiluminescent

samples. Part four of this guide describes how to use the Typhoon system
to scan in the chemiluminescence mode.

p1-6 ● Typhoon User’s Guide

 Chapter 1 Introduction to the Typhoon system

1.7 Before you begin

Before using the Typhoon system, you should become familiar with—

• Chapter 2—Important safety information.

• Chapter 3—Basic operational instructions for using the Typhoon

instrument and the Scanner Control software.

• Part five—Maintenance information for the Typhoon instrument and

accessories.

Typhoon User’s Guide ● p1-7

 Chapter 2 Safety

The Typhoon system is designed for safe operation. It is imperative that

you follow the precautions in this chapter. The topics in this chapter are—

• General safety precautions (section 2.1)

• Typhoon system serial numbers and safety labels (section 2.2)
• Electrical safety (section 2.3)
• Laser light safety (section 2.4)
• Pinching and general warnings (section 2.5)
• Hazardous materials precautions (section 2.6)

2.1 General safety precautions

Warnings The operator of the Typhoon system is assumed to be trained in the correct
operation of the system and the safety issues. Throughout the Typhoon User’s
Guide, the word “you” refers to this trained operator.

Using controls, making adjustments, or performing procedures other than

those specified in the Typhoon User’s Guide can result in hazardous exposure
to laser light, high voltage, or moving parts. Exposure to these hazards can
cause severe injury or death.

When using the Typhoon system, follow the precautions below—

• Make sure the instrument has at least 5 cm (2 in) of clearance on both

sides and behind it. Make sure you have 1.2 m (4 ft) of clearance above
the instrument. If the temperature of the room containing the instrument
exceeds 30 °C (86 °F), increase the clearance on all sides by 2.5 cm (1 in).

Caution Blocking the airflow to the Typhoon instrument can cause the instrument to
overheat, which can impact the instrument’s performance.

• (Typhoon 9400 and 9410 only) Make sure the blue laser module has at
least 7.5 cm (3 in) of clearance behind it and 20 cm (8 in) of clearance
on both sides. If the blue laser module is located under a laboratory bench,
you must provide 30 cm (12 in) of clearance on both sides of the module.
If the temperature in the room exceeds 30 °C (86 °F), you should use an
external fan to vent the exhaust out of the room.

Caution (Typhoon 9400 and 9410 only) If you do not use an external exhaust fan, the top of
the blue laser module can get very warm. Do not place any temperature-sensitive
materials on top of the blue laser module.

Typhoon User’s Guide ● p2-1

Part one Introduction

• If the cover or doors of the Typhoon instrument become damaged, do not

continue to use the instrument.

• (Typhoon 9400 and 9410 only) If the fiber-optic cable becomes damaged,
do not continue to use the instrument.

• If the Image Eraser becomes damaged, do not continue to use the eraser.

• If you add or remove optical (emission) filters, make sure you follow the
procedures in section 13.4. Because the instrument is turned on during
the procedures, you might be exposed to moving parts in the instrument.

• To protect your warranty, the Typhoon instrument and Image Eraser

should be serviced only by an authorized Technical Support representative.

If you have problems with the instrument or eraser, contact Technical Support
immediately. See Assistance in the preface for contact information.

2.2 Typhoon system serial numbers and

safety labels
When you call Technical Support, you will be asked for the serial number
of your instrument. The serial number of the Typhoon instrument is shown
in the Scanner Information area of the Scanner Control window (figure 2-1a)
and on the serial number certification label (figure 2-1b). The serial number
certification label also displays the model number of the instrument and the
Center for Devices and Radiological Health (CDRH) compliance information.
The label is located on the lower right side of the Typhoon instrument near
the plug. Figure 2-2 shows the locations of all the labels on the Typhoon
instrument.

(Typhoon 9400 and 9410 only) If you have a Typhoon 9400 or 9410
instrument, see figure 2-1c for the serial number label for the blue laser
module, and figure 2-3 for the locations of all the labels on the blue
laser module. The serial number certification label also displays the model
number of the blue laser module and the CDRH compliance information.

The serial number certification label (figure 2-1d) of the Image Eraser is
located on the lower right side of the eraser near the plug. Figure 2-4 shows
the locations of all the labels on the Image Eraser.

If any label becomes illegible or is missing for any reason, contact Technical
Support for a free replacement label. See Assistance in the preface for
contact information. While waiting for the replacement label, copy the figure
containing the missing label and attach the copy of the label to the instrument.

p2-2 ● Typhoon User’s Guide

 Chapter 2 Safety

(a) Serial number location in the Scanner Control window

Serial number of
Typhoon instrument

(b) Typhoon instrument

928 E. Arques Ave.

Sunnyvale, CA 94085-4520
9200 9210 or 9400 9410
/ /

(c) Blue laser module (d) Image Eraser

928 E. Arques Ave. 928 E. Arques Ave.

Sunnyvale, CA 94085-4520 Sunnyvale, CA 94086
MODEL # TYPHOON BLUE LASER MODULE
MODEL # 810-UNV T†V R h e i n l a nd

100-240V~ 2.2KVA 50/60Hz

100-120/220-240V 1.5A 50/60Hz gepr Ÿ fte
Sicherheit

SERIAL #
y

MONTH
Dec
Nov
r

Aug
Feb

Sep
Jun
Apr
Jan

Oct
Ma
Ma

Jul

MANUFACTURED
YEAR
02
01

07
99
00

05
06
97
98
96

03
04

T 1.5A/250V B1

Figure 2-1. The locations of the serial numbers. (a) The instrument serial number location in the Scanner Control
window. (b) The serial number labels for the Typhoon instrument. (c) The serial number label for the blue laser
module (Typhoon 9400 and 9410 only). (d) The serial number label for the Image Eraser.

Typhoon User’s Guide ● p2-3

Part one Introduction

Front view 1 Serial number

Safety interlock circuit 3
9200 9210

5 /

6
2
2 Laser-light eye exposure warning

Front cover CAUTION

Laser Radiation
when open.
AVOID EXPOSURE
TO BEAM.

Right side view

3 Laser-light direct exposure warning

1 9
4 Fuse
4 7

Top view
(with sample lid open)
5 General warning

8 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

I
K

I
6 High voltage
H H

G G

F F

E E

D D

C C

2 B

A
B

A
2
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

7 Laser-light international compliance

3 CLASS 1
LASER PRODUCT
Per IEC-825

Back view
8 Pinching hazard

5 9 Patents
6
2 US Patent 5,528,050
US Patent 5,091,652
Additional Patents Pending

Figure 2-2. Location of important labels on the Typhoon instrument.

p2-4 ● Typhoon User’s Guide

 Chapter 2 Safety

Front view 1 Serial number

928 E. Arques Ave.
Sunnyvale, CA 94085-4520
MODEL # TYPHOON BLUE LASER MODULE
100-240V~ 2.2KVA 50/60Hz

2 Laser-light direct exposure warning

3 Laser-light eye exposure warning

Back view
CAUTION
Laser Radiation
when open.
AVOID EXPOSURE
TO BEAM.

4 4 General warning
5
6

5 High voltage
Side view

6 Laser-light international compliance

2 CLASS 1
LASER PRODUCT
1 3 Per IEC-825

Figure 2-3. Location of important labels on the blue laser module (Typhoon 9400 and 9410 only).

Typhoon User’s Guide ● p2-5

Part one Introduction

Right side view 1 US flag

MADE IN U.S.A.

2 High-voltage warning

3 Serial number

928 E. Arques Ave.

Sunnyvale, CA 94086

MODEL # 810-UNV TÜV R h e i nl and

100-120/220-240V 1.5A 50/60Hz

2
geprüfte
Sicherheit

SERIAL #

y
MONTH

N ov
Dec
r

Aug
Feb

Sep
Jun
Apr
Jan

Oct
Ma
Ma

Jul
MANUFACTURED
YEAR

01
02

07
99
00

05
06
96
97
98

03
04
T 1.5A/250V B1

Figure 2-4. Location of important labels on the Image Eraser.

2.3 Electrical safety

You should follow the electrical safety information provided in this section to
make sure you are operating the Typhoon instrument and Image Eraser safely.

2.3.1 Electrical connections

Before you turn on the Typhoon instrument, Image Eraser, or computer,
check that the instrument, blue laser module (Typhoon 9400 and 9410 only),
eraser, computer, and monitor are plugged into surge protectors, and the
surge protectors are plugged in and turned on.

Note: The currents listed below refer to the minimum required circuit
breaker size.

Plug the Typhoon instrument into a grounded circuit capable of delivering

at least—

• 15 A for a 100–120 V~ power source

• 10 A for a 200–240 V~ power source

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 Chapter 2 Safety

(Typhoon 9400 and 9410 only) Plug the blue laser module into a grounded
circuit capable of delivering at least—

• 20 A for a 100–120 V~ power source (dedicated circuit)

• 13 A for a 200–240 V~ power source (dedicated circuit)

Plug the Image Eraser into a grounded circuit capable of delivering

at least—

• 15 A for a 100–120 V~ power source

• 10 A for a 200–240 V~ power source

Do not use circuits shared by equipment containing compressors, such as

refrigerators and centrifuges. Make sure power cords are in good condition
and are not frayed.

2.3.2 Operating voltage

When you turn on the Typhoon instrument, the instrument automatically
switches to the correct operating voltage. The Image Eraser does not
automatically switch to the correct operating voltage. You must manually
select the correct voltage (section 14.3).

Caution Before turning on the Image Eraser, make sure that the correct operating voltage
appears in the fuse window. Using the wrong voltage can severely damage the
eraser.

2.3.3 Fuses
Both the Typhoon instrument and the Image Eraser contain user-replaceable
fuses.

• On the Typhoon instrument—The fuse holder is on the lower right side

of the Typhoon instrument and contains two 5A, 250V ( , T5A, 250V)
slow-acting fuses. The fuse label contains the fuse specifications
(figure 2-5). The fuse holder accepts both 0.25-in by 1.25-in English
fuses (designated 3AG fuses) and 5-mm by 20-mm metric fuses.

• On the Image Eraser—The fuse holder is on the lower right side of

the Image Eraser and contains two 1.5A, 250V ( , T1.5A, 250V)
slow-acting fuses. The fuse holder accepts both 0.25-in by 1.25-in English
fuses (designated 3AG fuses) and 5-mm by 20-mm metric fuses.

(Typhoon 9400 and 9410 only) The blue laser module does not contain
any user-replaceable fuses. If the blue laser module does not turn on, check
the power cord and the communications cable. If the problem is not the
connections, contact Technical Support.

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Part one Introduction

250V

Figure 2-5. The fuse label on the Typhoon instrument.

To change the fuses on the Typhoon instrument, follow the instructions in

section 13.7. To change the fuses on the Image Eraser, follow the instructions
in section 14.3.

Warning If you need to change the fuses in the instrument or eraser, turn off the
instrument or eraser and disconnect the power cord. If a fuse requires repeated
replacement, the instrument or eraser could have an electrical problem. Do not
use a malfunctioning instrument or eraser. You could expose yourself to electrical
shock. Contact Technical Support. See Assistance in the preface for contact
information.

2.3.4 High-voltage hazard and precautions

Inside the Typhoon instrument, blue laser module (Typhoon 9400 and 9410
only), Image Eraser, computer, and monitor are high-voltage electronics.

Typhoon instrument
In general, you do not need to access the interior of the Typhoon instrument.
However, to install or remove an optical (emission) filter, you must remove the
front cover while the instrument is turned on. If you need to install or remove
emission filters, make sure you follow the procedures in section 13.4.

Warning Do not remove the front cover of the instrument unless you are installing
or removing optical (emission) filters. There are no other user-serviceable
components inside. When you change the optical filter selection, you
must leave the Typhoon instrument turned on. After you remove the front cover
of the Typhoon instrument and open the access and filter doors, make sure
you follow the procedures in section 13.4 to avoid injury.

When using the Typhoon instrument, follow the precautions below—

• Always plug the power cord into a grounded outlet.

• Before changing a fuse, always turn off the power and unplug the
instrument. Follow the instructions in section 13.7.

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 Chapter 2 Safety

• If the covers become damaged, do not use the instrument. Contact

Technical Support for repair. See Assistance in the preface for contact
information.

• If fuses must be replaced repeatedly, do not use the instrument. Contact

Technical Support for repair.

Figure 2-6 displays the high-voltage warning label on the Typhoon instrument.
See figure 2-2 for the location of the label.

Figure 2-6. High-voltage warning label.

Blue laser module (Typhoon 9400 and 9410 only)

You do not need to access the interior of the blue laser module. The module
has no user-serviceable parts or user-replaceable fuses.

Warning Do not remove the covers of the blue laser module. You could be exposed to
high voltages.

When using the Typhoon 9400 or 9410 instrument, follow the precautions
below—

• Always plug the power cord of the blue laser module into a grounded
outlet (dedicated circuit).

• If the covers of the blue laser module become damaged, do not use the
instrument. Contact Technical Support for repair. See Assistance in
the preface for contact information.

Figure 2-6 displays the high-voltage warning label on the blue laser module.
See figure 2-2 for the location of the label.

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Part one Introduction

Image Eraser
Warning Because the Image Eraser uses high voltage, you must disconnect the power cord
from the eraser before performing any maintenance task.

Figure 2-7 displays the high-voltage hazard label on the Image Eraser. See
figure 2-4 for the location of the label.

Figure 2-7. High-voltage hazard label on the Image Eraser.

Caution Disconnect power before servicing.

Attention Couper le courant avant l’entretien.

Warnung Vor der wartung vom netz trennen.

When using the Image Eraser, follow the precautions below—

• Always plug the power cord into a grounded outlet.

• Before cleaning the Image Eraser, always turn off the power and unplug the
eraser. Follow the instructions in section 14.1.

• Before changing a bulb, always turn off the power and unplug the eraser.
Follow the instructions in section 14.2.

• When changing a bulb, do not remove covers other than the front diffuser
panel. There are no user-serviceable parts inside.

• Before changing a fuse, always turn off the power and unplug the eraser.
Follow the instructions in section 14.3.

• If the covers become damaged, do not use the eraser. Contact Technical
Support for repair. See Assistance in the preface for contact information.

• If fuses must be replaced repeatedly, do not use the eraser. Contact

Technical Support for repair.

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 Chapter 2 Safety

Computer and monitor

See the manufacturer’s computer and monitor precautions before opening
the computer or monitor.

2.4 Laser light safety

Warning Using controls, making adjustments, or performing procedures other than those
specified herein can result in hazardous laser light exposure.
The Typhoon instrument is a Class I laser instrument that houses two
Class IIIB lasers inside the instrument. Under the specified operating
procedures, the instrument does not allow operator exposure to laser light.
The lasers, with power of 10–20 mW, are accessible in the interior of the
instrument.
(Typhoon 9400 and 9410 only) The blue laser module contains one
Class IIIB laser. The blue laser, with power at 30 mW, is accessible in the
interior of the module.
The safety interlocks (figure 2-2) in the Typhoon instrument are designed to
prevent you from being exposed to the laser beams. If you open the sample
lid while the scanner is in operation, the laser shutter closes and blocks the
light from the lasers.
Warning Do not attempt to defeat the safety interlocks on the sample lid or try to gain
access to the interior of the instrument through any other opening. Exposure to
laser light can cause injury. For example, viewing the laser light directly can
cause blindness.

2.4.1 Laser-light warning labels

The labels shown in figure 2-8 warn of exposure to laser light. The locations
of the labels are shown in figures 2-2 and 2-3.

CAUTION
CLASS 1 Laser Radiation
LASER PRODUCT when open.

Per IEC-825 AVOID EXPOSURE

TO BEAM.

International compliance Eye exposure Direct exposure

Figure 2-8. Laser-light warning labels.

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Part one Introduction

Caution Danger—Laser radiation when open and interlock defeated. Avoid direct exposure
to beam.
Vorsicht Gefahr—Laserstrahlung, wenn offen und Verriegelung ausgeschaltet. Direkte
bestrahlung vermeiden.
Attention Danger—L’ouverture du couvercle entraîne une exposition au rayonnement laser si
le dispositif de verrouillage a été mis hors service. Éviter toute exposition directe
au faisceau.

2.4.2 Instrument safety precautions

Warning Caution—Use of controls or adjustments or performance of procedures other than
those specified herein can result in hazardous radiation exposure.
The Typhoon instrument has been designed to protect you from the laser beam
emissions during normal operation. Nevertheless, laser power of 10–30 mW
can be accessed from within the interior of the instrument.
The Typhoon instrument contains a red laser and a green laser. The output
of the red visible laser is specified at a maximum of 10 mW at 633 nm in a
diverging beam. The output of the green visible laser is specified at a maximum
of 20 mW at 532 nm in a diverging beam.
When using the Typhoon instrument, follow the precautions below—
• Do not remove the front cover (figure 2-2) of the Typhoon instrument
except to install or remove optical (emission) filters. There are no other
user-serviceable components inside, and you can be exposed to laser light.
• Do not defeat the safety interlocks of the sample lid (figure 2-2). The safety
interlocks are designed to protect you from exposure to the laser light. If
you lift the sample lid during a scan, the safety interlocks signal the laser
shutters to close and block the light from the lasers.
• Do not continue to use the instrument—
- If a cover or the sample lid becomes damaged and the instrument is
no longer light tight.
- If fuses must be replaced repeatedly.
Contact Technical Support immediately to arrange for repair. See
Assistance in the preface for contact information.
To protect your warranty and for proper operation, your Typhoon
instrument should be serviced only by an authorized Technical Support
representative. If the instrument is not working correctly, contact Technical
Support. See Assistance in the preface for contact information.

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2.4.3 Blue laser module safety precautions

(Typhoon 9400 and 9410 only)
The blue laser module contains the blue laser and the power supply for the
blue laser. The fiber-optic cable that connects the instrument and the blue laser
module transmits the output of the blue visible laser at a maximum of 30 mW
at wavelengths from 457 nm to 488 nm in a diverging beam. The cable must
be connected by an authorized Service Support engineer. See Assistance in the
preface for contact information.

Caution The core of the fiber-optic cable is protected by a flexible metal sheath, but you
still must take precautions to protect the cable from damage.

To protect the cable from damage—

• Position the fiber-optic cable away from the high-traffic areas in the
laboratory.

• Do not coil the cable into a circle with a diameter smaller than
15.24 cm (6 in).

• Make sure you do not stretch the cable.

• If the fiber-optic cable becomes damaged, do not continue to use the

instrument. Contact Technical Support. See Assistance in the preface for
contact information.

2.5 Pinching and general warnings

A pinching hazard label (figure 2-9a) appears near the support bars for the
sample lid. This label warns you that your fingers could be pinched if the
sample lid closes unexpectedly.

A general warning label (figure 2-9b) appears on the back of the Typhoon
instrument near the power supply fan exhaust. This label warns you that
you could be exposed to the moving parts when the instrument is running.

A general warning label appears near the access door to the optical filter
changer. This label warns you that you could be exposed to moving parts if
you open the access door while the instrument is running.

(Typhoon 9400 and 9410 only) A general warning label appears on the back
of the blue laser module near the power supply fan exhaust. This label warns
you that you could be exposed to the moving parts when the module is
running.

Figure 2-2 shows the locations of pinching hazard and general warning labels.

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Part one Introduction

(a) The pinching hazard label (b) The general warning label

Figure 2-9. (a) The pinching hazard label. (b) The general warning label.

2.6 Hazardous materials precautions

Some materials used to label samples can be hazardous. Use good laboratory
procedures and follow the manufacturer’s precautions when working with
these materials.

Before using the Typhoon system, become familiar with your laboratory’s
hazardous materials procedures.

Warning Amersham Biosciences is not responsible or liable for any damages or injuries
caused by or as a consequence of the use of any hazardous material.

Cautions Do not expose the Typhoon instrument and storage phosphor screen to volatile
organic solvents, such as methanol, chloroform, or acetone. Make sure thin-layer
chromatography (TLC) plates are completely dry. Always remove corrosive liquids
before loading the sample.

Do not use scintillants or enhancers on your sample. These compounds interfere

with the proper function of the storage phosphor screens.

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This chapter describes the procedures for using the Typhoon system.
The topics in this chapter are—
• Turning on and warming up the Typhoon instrument (section 3.1)
• Turning on the computer (section 3.2)
• Starting the Scanner Control software (section 3.3)
• About the Typhoon instrument states (section 3.4)
• Workflows for scanning (section 3.5)
• Customizing the scan area for multiple samples (section 3.6)
• Saving the scan parameters as a template (section 3.7)
• Closing the Scanner Control software (section 3.8)
• Turning off the Typhoon instrument (section 3.9)
• Turning off the computer (section 3.10)

3.1 Turning on and warming up the Typhoon

instrument
To turn on the Typhoon instrument, press the on/off switch on the lower
right side of the instrument (figure 3-1). The power indicator light on the front
of the instrument turns on and remains red during the self-test sequence, which
takes a few seconds. During the initialization, the instrument flashes the green
Power light for approximately 45 seconds. After initialization, the flashing
green light turns solid green.

Important After you turn on the Typhoon instrument, wait approximately 30 minutes for
the instrument to warm up before you start the first scan. Scanning before the
instrument is warmed up can affect the accuracy of the collected data.

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Typhoon 8610, 9200, and 9210 only

Typhoon instrument
(right side view)

Power indicator light

Front Back

On/off switch

Ethernet connection
to computer

Typhoon 9400 and 9410 only

Typhoon instrument
(right side view)

Power indicator light

Front Back

On/off switch

Ethernet connection
to computer
Laser control cable Fiber-optic cable

Cables to blue laser module

Blue laser module (front view)

Power indicator light

Figure 3-1. Right side views of the Typhoon instruments and the front of the blue laser module. Note: The laser
control cable and the fiber-optic cable are used on the Typhoon 9400 and 9410 only.

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(Typhoon 9400 and 9410 only) The blue laser module does not have a power
switch. When you start the Typhoon instrument, the blue laser module turns
on automatically. The Power light on the front of the blue laser module
turns green, and then the Connection light turns green, which indicates the
instrument is communicating with the blue laser module. The blue laser starts
running after the Typhoon instrument completes the self-test (approximately
1 minute), and then the Laser On light turns green.

3.2 Turning on the computer

So that the computer can communicate with the Typhoon instrument, the
instrument must be turned on first, and the power indicator light must be
solid green. Use the computer manufacturer’s instructions for turning on the
computer.

3.3 Starting the Scanner Control software

After the computer is turned on, log on to Windows. Locate and double-click
the Scanner Control shortcut icon on the desktop. (Alternatively, you can
start the Scanner Control software using the Start menu.) The Scanner Control
window appears (figure 3-2).

Instrument State area

Figure 3-2. The Scanner Control window.

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3.4 About the Typhoon instrument states

The Typhoon instrument can be in one of five states. The Scanner Control
window displays the current instrument state and an Initialize Scanner button
(figure 3-2).

The instrument states are—

• Warming Up—Scanner Control displays the Warming Up message for

5 minutes after you turn on the system or click the Initialize Scanner
button. During the 5 minutes, the Typhoon system stabilizes the lasers
and system components. However, complete warm-up takes 30 minutes
when you first turn on the instrument.

• Ready—The instrument is ready to scan. If you just turned on the

instrument, the Ready message appears after approximately 5 minutes.
However, for best performance, you should let the instrument warm up
for the full 30 minutes before scanning.

• Sleep—The instrument has not been used for the amount of time you
set using the Typhoon Direct Instrument Access software (section 13.2).
(Note: The default setting is 4 hours.) After the selected time elapses,
the lasers shut off and the Sleep message appears in the Scanner Control
window.

• Initialization—After you click the Scan button, the Initialization message

appears. The Initialization message remains displayed until the instrument
begins scanning. If the prior instrument state was Ready, the initialization
takes approximately 1 minute. If the prior instrument state was Sleep
or Warming Up, the initialization takes approximately 5 minutes.

• Scanning—The Scanning message appears while the instrument is scanning.

Note: If the Service message appears, the instrument requires servicing.

You should call Technical Support. See Assistance in the preface for contact
information.

While you are preparing the sample, you can click the Initialize Scanner button
to reset the sleep clock and bring the instrument to the Ready state. When
your sample is ready to scan, the instrument scans without delay. If the sample
is already in position on the glass platen, you can start the scan even if the
instrument is in the Sleep state. If this is the case, 5 minutes are added to the
initialization time to allow the lasers and other system components to stabilize
before the scan starts.

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3.5 Workflows for scanning

You can scan three types of samples on the Typhoon instrument:

• A storage phosphor screen that has been exposed to a radioactive sample

(section 3.5.1)

• A fluorescent sample (section 3.5.2)

• A chemiluminescent sample (section 3.5.3)

This section provides an overview of the workflow for each sample type and
indicates where in this user’s guide you should look for detailed information.

3.5.1 Workflow for storage phosphor scanning

Table 3-1 describes the workflow for storage phosphor scanning and lists the
sections in this user’s guide that contain the procedural steps for each task.

Table 3-1. Storage phosphor scanning workflow

Task Description Section

Preparing for storage phosphor screen autoradiography

1. Prepare the sample. Prepare a sample using a radioactive isotope that can be collected 5.1
by the general-purpose (GP), low-energy (LE), or tritium (TR) storage
phosphor screen. Use the laboratory procedures established for
the type of sample you are preparing. If you are preparing a wet gel,
wrap the gel in plastic wrap or polyester film before exposing it to
the GP screen. Do not use the LE or TR screens with a wet gel.

2. Prepare the storage Decontaminate (optional), clean, and erase the GP or LE screen. 5.2
phosphor screen. Erase the TR screen. Protect the Image Eraser from contamination
when erasing the TR screen.

3. Prepare the exposure Decontaminate (optional) and clean the exposure cassette. 14.4
cassette.

4. Place the sample Place the sample in the exposure cassette and note the grid 5.5
in the exposure coordinates where you placed the sample. If the sample is thick or
cassette. wet, do not use the exposure cassette. Instead, expose the sample
to the screen in a light-tight environment, such as a light-tight drawer.

5. Place the storage Place the screen on the sample. To avoid a double image of the 5.6
phosphor screen sample, do not reposition the screen after it has touched the sample.
on the sample.

6. Expose the storage Leave the screen in the exposure cassette (or light-tight drawer) until 5.7
phosphor screen the screen is exposed. To determine the length of exposure, consider
to the sample. a 2-hour exposure to the screen to be equal to an overnight exposure
to basic x-ray film.

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Table 3-1. Storage phosphor scanning workflow (continued)

Task Description Section

Scanning the storage phosphor screen

1. Prepare the Decontaminate (optional) and clean the glass platen and sample lid 6.1
Typhoon instrument. of the Typhoon instrument.

2. Place the storage In subdued light, remove the storage phosphor screen from the 6.2, 6.3
phosphor screen exposure cassette (or light-tight drawer). Keep the screen face down
in the Typhoon while you move it from the cassette to the instrument. With the screen
instrument. still face down, position the screen on the glass platen so that the
A1 corner of the screen aligns with the A1 corner of the glass platen.
Close the sample lid.

3. Select scan In the Scanner Control window, select an existing template that contains 6.5
parameters using the scan parameters you want to use, or manually select the parameters.
the Scanner Control To manually select the parameters, make sure Storage Phosphor is
software. the selected scan acquisition mode. Choose whether you want best
sensitivity or best resolution. Select the grid area or tray template, pixel
size, sample orientation, and image analysis software. Note: In the storage
phosphor scan acquisition mode, selecting DIGE File Naming Format
has no effect on the way the software saves the image file.
Type comments you want saved with the image.

4. Start the scan. Click Scan. Type a file name and click Save. (If you are creating 6.6
multiple images, type a base file name and click Set, or click
Edit Sample File Name, type separate image file names, and click OK.
Optionally, click the Folder Browse button, select a new storage location,
and click Set. Click Scan to start the scan.) The ImageQuant Preview
window appears. While the Typhoon instrument scans the screen, an
image of the screen appears in the window.

5. Evaluate the results. During scanning, check the image in the ImageQuant Preview window 6.6.6
for saturation. Saturated pixels appear in red. If the image appears
saturated, you might need to expose a clean screen to the sample for
a shorter amount of time. If the image appears faint, you might need
to expose a clean screen for a longer amount of time. If the image
appears usable, continue with the next scan. If you are scanning another
screen, make sure you clean the glass platen and sample lid before
you place the next screen in the instrument.

6. Clean up after Remove the sample from the exposure cassette and dispose of the 6.7, 6.8
the scan. sample using the appropriate laboratory procedures. Decontaminate
and clean the Typhoon instrument, exposure cassette, and Image Eraser.
Decontaminate, clean, and erase a GP or LE screen. Erase a TR screen.
Store the screen in the exposure cassette or another dark place.

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3.5.2 Workflow for fluorescence scanning

Table 3-2 describes the workflow for fluorescence scanning and lists the
sections in this user’s guide that contain the procedural steps for each task.

Table 3-2. Fluorescence scanning workflow

Task Description Section

Preparing for fluorescence scanning

1. Prepare the sample. Prepare the sample using fluorescent dyes that are compatible with 8.1
the green (532 nm) or the red (633 nm) excitation mode.
(Typhoon 9400 and 9410 only) Prepare the sample using fluorescent
dyes that are compatible with the blue (457 nm or 488 nm) excitation
modes.

2. Prepare the Typhoon Decontaminate (optional) and clean the glass platen and sample lid 8.2
instrument. of the Typhoon instrument.

Scanning the fluorescent sample

1. Place the sample In subdued light, position the sample on the glass platen. Make 8.3
in the Typhoon a note of the grid coordinates on the glass platen. Close the
instrument. sample lid.

2. Select scan In the Scanner Control window, select an existing template that 9.2, 9.3
parameters using contains the scan parameters you want to use, or manually select
the Scanner Control the parameters. To manually select the parameters, make sure
software. Fluorescence is the selected scan acquisition mode. Then select
the grid area or tray template, pixel size, sample orientation,
press sample (optional), focal plane, DIGE file format naming for
multichannel images (optional), and image analysis software from
the Scanner Control window. Note: For a single-channel scan,
selecting DIGE File Naming Format has no effect on the way the
software saves the image file.
Then click Setup. In the Fluorescence Setup window, select the
emission filter, PMT voltage, laser, and sensitivity for each scan.
Optionally, you can select scans that can be linked. Click OK.
In the Scanner Control window, type comments you want saved
with the image.

3. Start the scan Click Scan. Type a file name and click Save. (If you are creating 9.4
multiple images, type a base file name and click Set, or click
Edit Sample File Name, type separate image file names, and click OK.
Optionally, click the Folder Browse button, select a new storage location,
and click Set. Click Scan to start the scan.) The ImageQuant Preview
window appears. While the Typhoon instrument scans the sample,
an image of the sample appears in the window.

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Table 3-2. Fluorescence scanning workflow (continued)

Task Description Section

4. Evaluate the results. During scanning, check the image in the ImageQuant Preview window 9.4.7
for saturation. Saturated pixels appear in red. If the image appears
saturated, you might need to repeat the scan. If the image appears
usable, continue with the next scan. If you are scanning another
sample, make sure you clean the glass platen and sample lid before
you place the next sample in the instrument.

5. Clean up after Remove the sample from the Typhoon instrument and dispose of 9.5, 9.6
the scan. the sample using the appropriate laboratory procedures. Clean the
Typhoon instrument.

3.5.3 Workflow for chemiluminescence scanning

Table 3-3 describes the workflow for chemiluminescence scanning and lists the
sections in this user’s guide that contain the procedural steps for each task.

Table 3-3. Chemiluminescence scanning workflow

Task Description Section

Preparing for chemiluminescence scanning

1. Prepare the sample. Prepare the sample using chemiluminescent enzyme substrate 11.1
systems. To create two images with a single scan, use substrates
that can be collected and separated using a beamsplitter.

2. Prepare the Typhoon Decontaminate (optional) and clean the glass platen and sample lid 11.2
instrument. of the Typhoon instrument.

Scanning the chemiluminescent sample

1. Place the sample In subdued light, position the sample on the glass platen. Make a note 11.3
in the Typhoon of the grid coordinates on the glass platen. Close the sample lid.
instrument.

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Table 3-3. Chemiluminescence scanning workflow (continued)

Task Description Section

2. Select scan In the Scanner Control window, select an existing template that 12.2,
parameters using contains the scan parameters you want to use, or manually select 12.3
the Scanner Control the parameters. To manually select the parameters, make sure
software. Chemiluminescence is the selected scan acquisition mode. Then
select the grid area, pixel size, sample orientation, press sample
(optional), focal plane, and image analysis software from the
Scanner Control window. Note: For a single-channel scan, selecting
the DIGE File Naming Format has no effect on the way the software
saves the image file. Then click Setup. In the Chemiluminescence Setup
window, select the sensitivity and PMT voltage for the scan. To create
two images with a single scan, select a beamsplitter and a second
PMT voltage. Click OK.
In the Scanner Control window, type comments you want saved with
the image.

3. Start the scan. Click Scan. Type a file name and click Save. (If you are creating 12.4
multiple images, type a base file name and click Set, or click
Edit Sample File Name, type separate image file names, and click OK.
Optionally, click the Folder Browse button, select a new storage location,
and cllck Set. Click Scan to start the scan.) The ImageQuant Preview
window appears. While the Typhoon instrument scans the sample,
an image of the sample appears in the window.

4. Evaluate the results. During scanning, check the image in the ImageQuant Preview window 12.4.7
for saturation. Saturated pixels appear in red. If the image appears
saturated, you might need to repeat the scan. If the image appears
usable, continue with the next scan. If you are scanning another
sample, make sure you clean the glass platen and sample lid before
you place the next sample in the instrument.

5. Clean up after Remove the sample from the Typhoon instrument and dispose of 12.5,
the scan. the sample using the appropriate laboratory procedures. Clean the 12.6
Typhoon instrument.

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Part one Introduction

3.6 Customizing the scan area for multiple samples

If you are scanning multiple samples (for example, DIGE gels), you can use the
Tray Editor window (figure 3-3) to create a separate scan area for each sample.
You provide a name for each scan area. When you select the scan parameters,
you choose the tray definition from the Tray list. When you scan the samples,
Scanner Control creates a separate image for each scan area defined in the
selected tray definition.

Figure 3-3. The Tray Editor window.

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 Chapter 3 Getting started

Scanner Control includes four predefined tray definitions. They are—

• User Select—Allows you to define one scan area by selecting the area
using the grid in the Scanner Control window.

• DIGE Ettan DALT—Contains two predefined scan areas for use with
the DIGE Ettan DALT gel alignment guide. In the Tray area in the
Scanner Control window, you can choose to scan one scan area or both.

• DIGE SE600—Contains four predefined scan areas for use with the
DIGE SE600 gel alignment guide. In the Tray area in the Scanner Control
window, you can choose to scan one through four scan areas.

• MicroArray 2 Slides—Contains two predefined scan areas for use with

the microarray slide holder. In the Tray area in the Scanner Control
window, you can choose to scan one scan area or both.

3.6.1 Creating a new tray definition

You define the new tray by selecting the sample dimensions and the sample
placement of each sample you want included in the tray definition.

To create a tray definition—

1. Choose Tray Editor from the Tray menu. The Tray Editor window appears
and displays the current list of defined trays (figure 3-3).

2. Click New Tray. The New Tray window appears (figure 3-4).

Figure 3-4. The New Tray window.

3. Type a name for the tray definition in the New Tray Name box and
click OK. A window appears and tells you to select New Sample to enter
the sample dimensions.

4. Click OK. The name you typed appears in the Tray list.

5. Click Save Current Tray to save the tray definition name.

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Part one Introduction

6. Click the new tray definition name in the Tray list.

7. Click New Sample. The New Sample Tray window appears (figure 3-5).

Figure 3-5. The New Sample Tray window.

8. Using the grid coordinates on the glass platen of the Typhoon instrument,
determine where the lower left and upper right corners will be for the
first sample.

9. Select the coordinates in the New Sample Tray window and click Add.

10. Repeat steps 7 through 9 for each sample you will be placing on the
glass platen. After you enter the last set of coordinates, click Close instead
of Add to close the New Sample Tray window and return to the Tray
Editor window. The Tray area displays the name of the tray you defined
and the number of samples you defined for the tray.

11. (Optional) If you want to change the coordinates for a sample, click
Edit Sample. The Edit Sample Tray window appears (figure 3-6). Change
the grid coordinates for the sample and click OK.

Figure 3-6. The Edit Sample Tray window.

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12. (Optional) If you want to delete the coordinates for a sample, click the
coordinates in the Sample list and then click Delete Sample. The sample
coordinates disappear from the list.

13. Click Preview. The Preview Sample Tray window appears and displays
the scan areas for the samples you defined (figure 3-7).

Figure 3-7. The Preview Sample Tray window.

14. Click Close to close the Preview Sample Tray window and return to the
Tray Editor window.

15. (Optional) To modify the grid coordinates for any scan area that you
incorrectly defined, repeat step 11.

16. Click Save Current Tray to save the tray configuration.

3.6.2 Copying a tray definition

You can copy a tray definition so that you can create a new tray definition.
To do this—

1. Choose Tray Editor from the Tray menu. The Tray Editor window appears
and displays the current list of defined trays (figure 3-3).

2. Click the tray definition that you want to copy.

3. Click Copy Tray. The Copy Tray window appears.

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Part one Introduction

Figure 3-8. The Copy Tray window.

4. Type a name for the new tray definition in the New Tray Name box and
click OK.

5. Click Save Current Tray to save the tray definition name.

6. Click the new tray definition name in the Tray list.

7. Modify the grid coordinates to match how you will place the samples on
the glass platen of the Typhoon instrument. You can—

- Change the coordinates for an existing sample—Click Edit Sample.

The Edit Sample Tray window appears (figure 3-6). Change the grid
coordinates for the sample and click OK.

- Delete the coordinates for an existing sample—Click the coordinates

in the Sample list, and then click Delete Sample. A window appears
asking you to confirm that you want to delete the coordinates.
Click Yes. The sample coordinates disappear from the list.

- Add a new set of coordinates—Click New Sample. The New Sample

Tray window appears (figure 3-5). Select the coordinates in the
New Sample Tray window and click Close.

8. Click Preview. The Preview Sample Tray window appears and displays
the scan areas for the samples you defined (figure 3-7).

9. Click Close to close the Preview Sample Tray window and return to the
Tray Editor.

10. (Optional) To modify the grid coordinates for any scan area that you
incorrectly defined, repeat step 7.

11. Click Save Current Tray to save the tray configuration.

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 Chapter 3 Getting started

3.6.3 Deleting a tray definition

You can delete a tray definition that you no longer need from the list in the
Tray Editor window (figure 3-3).

Important If you created a template that includes a tray definition as one of the scan
parameters, the software will not delete the tray definition until you modify
the template to remove the tray definition. For more information on modifying
templates, see section 3.7.3.

To delete a tray definition—

1. Click the name of the tray definition that you want to delete.

2. Click Delete Tray. A window appears asking you to confirm that you
want to delete the definition.

3. Click Yes. The software removes the definition from the Tray list.

3.7 Saving the scan parameters as a template

The Scanner Control software allows you to save the scan parameters you
use frequently as a uniquely named template. You use the template name
to retrieve the parameters and display them in the Scanner Control and
Setup windows.

Important When you create a template for the fluorescence acquisition mode, you select
an emission filter or filters from the filters installed in the Typhoon instrument
and, for a multichannel scan, a beamsplitter from the beamsplitters installed
in the Typhoon instrument. If you remove an emission filter or a beamsplitter
from the instrument, Scanner Control removes all the templates from the template
list that used the filter or beamsplitter. If you reinstall the filter or beamsplitter,
the templates reappear in the list.

3.7.1 Creating a new template

To create a template—

1. In the Setup area of the Scanner Control window (figure 3-9), select the
parameters you want saved with the template. Note that comments in
the User Comment box are not saved with the template.

For a description of the setup parameters, see section 3.6 (scan area
definitions for multiple samples), section 6.5 (storage phosphor),
section 9.2 (fluorescence), or section 12.2 (chemiluminescence).

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Part one Introduction

1. Select the scan area.

2. Select the scan
acquisition mode.
3. Select a tray
definition.
4. (Storage phosphor
only) Choose
best sensitivity or
best resolution.
5. Select the sample
orientation.
6. Select the pixel size.
7. Select the focal plane.

8. Select the image

analysis software.

Figure 3-9. Selecting parameters in the Setup area of the Scanner Control window.

2. (Storage phosphor only) Select whether you want to scan using the
Best Resolution or the Best Sensitivity. For more information on these
parameters, see section 6.5.5.

3. (Fluorescence and chemiluminescence only) Click the Setup button

and select the parameters in the Setup window (figure 3-10). For more
information on selecting parameters, see section 9.3 (fluorescence) or
section 12.3 (chemiluminescence).

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(a) Fluorescence Setup window

1. Select the 2. For each scan, select— 3. Link scans.

number of scans.

Emission filter PMT voltage Laser Sensitivity

4. Click OK.

(b) Chemiluminescence Setup window

1. Select sensitivity.

2. Select beamsplitter.
3. Select PMT voltage.

4. Click OK.

Figure 3-10. Selecting parameters in the (a) Fluorescence Setup window or (b) Chemiluminescence Setup
window.

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Part one Introduction

4. Choose Save As Template from the Templates menu. The Save As Template
window appears (figure 3-11).

Figure 3-11. The Save As Template window.

5. Type a new name for the template in the box. Note: Because the
Template list displays all the available templates, you might want to
label the templates by scan acquisition mode. For example, a template
for storage phosphor can be named TemplateName_Phos.

Important A template name can be a maximum of 32 characters, and you should type
an underscore instead of a space.

6. (Optional) If you want the template to become the new default,

select the Set as Default Template check box. Note: You can select the
original default template (system) supplied with the instrument from
the Templates menu.

7. Click OK. The template name appears above the grid area in the
Scanner Control window.

3.7.2 Selecting a template

If you want to use a different template, choose Load from the Templates
menu and then select the template name from the list.

3.7.3 Modifying a template

You can modify a template and use the modified parameters to scan a sample.
After you change a parameter, an asterisk appears next to the template name
to show that the parameters have been changed. If you want to use the original
unmodified parameters, select the template from the Load menu again. The
original parameters appear in the Scanner Control window.

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Scanner Control will not allow you to overwrite the existing parameter
values in the original template. If you want to save a modified template using
the same name, you must delete the old template (section 3.7.5). Next, select
the new parameters and save the template using the name of the template
you deleted.

3.7.4 Selecting a template to use as a default

If you use the same scan acquisition mode when scanning samples, you
can create a template using a standard set of parameters for that mode.
You can select the template as the default template to load when you start
the Scanner Control software. For example, if you typically scan fluorescently
labeled samples, set up the scan parameters for a fluorescent scan and save the
parameters as the default template. The next time you start Scanner Control,
the parameters appear in the Scanner Control window and the Fluorescence
Setup window.

To select a template to use as the default, choose Set Default/Load from the
Templates menu and select the template name from the list. The template name
and parameters appear in the Scanner Control window. Each time you start
the Scanner Control software, the parameters for the template you selected
as the default appear in the Scanner Control window. If the default template
uses the fluorescence or chemiluminescence scan acquisition mode, the
parameters also appear in the Setup window.

3.7.5 Deleting a template

If you want to delete a template, choose Delete from the Templates menu.
The Delete Template(s) window appears (figure 3-12). Select the template name
that you want to delete and click Delete.

Note: Because you cannot delete the template displayed in the Scanner Control
window, this template name does not appear in the list. To delete the template
in use, close the Delete Template(s) window, select a different template from
the Load list, and then choose Delete from the Templates menu again. You
should see the template name in the list.

To delete all the templates except the template displayed in the Scanner Control
window, click Select All and then click Delete.

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Part one Introduction

Figure 3-12. The Delete Template(s) window. Note: The Templates list does not
include the template currently displayed in the Scanner Control window.

3.8 Closing the Scanner Control software

Although it is not necessary, you can close the Scanner Control software
after you finish scanning.

Important Before installing or removing an emission filter, you must close the Scanner
Control software. See section 13.4 for more information on changing an
emission filter.

To close the Scanner Control software, choose Exit from the File menu.

3.9 Turning off the Typhoon instrument

Caution Do not turn off the Typhoon instrument while the instrument is scanning. Doing
so can damage the internal mechanism of the instrument.

To turn off the Typhoon instrument, press the on/off switch on the lower
right side of the Typhoon instrument (figure 3-1) to the off position. The power
indicator light turns off. You can continue to use the computer after you turn
off the Typhoon instrument.

(Typhoon 9400 and 9410 only) The blue laser module does not have a power
switch. After you turn off the Typhoon instrument, the Connection light on
the blue laser module turns off. After 10 seconds, the Laser On light turns off.
The laser cooling fan continues to run for approximately 3 minutes to allow
the blue laser to cool down. Approximately 5 minutes after you turn off the
Typhoon instrument, the blue laser module turns off, and the Power light
turns off.

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 Chapter 3 Getting started

3.10 Turning off the computer

Before you turn off the computer, you should save and close all open files,
and then close all open applications. Use the manufacturer’s instructions
for shutting down the operating system and turning off the computer.

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Part two

Scanning in the storage phosphor

mode
Chapter 4 About storage phosphor
screen autoradiography

This chapter describes storage phosphor screen autoradiography. The topics

in this chapter are—
• How the Typhoon instrument generates an image (section 4.1)
• Advantages of storage phosphor screen autoradiography (section 4.2)
• Types of storage phosphor screens (section 4.3)

4.1 How the Typhoon instrument generates an

image
Generating an image from a storage phosphor screen is a two-step process.
First, you expose an erased storage phosphor screen to the radioactively
labeled sample using an exposure cassette. An imprint of the sample is created
on the screen from the radiation energy that is trapped in the crystal lattice
of the screen.
Next, you use the Typhoon instrument to scan the exposed storage phosphor
screen. The instrument captures the stored information on the screen in the
form of a digital image.

4.1.1 Storing the image

The storage phosphor screens are composed of fine crystals of BaFBr:Eu+2
in an organic binder. When the screen is exposed to a radioactive sample, the
radiation excites Eu+2 electrons to a state in which the electrons move easily
within the phosphor. During the exposure process, Eu+2 is oxidized to Eu+3,
-
and BaFBr is reduced to BaFBr . These ions remain oxidized and reduced after
the screen is removed from the sample. In this way, the phosphor stores the
energy from ionizing radiation. Most of the energy (from ionizing radiation)
stored on the screen remains for as long as several weeks.

4.1.2 Releasing the stored information

Storage phosphors release stored energy when stimulated by light of
appropriate wavelengths. The Typhoon instrument scans the screen using a
-
red light at 633 nm. The charged BaFBr complexes in the screen absorb light
in this range (figure 4-1), freeing electrons and reducing the Eu+3 to Eu+2*
(an Eu+2 ion with an electron in an excited state). As the excited electron falls

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Part two Scanning in the storage phosphor mode

to the ground state, it releases energy in the form of blue light. The Typhoon
instrument uses a band-pass filter, which allows the light near the peak
emissions of the screen to pass through to the detector. The detector collects
and measures the light. The emitted light intensity is proportional to the
radioactivity in the sample.

Emission Absorption
390 ~600 Excitation
633

300 400 500 600 700 800

Wavelength (nm)

Figure 4-1. Emission (— —) and absorption (---) spectra of the activated storage
phosphor screen. The wavelength with maximum stimulation or emission is shown
above the curves. (These curves are approximations based on data presented in an
article by Sonoda et al., 1983. See appendix C for a reference list.)

4.2 Advantages of storage phosphor screen

autoradiography
Storage phosphor screen autoradiography offers many advantages over
traditional film autoradiography—

• Exposure time is approximately one-tenth that of traditional

autoradiography using x-ray film.

• Sensitivity is 10 to 100 times that of film, depending on the isotope used

and the sample type.

• The linear dynamic range is 1 to 100 000 (5 orders of magnitude). Film

has a linear dynamic range of only 1 to 500 (2.5 orders of magnitude). The
linear dynamic range of the storage phosphor screen allows both weak and
strong signals to be visualized and quantitated in a single exposure, which
eliminates the need for multiple exposures.

• The storage phosphor screens are reusable.

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 Chapter 4 About storage phosphor screen autoradiography

• The storage phosphor screens are placed on the samples in ambient light,
and exposure takes place at room temperature.

• No chemicals, darkroom, or special treatment are required.

• Results are in a digital format and can be analyzed qualitatively and

quantitatively using ImageQuant.

4.3 Types of storage phosphor screens

The storage phosphor screen detects the beta and gamma ionizing radiation
from most isotopes. You can use any of the three types of storage phosphor
screens:

• General-purpose (GP) storage phosphor screen (section 4.3.1)

• Low-energy (LE) storage phosphor screen (section 4.3.2)

• Tritium (TR) storage phosphor screen (section 4.3.3)

The TR screen is available in one size: 19 cm × 24 cm (7.4 in × 9.4 in).

Unless noted below, the GP and LE screen types are available mounted on
an aluminum backing or unmounted in the following sizes:

• The small screen, which is 20 cm × 25 cm (7.8 in × 9.8 in).

• The half-size screen, which is 17.5 cm × 43 cm (6.8 in × 16.8 in).

• The large screen, which is 35 cm × 43 cm (13.7 in × 16.8 in).

• The macroarray screen, which is 24 cm × 30 cm (9.4 in × 11.7 in). The

macroarray screen is available in the unmounted style only.

In general, you expose the screen to the sample in an exposure cassette. (See
chapter 5 for guidelines on exposing different sample types.) The exposure
cassettes come in four styles:

• Small cassette for small mounted screens

• Small cassette for small unmounted screens

• Large cassette for large and half-size mounted screens

• Large cassette for large unmounted or macroarray screens

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Part two Scanning in the storage phosphor mode

4.3.1 General-purpose storage phosphor screen

Caution You should handle the general-purpose (GP) screen carefully. Scratching the
surface of the screen will remove the protective overlay. Always follow the
guidelines and instructions provided in chapter 5 when handling the GP screen.
If you use the Typhoon instrument for a wide variety of applications, you
should use the GP storage phosphor screen. The GP screen is protected from
radioactive contamination by a durable cellulose acetate overlay that covers
the phosphor layer.
The phosphor layer of the GP screen can detect energy from most isotopes. The
isotopes include, but are not limited to, 32P, 33P, 125I, 35S, and 14C. Typical
samples that can be exposed to a GP screen include 32P Northern blots,
32P Southern blots, 125I Western blots, and a variety of gels.

4.3.2 Low-energy storage phosphor screen

Caution You should handle the low-energy (LE) screen carefully. Scratching the surface
of the screen will remove the thin protective overlay. Exposing the LE screen to wet
or moist samples damages the screen. Because wrapping wet samples in plastic
film might not prevent damage, make sure the sample is dry before exposing the
sample to the LE screen. Always follow the guidelines and instructions provided
in chapter 5 when handling the LE screen.
If you use the Typhoon instrument for applications that require more
sensitivity, you should use the LE storage phosphor screen. The phosphor
layer of the LE screen is coated with a thin layer of the durable cellulose acetate
overlay and a small amount of iodide, which increases the efficiency of the
energy stored and released by the screen.
You can use the LE screen to record 33P, 35S, and 14C emissions. Typical
samples that can be exposed to an LE screen include 35S sequencing gels,
35S protein gels, and 33P macroarrays.

4.3.3 Tritium storage phosphor screen

Caution You should handle the tritium (TR) screen carefully. Because you cannot clean
a contaminated TR screen, make sure the sample is as dry as possible before
exposing it to the TR screen. You can erase an exposed TR screen that is not
contaminated and reuse it. Always follow the guidelines and instructions provided
in chapter 5 when handling the TR screen.
You use the TR storage phosphor screen to record 3H emissions. Because
the screen is not coated with the protective cellulose acetate overlay, the
TR screen can detect the weak energy emitted by 3H. Typical samples that
can be exposed to a TR screen include tissue sections on glass and whole
body autoradiography.

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Chapter 5 Preparing for
storage phosphor screen
autoradiography

This chapter provides guidelines for sample preparation and instructions

on exposing the sample to both mounted and unmounted storage phosphor
screens. The topics in this chapter are—

• Guidelines for preparing the samples (section 5.1)

• Preparing the storage phosphor screen for exposure (section 5.2)
• Guidelines for exposing the storage phosphor screen (section 5.3)
• Guidelines for placing the sample in the exposure cassette (section 5.4)
• Placing the sample in the exposure cassette (section 5.5)
• Placing the screen in the exposure cassette (section 5.6)
• Exposing the storage phosphor screen (section 5.7)

5.1 Guidelines for preparing the samples

This section provides guidelines for preparing samples for use with the
storage phosphor screen.

5.1.1 General
Use the following guidelines when preparing the samples:

• Follow all the laboratory procedures for the type of sample you are
preparing.

• Make sure that thin-layer chromatography (TLC) plates are completely

dry before placing them with the screen. To keep flecks off the screen, cover
the dry TLC plate with plastic wrap or strong, thin polyester film, such as
5-mm Mylar™.

• If you also use the Typhoon instrument for fluorescence scanning, make
sure you wear powder-free gloves when handling the samples. Always
rinse the gloves thoroughly with distilled or tap water before handling
the samples. Dust and powder fluoresce and scatter light, which can
affect the quality of images created from fluorescent samples.

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Part two Scanning in the storage phosphor mode

• Neutralize alkaline denaturing gels and make sure the sample is free from
acetic acid vapors and organic solvents. These materials are harmful to
the storage phosphor screens and can penetrate the plastic wrapping or
polyester film on wet samples.

• Do not use scintillants or enhancers, such as PPO or Amplify™. These

products interfere with the proper function of the screen.

5.1.2 Using wet gels with the storage phosphor screen

In addition to the general guidelines in section 5.1.1, use the following
guidelines when exposing the screen to a wet gel:

• Do not directly expose the storage phosphor screen to wet chemicals of

any kind, especially organic solvents.

Caution Because organic solvents penetrate plastic, plastic wrap will not protect the
storage phosphor screens from organic solutions.

• Protect the general-purpose (GP) screen from contamination by separating

a wet gel from the screen with a piece of plastic wrap or polyester film.
Wrap the plastic wrap completely around the gel so that liquid cannot
leak out. This precaution reduces screen contamination with minimum
attenuation of the signal.

• You can expose a wrapped wet gel in the exposure cassette, but do not
lock the clamps on the exposure cassette to secure the screen. Doing so can
cause liquid to leak into the exposure cassette. If possible, dry a thin wet gel
on blotting paper, such as Grade 3MM Chr by Whatman™ Incorporated,
before placing the gel in the exposure cassette.

• Some wet gels are too thick for use in the exposure cassette. Expose these
wet gels in a light-tight drawer or other light-tight enclosure.

• Because a low-energy (LE) screen can be damaged by long exposure to

liquid, do not expose a wet or moist gel to an LE screen. Wrapping wet gels
in plastic film might not prevent damage. Therefore, make sure the gel is
dry before exposing the gel to the LE screen.

• Because you cannot clean a tritium (TR) screen, do not expose a wet gel to
a TR screen. The TR screen does not have the cellulose acetate layer that
protects the GP screen.

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 Chapter 5 Preparing for storage phosphor screen autoradiography

5.1.3 Using radioactive standards

By exposing your sample in conjunction with a set of radioactive standards,
you can convert Typhoon system counts, which are arbitrary units, to the units
of your choice, such as disintegrations per minute.

Keep the following in mind when using standards:

• The range of activities of the standards should bracket expected levels in

your sample.

• Increasing the number of steps in the standard series will increase the
accuracy in the conversion process.

• For accurate quantitation, load the standards as part of the sample.

• If you cannot load the standards as part of the sample, the standards
should be in a matrix similar to the final sample. For example, if the sample
is a dried 10% polyacrylamide gel, the standards should be made in a 10%
polyacrylamide gel and dried as well.

Standards are commercially available from a number of companies that sell

radioactive products. Contact these companies for assistance in choosing an
appropriate set of standards for your application. Alternatively, you can make
your own standards.

5.2 Preparing the storage phosphor screen for

exposure
Before exposing the sample to the storage phosphor screen, you should clean,
erase, and if necessary, decontaminate the screen.

5.2.1 Protecting the storage phosphor screen

The storage phosphor screens consist of a relatively soft matrix. To protect the
screen—

• Handle the screen on the edges or back only. Do not touch the white
phosphor surface.

• Do not fold, roll, or gouge an unmounted screen.

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Part two Scanning in the storage phosphor mode

5.2.2 Verifying that the storage phosphor screen is clean

Between exposures or if the screen has not been used for several days, verify
that the storage phosphor screen is clean using the following procedure:

1. Clean and erase the screen using the procedures in sections 5.2.3 and 5.2.4.

Important Before you erase the screen, check the Image Eraser for contamination from
radioactive samples. To clean the eraser, see section 14.1.

2. Store the screen in a clean, light-tight box.

3. Provide enough time to register the contamination as an image on

the screen.

4. After storage, scan the screen and examine the image. If no hot spots
appear on the image, erase the screen again and begin the next exposure.

5.2.3 Cleaning the storage phosphor screen

Use the cleaning method appropriate for the type of screen you are cleaning.

• GP and LE screens—Use a soft cotton cloth and an intensifying-screen

cleaner (for example, Kodak™ Intensifying Screen Cleaner). Follow the
directions on the bottle. Alternatively, use a small amount of alcohol and
distilled water. Do not use a powdered detergent. Any undissolved particles
can scratch the surface of the screen. This cleaning procedure removes dust,
fingerprints, static electricity, and mild contamination from radioactive
samples.

• TR screen—Use a gentle gas stream or soft brush to remove any particulate

matter from the unprotected surface of the screen.

Caution To avoid damaging the TR screen, do not expose the screen to liquids of any sort.
To avoid damaging the LE screen, make sure you dry the screen completely after
you clean the screen using an intensifying-screen cleaner.

5.2.4 Erasing the storage phosphor screen

After you clean the storage phosphor screen, you use the Image Eraser to
erase any residual signal from the screen.

Use the following guidelines when erasing the screen:

• To avoid contaminating the screen or the eraser, make sure that both the
screen and eraser are free from radioactive contamination before placing
the screen on the eraser.

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 Chapter 5 Preparing for storage phosphor screen autoradiography

• Erase the screen immediately before exposure as well as after scanning the
screen in the instrument. Cosmic radiation creates background on screens
left unused for long periods of time.

• Erase the screen until the recorded signal is fully removed.

• Because you cannot decontaminate a TR screen, you should protect the

eraser and the screen from possible contamination by placing plastic wrap
or polyester film between the TR screen and the eraser surface.

To erase the screen—

1. Hold the screen by its edges with the white side facing the eraser.

2. Place the screen on the eraser as shown in figure 5-1. Rest the screen on the
lip of the eraser. To erase two small screens at once, suspend an unmounted
screen from the clip at the top of the eraser.

Caution Do not use the clip on the TR screen. The clip can damage the surface of
the screen.

3. Set the eraser time by pressing the Time button. Figure 5-1 shows the
button positions for Normal (out) and Extended (in). Select—

• Normal for typical samples. The Normal setting takes approximately

10 minutes.

• Extended if the background or residual image is high. For example,

the original image contained readings of 104 counts and higher. The
Extended setting takes approximately 20 minutes.

4. Press the Erase button.

If the Image Eraser is unavailable, you can use a fluorescent light box and
double the erasure time. If a fluorescent bulb in the Image Eraser needs to be
replaced, you should replace all four bulbs before using the eraser. To replace
the bulbs, see section 14.2.

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Part two Scanning in the storage phosphor mode

Front view Side view

Image Eraser

Clip

Storage phosphor screen:

white side toward eraser

Lip
Time Erase

Normal Extended Time Erase button Power switch

Figure 5-1. Erasing the storage phosphor screen.

5.3 Guidelines for exposing the storage phosphor

screen
Use the following guidelines when exposing the storage phosphor screen:
• Use an exposure cassette to expose the screen to the sample. The exposure
cassette seals out light and keeps the sample flat against the storage
phosphor screen during exposure.
• To expose multiple samples on the same screen, make sure the samples are
the same thickness. If the samples are not the same thickness, the thinner
sample will not contact the screen uniformly, which can result in a bad
exposure, poor image, and poor quantitation results.
• Some samples, such as wet gels or TLC plates, are too thick to fit in an
exposure cassette. For thick samples, expose the screen in a light-tight
drawer or other light-tight enclosure.
• Place the screen on the sample correctly the first time.

Caution Adjusting the position of the screen following initial placement can result in a
double image. If you must adjust the position, remove the screen and erase it.
Then place the screen on the sample again.

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 Chapter 5 Preparing for storage phosphor screen autoradiography

5.4 Guidelines for placing the sample in the

exposure cassette
Use the following guidelines when placing the sample in the exposure cassette:
• In general, place the sample in the cassette in the orientation you want to
view the scanned image (face up on the grid and with the top of the sample
toward the top end of the cassette).
• To avoid possible edge effects on the image, you should place the sample
at least 1 cm (0.4 in) from the edge of the screen. For example, use the area
B2 through J13 for the small screens and the area B2 through Q21 for the
large screens, as shown in figure 5-2.
• To minimize the scan time—
- Place the sample near the upper left corner of the grid (for example,
start in grid square B2).
- Position a rectangular sample so that the shortest edge is along the
numbered side of the exposure cassette as shown in figure 5-2. Because
each pass of the scan head moves the entire length of the glass platen
(from front to back), placing the longest edge of the sample along the
scan head path minimizes the scan time. The scan head path is from
A to R.

Coordinates of this grid square, B2

1 1

1 A
2
B C D E F G H I J K L M N O P Q
2
R

3 3

4 4

5 5

6 6

7
Sample 7

8 8

9 9

10 10
Coordinates
11 11

12 12
of this grid square,
13 13
M10
14 14

15 15

16 16

17 17

18 Exposure Cassette 18

19 19

20 20 Plastic surface
21 21
A B C D E F G H I J K L M N O P Q R

22 22 22

A R

Figure 5-2. Placing the sample in the exposure cassette.

Typhoon User’s Guide ● p5-7

Part two Scanning in the storage phosphor mode

• To minimize the size of the image file—

- Scan only the grid squares that are covered by the sample. If you do not
want to scan the entire sample, scan the squares that contain the part
of the sample you are interested in analyzing.

- (Typhoon 8610, 9210, and 9410 only) Use the 10-µm pixel size to scan
smaller samples only. Because the 10-µm pixel size creates a large file,
you can only scan approximately two-thirds of a large screen before
you exceed the 1-GB file size limit. Scanner Control warns you if you
try to select a scan area that exceeds the two-thirds limit.

• To use one screen to expose multiple samples of the same thickness, place
the samples close together.

• Align the lanes and rows of the sample with the edges of the grid so that
the scanned image will be straight, as shown in figure 5-2.

5.5 Placing the sample in the exposure cassette

The exposure cassette comes in two styles: one for mounted screens and one
for unmounted screens. Each style of exposure cassette comes in two sizes:
one for the small screens and one for the large screens. Select the exposure
cassette size and style that matches the storage phosphor screen you want to
use with the sample. All exposure cassettes come with grid markings inside
to facilitate sample positioning.

Caution Do not put uncovered wet gels in the exposure cassette. For the GP screen,
make sure wet gels are properly covered. Do not expose the LE or TR screen
to wet gels.

To place the sample in the exposure cassette—

1. Use a damp cloth to clean the grid surface inside the exposure cassette
and remove any contamination (section 14.4).

2. Place the sample on the grid using the guidelines in section 5.4.

3. Make a note of the grid coordinates of the area you want to scan (as shown
in figure 5-2). The grid coordinates in the exposure cassette also appear
in the Typhoon instrument (section 6.3) and in the Scanner Control
window (section 6.5.3).

p5-8 ● Typhoon User’s Guide

 Chapter 5 Preparing for storage phosphor screen autoradiography

5.6 Placing the screen in the exposure cassette

You should perform storage phosphor screen autoradiography at room
temperature. Exposing the screen at subzero temperatures provides no
advantage.

Cautions Condensation can destroy the screen. If you are exposing a screen to a frozen
sample, place the screen in a sealed, dry environment, such as a sealed bag.
After exposure, allow the screen to come to room temperature before removing
it from the bag and scanning.

Make sure you place the screen in the correct position when you first set it down.
Because the screen is extremely sensitive, adjusting the position of the screen
can result in a double image.

5.6.1 Positioning a mounted screen

To position a mounted screen in the exposure cassette—

1. Make sure the clamp or clamps on the cassette are rotated out of the way.

2. Remove the screen from the eraser.

3. Note the groove along the side of the exposure cassette opposite the clamp
or clamps. Place the edge of the screen into the groove. The white side of
the screen should be face down, toward the sample. The top of the label
on the screen should be toward the top of the cassette (figure 5-3).

4. Gently lower the screen into place in the corner guides, making sure
the screen fits into the guides correctly.

Caution Do not reposition the screen after it has touched the sample. Because the
screen is extremely sensitive, adjusting the position of the screen can result
in a double image.

Typhoon User’s Guide ● p5-9

Part two Scanning in the storage phosphor mode

Exposure cassette Phosphor screen

1 1

A B C D E F G H I J K L M N O P Q R
2 2

3 3
Corner guide
Groove 4 4

Labels
5 5

6 6

7
Sample 7

8 8

9 9

10 10

11 11
Swing the
12

13
12

13
clamps out of
14 14 the way into the
15

16
15

16
position shown.
17 17

18 Exposure Cassette 18

Groove 19 19

20

21
20

21
Corner guide
A B C D E F G H I J K L M N O P Q R

22 22

Phosphor screen:
white side down,
label toward the
A
1

2
B C D E F G H I J K L M N O P Q
1

2
R top of the sample.
3 3
Sa m p le

4 4

5 5

6 6

7 7

8 8

9 9

10 10

11 11

12 12

13 13

14 14

15 15

16 16

17 17

18 Exposure Cassette 18

19 19

20 20

21 21
A B C D E F G H I J K L M N O P Q R

22 22

Figure 5-3. Loading the large-format mounted screen into the exposure cassette.

p5-10 ● Typhoon User’s Guide

 Chapter 5 Preparing for storage phosphor screen autoradiography

5. Close the exposure cassette by rotating each clamp counterclockwise until

it stops at the pin (figure 5-4) and then flipping the lever over to lock the
screen into place.

Exposure cassette Exposure cassette

Screen Pin

1. Rotate the lever 90 degrees. 2. Flip the lever down over the
screen to lock it into place.

Figure 5-4. Closing the exposure cassette for mounted screens.

5.6.2 Positioning an unmounted screen

To position an unmounted screen in the exposure cassette—

1. Remove the screen from the Image Eraser.

2. Hold the white side of the screen facing down, toward the sample. The
top of the label on the screen should be toward the top end of the cassette.

3. Gently lower the screen into place over the grid area in the cassette. The
screen should be centered over the grid area and should lie straight and
flat in the cassette (figure 5-5).

Caution Do not reposition the screen after it has touched the sample. Because the
screen is extremely sensitive, adjusting the position of the screen can result
in a double image.

4. Close the exposure cassette and press the lid shut until the lock or
locks click.

Typhoon User’s Guide ● p5-11

Part two Scanning in the storage phosphor mode

Exposure cassette
Inside lid Outside lid Locks

1
A B C D E F G H I J
2

Sample
4

10 Exposure Cassette

11

12

13

Phosphor screen:
white side down.
1. Place the screen in the exposure cassette. 2. Press the lid shut until both locks click.

Figure 5-5. Loading a large unmounted screen into the exposure cassette.

5.7 Exposing the storage phosphor screen

The storage phosphor screen requires approximately one-tenth the exposure
time of normal x-ray film. When determining the exposure time, consider a
2-hour exposure to the storage phosphor screen to be equal to an overnight
exposure to basic x-ray film. Because the storage phosphor screen has a wide
linear dynamic range, it is unlikely that you will overexpose the sample to the
screen. This allows you to capture both the strong and weak sample signals
with only one exposure to the sample.

p5-12 ● Typhoon User’s Guide

Chapter 6 Scanning a
storage phosphor screen

This chapter provides step-by-step instructions for scanning a storage

phosphor screen. The topics in this chapter are—

• Verifying the Typhoon instrument is clean (section 6.1)

• Removing the exposed screen from the exposure cassette (section 6.2)
• Loading the storage phosphor screen into the instrument (section 6.3)
• Checking the instrument state (section 6.4)
• Selecting the scan parameters in the Scanner Control window (section 6.5)
• Starting a scan and checking the progress (section 6.6)
• Cleaning up after the scan (section 6.7)
• Storing the storage phosphor screen (section 6.8)
• Analyzing or preprocessing the scanned image (section 6.9)

6.1 Verifying the Typhoon instrument is clean

You should check the Typhoon instrument for all types of contamination
before placing the storage phosphor screen in the instrument.

6.1.1 Checking for radioactive contamination

Periodically, you should check the instrument for contamination from
radioactive samples.

To check the instrument for radioactive contamination, use the following

procedure:

1. Select a storage phosphor screen that is free from radioactive

contamination.

2. Erase the screen, scan the screen to make sure it is not contaminated,
and then erase the screen again. (If, during scanning, an image that looks
like a gel or a blot appears in the ImageQuant Preview window, the screen
might be contaminated. Erase the screen. Rotate the screen or place the
screen on a different part of the glass platen, and scan the screen again.
If the same image appears at the new position in the ImageQuant Preview
window, the screen is contaminated. Select a different screen and repeat
this step.)

Typhoon User’s Guide ● p6-1

Part two Scanning in the storage phosphor mode

3. Place the white side of the screen on the glass platen of the Typhoon
instrument.

4. Leave the screen in the instrument overnight.

5. Scan the screen. If an image appears in the ImageQuant Preview

window that looks like a gel or blot, the instrument is contaminated.
Note: If a white or gray image appears, the image was probably created
by background contamination, and the instrument is not contaminated.

To clean the instrument, follow the instructions in sections 6.1.2 and 6.1.3.

6.1.2 Cleaning the glass platen

The glass platen of the Typhoon instrument should be kept free of
contamination from a radioactive sample. In addition, you should clean
the glass platen before and after you scan each sample.

Important To protect your hands from the ethanol and hydrogen peroxide used in this
procedure and to avoid transferring oils from your hands onto the glass platen,
you should wear gloves. If you scan fluorescent samples using the Typhoon
instrument, make sure the gloves are powder free.

To clean the glass platen—

1. Push up on the lid release under the center front of the sample lid until
the lid opens (figure 6-1).

2. (Optional) If you use the instrument for fluorescent scanning and

fluorescent material has come in direct contact with the glass platen,
moisten a lint-free cloth with 10% hydrogen peroxide and wipe the glass
several times.

3. Clean the glass with distilled water and a clean, lint-free cloth or paper. If
visible spots remain, clean the glass first with 75% ethanol and then with
distilled water.

Caution Because window cleaners contain ingredients that can fluoresce, do not use
window cleaners to clean the glass platen. In addition, the use of acetone or the
excessive use of ethanol can shorten the lifetime of the instrument. Protect the
glass from scratches. Scratches interfere with accurate imaging and quantitation.

p6-2 ● Typhoon User’s Guide

 Chapter 6 Scanning a storage phosphor screen

Push up on the
lid release.

Sample lid
(open)

Lid release

Sample lid

Figure 6-1. Opening the sample lid.

6.1.3 Cleaning the sample lid

Under normal circumstances, the surface of the inner lid should not come in
contact with contaminants. However, it is good laboratory practice to check
the surface periodically for contamination. For example, you can perform
a wipe test, or use the procedure that you used to check the glass platen
(section 6.1.1), except place the screen in the instrument with the phosphor
side up.

The surface of the inner lid should be clean and free of contamination
from radioactive samples. If necessary, clean the surface with a damp (not
saturated) cloth moistened with a small amount of distilled water. If visible
spots remain, clean the surface first with 75% ethanol and then with distilled
water. Note: You should wear gloves to protect your hands when cleaning
the sample lid using 75% ethanol. To prevent liquid from seeping inside
the lid or rolling down onto the glass platen, do not spray liquid on the lid.

Typhoon User’s Guide ● p6-3

Part two Scanning in the storage phosphor mode

6.2 Removing the exposed screen from the exposure

cassette
Important The image on an exposed storage phosphor screen is light sensitive. When
transferring the screen from the exposure cassette to the instrument, keep the
screen face down. After placing the screen on the glass platen, close the lid
immediately. Exposure to direct light will erase some of the signal on the screen.

To remove the storage phosphor screen from the exposure cassette—

1. Open the latch on the cassette.

• For mounted screens—Flip the lever or levers on the cassette

(figure 6-2), and then rotate the clamp or clamps clockwise so that they
no longer cover the screen.

• For unmounted screens—Open the latch or latches and raise the lid of
the cassette.

Exposure cassette Exposure cassette

Screen

1. Flip the lever up away from the screen. 2. Rotate the lever 90 degrees.

Figure 6-2. Opening the exposure cassette for mounted screens.

2. Remove the screen. Handle the screen by the edges only. Do not touch the
white surface of the screen. If the sample sticks to the screen, gently peel
off the sample.

Note: To keep unmounted screens from moving and causing a double

image, press down on one edge of the screen, and then lift up the opposite
edge of the screen.

3. Protect the screen from direct light and proceed immediately to the next
section.

p6-4 ● Typhoon User’s Guide

 Chapter 6 Scanning a storage phosphor screen

6.3 Loading the storage phosphor screen into the

instrument
To load the storage phosphor screen into the Typhoon instrument—

1. If the sample lid is not already open, push up on the lid release under the
center front of the sample lid until the lid opens (figure 6-1).

2. Make sure the white phosphor side of the screen is face down.

3. Use the grid markings that surround the glass platen to align the A1
corner of the screen with the A1 corner of the glass platen (figure 6-3).

Important If you place a small screen so that the J1 corner of the screen aligns with
the A1 corner of the glass platen, make sure you use the orientation buttons
(section 6.5.4) in the Scanner Control window to rotate the scanned image.

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

O
P

O
Glass platen
N N

M M

L L

K K

J J

I I Small screen
as viewed
H H

G G

E
F

E
from above
D

C
D

C
Label
B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner
Front of the Typhoon instrument

Figure 6-3. Load the screen onto the glass platen of the Typhoon instrument.

Typhoon User’s Guide ● p6-5

Part two Scanning in the storage phosphor mode

4. Gently lower the screen on the glass platen.

Note: The unmounted screen might not lie completely flat against the glass
at this time. When you initiate the scan, the instrument lowers the inner
section of the lid to hold the screen flat.

5. Close the sample lid and press the lid down until the latch clicks. The
screen is ready to scan.

6.4 Checking the instrument state

If time is critical for your experiment, you can make sure the instrument is
ready to scan the storage phosphor screen by checking the instrument state,
which is displayed at the top left of the Scanner Control window (figure 6-4).
If the instrument state is Ready, you can select the scan parameters, place the
screen on the glass platen, and start the scan.

If the instrument is in the Sleep state, click the Initialize Scanner button to
bring the instrument to the Ready state. The Instrument State area displays
a Warming Up message. The warm-up period takes approximately 5 minutes.
During the warm-up period, you can select the scan parameters in the
Scanner Control window.

If time is not critical for your experiment, you can select the scan parameters,
place the screen on the glass platen, and start the scan while the instrument
is in the Sleep state. The instrument takes approximately 4 minutes during
the initialization to stabilize the lasers and system components before starting
the scan. The instrument takes approximately 1 additional minute to position
the scan head, select the correct emission filter (if the filter is not in place),
and lower the sample lid.

For more information on the instrument states, see section 3.4.

p6-6 ● Typhoon User’s Guide

 Chapter 6 Scanning a storage phosphor screen

Instrument State area

Figure 6-4. The Scanner Control window set for a storage phosphor scan.

6.5 Selecting the scan parameters in the

Scanner Control window
You use the Scanner Control window (figure 6-4) to select the scan parameters
you want to use when you scan the storage phosphor screen. If the Scanner
Control window is not open, see section 3.3.

In the storage phosphor scan acquisition mode, two parameters cannot be

changed. The Press Sample parameter is selected so that the screen is pressed
tightly against the glass platen for scanning. The Platen parameter is selected
as the Focal Plane so that the Typhoon instrument scans the area just above the
glass platen.

Typhoon User’s Guide ● p6-7

Part two Scanning in the storage phosphor mode

6.5.1 Selecting a template

If a template exists with the parameters you want to use, you can select the
template, review the parameters, add user comments (section 6.5.8), and
then start the scan (section 6.6). For more information on creating and using
templates, see section 3.7.

To select a template, choose Load from the Templates menu and then select
the template name from the list.

If a template does not exist, select the parameters using the instructions in
sections 6.5.2 through 6.5.8.

6.5.2 Selecting the storage phosphor scan acquisition mode

Make sure Storage Phosphor is the selected acquisition mode. If it is not, select
Storage Phosphor from the Acquisition Mode list. The parameters for the
storage phosphor acquisition mode appear in the Scanner Control window
(figure 6-4).

6.5.3 Selecting the scan area

The grid in the Scanner Control window allows you to select the area
to scan. The letter and number markings correspond to the markings in the
exposure cassette and on the glass platen of the Typhoon instrument. The
white rectangle on the grid designates the area you want to scan. You can
either use the current scan area, select a predefined scan area from the Tray
list, or select a new scan area using the grid.

If you are selecting a predefined scan area from the Tray list, select the
tray definition that matches how you are placing the samples on the storage
phosphor screen and how you are placing the storage phosphor screen on the
glass platen. The grid changes to the parameters for the tray definition you
selected. If you are scanning fewer samples than defined in the tray definition,
select the number in the Tray number list that corresponds to the number
of samples you are scanning. The grid changes to reflect the number of scan
areas you selected.

Important In the Tray area, the User Select parameter allows you to select the scan area
using the procedure below. The 1 parameter indicates that you can select only
one scan area. However, if you exposed the storage phosphor screen to multiple
samples, you can customize the scan area using the Tray Editor to define a
separate scan area for each sample (section 3.6).

p6-8 ● Typhoon User’s Guide

 Chapter 6 Scanning a storage phosphor screen

To select a new scan area using the grid—

1. In the Tray list, choose User Select.

2. Place the pointer in the grid square that corresponds to the lowest lettered
and numbered grid square of the area you want to scan.

For example, if you placed the upper left corner of the sample on the
B2 grid square in the exposure cassette, and then aligned the A1 corner
of the screen with the A1 corner of the glass platen, place the pointer on
the B2 grid square.

3. Drag the pointer to the grid square that corresponds to the highest lettered
and numbered grid square of the area you want to scan (figure 6-5).

4. Release the mouse button. The scan area you selected appears in white. The
Scanning Information area displays the approximate image file size, the
approximate scan time, and the number of lines per channel.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

J J

I I

H H

G G

F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

Figure 6-5. Selecting the scan area.

Typhoon User’s Guide ● p6-9

Part two Scanning in the storage phosphor mode

6.5.4 Selecting the sample orientation

You select the sample orientation from the Options area in the Scanner Control
window (figure 6-4). The orientation buttons allow you to change how the
scanned image will be displayed in ImageQuant. To do this, select an icon that
represents how you aligned the upper left corner of the sample with the grid
markings on the exposure cassette and how you aligned the A1 corner of the
screen with the grid markings on the glass platen. Figure 6-6 describes each
sample orientation parameter.

Important Make sure you accurately match the orientation of the sample on the screen
and the orientation of the screen on the glass platen before you select an
orientation button. Depending on how you positioned the sample on the screen
and how you positioned the screen on the glass platen, the top of the sample
may be rotated several times.

To display the orientation buttons, place the pointer on the button next
to Orientation in the Options area and hold down the mouse button. The
orientation buttons appear. Using figure 6-6 as a guide, select the orientation
button that you want to use, and then release the mouse button. During the
scan, the software maps the pixels to permit display of the sample image face
up and top-end up in ImageQuant.

p6-10 ● Typhoon User’s Guide

 Chapter 6 Scanning a storage phosphor screen

Orientation buttons

Sample placement in the Screen placement on the For face-up sample, For face-down sample,
exposure cassette— glass platen— select— select—

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q
3 P P

O O
4
N N

6
Top M

K
M

J J

I I
7
H H

G G
8
F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

A1 corner A
1

2
B C D E F G H I J
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q
3 P P

O O
4

5 Top N

L
N

K K
6
J J

I I
7
H H

8 G G

F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

3 P P

O O
4 N N

M M
5
L L

K K
6

7
Top J

H
J

G G
8
F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

3 P P

O O
4

5
Top N

L
N

K K
6
J J

I I
7
H H

G G
8
F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

Figure 6-6. Determining which orientation button to use.

Typhoon User’s Guide ● p6-11

Part two Scanning in the storage phosphor mode

Orientation buttons

Sample placement in the Screen placement on the For face-up sample, For face-down sample,
exposure cassette— glass platen— select— select—

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

3 P P

O O
4 N N

6
Top M

K
M

J J

I I
7
H H

G G
8
F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

3 P P

O O
4

5 Top M
N

L
N

K K
6
J J

I I
7
H H

G G
8
F F

E E
9
D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

3 P P

O O
4 N N

M M
5
L L

K K
6

7
Top J

H
J

G G
8
F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

A1 corner A
1

2
B C D E F G H I J 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q
3 P P

O O
4

5
Top M
N

L
N

K K
6
J J

I I
7
H H

G G
8
F F

9 E E

D D

10 Exposure Cassette C C

B B

11 A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

12

13

A1 corner

Figure 6-6. Determining which orientation button to use. (continued)

p6-12 ● Typhoon User’s Guide

 Chapter 6 Scanning a storage phosphor screen

6.5.5 Selecting how to scan the sample

You select whether you want to scan the storage phosphor screen using
the best resolution or the best sensitivity. You select one of the parameters
from the Phosphor Mode area in the Scanner Control window (figure 6-4).

• Best Resolution—Use this parameter if you require higher resolution

than sensitivity. The instrument lowers the laser light on the screen to
resolve smaller sample features. The increase in resolution is achieved
by significantly reducing the amount of laser light that is scattered
by the screen. Use Best Resolution with the 50- and 25-µm pixel sizes.

• Best Sensitivity—Use this parameter if you require higher sensitivity

(limit of detection) than resolution. The instrument increases the laser
power to improve the data collection. The higher laser power releases
all the stored energy in the storage phosphor screen. Use Best Sensitivity
with the larger pixel sizes (above 100 µm).

6.5.6 Selecting the pixel size

Pixel size refers to the size of each individual picture element that is recorded
and, together with the thousands of other pixels, forms the image. You select
the pixel size from the Pixel Size list in the Setup area of the Scanner Control
window (figure 6-4). After you change the pixel size, Scanner Control updates
the image size, the scan time, and the number of data lines per channel in
the Scanning Information area.

Table 6-1 lists the available pixel sizes.

Caution You should not use the 1 000- and 500-µm pixel sizes to perform a prescan
of a storage phosphor screen. Because the scanning process destroys the signal
on the screen, an exposed storage phosphor screen can be scanned once per
exposure.

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Part two Scanning in the storage phosphor mode

Table 6-1. Pixel sizes

Pixel size Description

1 000 µm For a very low resolution scan of the screen, select 1 000 microns. The 1 000-µm pixel size
produces 10 data points per centimeter and 20 data lines per grid square. Note: The 1 000-µm
pixel size produces very rough data that is not recommended for quantitative analysis.

500 µm For a low resolution scan of the screen, select 500 microns. The 500-µm pixel size produces
20 data points per centimeter and 40 data lines per grid square.

200 µm For most standard electrophoresis samples, select 200 microns. The 200-µm pixel size
produces 50 data points per centimeter and 100 data lines per grid square.

100 µm For samples requiring high resolution (such as DNA sequences), select 100 microns. The
100-µm pixel size produces 100 data points per centimeter and 200 data lines per grid square.

50 µm For samples requiring a higher resolution (such as whole body autoradiography), select
50 microns. The 50-µm pixel size produces 200 data points per centimeter and 400 data
lines per grid square.

25 µm For samples requiring an even higher resolution (such as high-density macroarrays), select
25 microns. The 25-µm pixel size produces 400 data points per centimeter and 800 data lines
per grid square.

10 µm For samples requiring the highest resolution (such as microarrays), select 10 microns. The
(Typhoon 8610, 10-µm pixel size produces 1 000 data points per centimeter and 2 000 data lines per grid
9210, and square. Note: Because of file size limitation, you can only scan approximately two-thirds
9410 only) of the large storage phosphor screen. For more information on minimizing the file size, see
section 5.4.

Important (Typhoon 8610, 9210, and 9410 only) The resolution of a storage phosphor
screen is limited by the crystalline structure of the screen. Depending on the
screen, scanning at 25 µm or 10 µm might not improve the resolution of the image.
If you select 25 microns or 10 microns from the Pixel Size list, make sure you
select Best Resolution so that the instrument can make the best use of the smaller
pixel sizes.

6.5.7 Selecting the image analysis software

If you want to analyze the scanned image after you finish scanning, you can
select the analysis software you want to use from the Image Analysis list in the
Setup area of the Scanner Control window (figure 6-4). After the instrument
finishes scanning, the selected software starts and displays the image.

If you select None from the Image Analysis list, the Scanner Control window
remains active so that you can perform another scan.

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 Chapter 6 Scanning a storage phosphor screen

6.5.8 Entering user comments (optional)

Important The user comments are not saved as part of a template. If you want to include
comments, you must type the comments each time you scan.

In the User Comment box, type any comments you want to save with the image
(approximately 4 000 characters, including spaces). The comments are for
reference only and do not affect the scan. After the scan, you can view, but
not change, the comments in ImageQuant.

6.6 Starting a scan and checking the progress

Warning Do not attempt to defeat the safety interlocks on the sample lid. These interlocks
are designed to protect you from laser light exposure.

Caution Never turn off the Typhoon instrument or disconnect the Ethernet cable while
scanning. You can damage the internal mechanism of the instrument.

Important Keep the sample lid closed during the scan. Opening the lid causes the instrument
to close the laser shutter and block the laser light. Then Scanner Control aborts
the scan and saves the data already collected.

During the scanning process, light illuminates each position on the sample
only while the corresponding pixel is being recorded. The position is only
minimally exposed during the rest of the scan.

Scanner Control creates an image file and stores it using the Data File (.gel)
extension type.

6.6.1 Starting a scan of a single sample or scan area

If you exposed the storage phosphor screen to a single sample or included
multiple samples in a single scan area, you create one image file.

To start the scan—

1. Make sure that the storage phosphor screen is in place, the sample lid is
shut, and all the parameters are correct in the Scanner Control window.

2. Make sure the DIGE File Naming Format check box is not selected.

3. In the Scanner Control window, click the Scan button. The Save as window
appears (figure 6-7).

4. In the Save as window, type a name in the File name box. The file type is
automatically set to Data File (.gel).

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Part two Scanning in the storage phosphor mode

Caution If you type a name that is already used, a message appears and asks you if you
want to replace the existing file. Before you click Yes, make sure you do not want
to keep the existing image file. Clicking Yes deletes the existing image and all the
associated auxiliary files. If you have analyzed the image using ImageQuant, all
the data will be deleted.

Figure 6-7. The Save as window.

5. (Optional) Select a different folder. Otherwise, the software saves the image
file in the Data folder.

Caution Using a network to save the scanned data to a folder on a remote computer can
slow or delay the scan. For the best results, select a folder on the local hard drive.
After you scan the screen, move the image file to the remote computer.

6. To start the scan, click Save.

6.6.2 Starting a scan of multiple samples and scan areas

If you exposed the storage phosphor scan to multiple samples and you created
separate scan areas for each sample, you can create a separate image file for
each scan area.

To start the scan—

1. Make sure that the storage phosphor screen is in place, the sample lid is
shut, and all the parameters are correct in the Scanner Control window.

Important Make sure the tray definition and number of samples in the Tray area match the
positions of the samples on the storage phosphor screen.

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 Chapter 6 Scanning a storage phosphor screen

2. In the Scanner Control window, click the Scan button. The Multiple Sample
Naming window appears (figure 6-8). Default file names appear for each
sample.

Figure 6-8. The Multiple Sample Naming window.

3. In the Use Common Setting for All Samples area, click Browse and locate
an existing folder in the Save Folder to window. Click OK to close the
Save Folder to window, and then click Set in the Multiple Sample Naming
window.

Caution Using a network to save the scanned data to a folder on a remote computer can
slow or delay the scan. For the best results, select a folder on the local hard drive.
After you scan the screen, move the image file to the remote computer.

4. To name—

• Each file individually—In the File Name list, click the file name that
you want to change and then click Edit Sample File Name. The Save As
window appears. Type the name you want to use in the File Name box,
and click Save to close the window and return to the Multiple Sample
Naming window. Click the next file name that you want to change and
repeat the steps in this bullet.

• Each file using the same base file name—In the Use Common Setting for
All Samples area, type a name in the Base File Name box, and click Set.
The software displays the base file name in the File Name list.

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Part two Scanning in the storage phosphor mode

• Each file using an existing base file name—In the Use Common Setting
for All Samples Area, click Browse, and locate the file name you want
to use in the Name File window. Click OK to close the window, and
then click Set in the Multiple Sample Naming window. The software
displays the base file name in the File Name list.

5. Click Scan to start the scan.

After the scan, the software saves each image in the folder you selected.

• If you used unique names, the folder contains an image file for each file
name.

• If you used a base file name, the software appends a number to each file
name to make the names unique. For example, the file name for sample one
will be basefilename1, where basefilename is the name you entered in the
Base File Name box. All the files have the .gel file extension.

6.6.3 The initialization process

Before the Typhoon instrument begins the scan, an initialization process
occurs. Depending on the state of the instrument and the scan parameters you
selected in Scanner Control, the initialization can take as long as 5 minutes.
A timer displays the time estimated for initialization. The timer counts down
as the initialization proceeds.

The initialization procedures include—

• Moving the scan head into position

• Changing the filters to match the scan parameters

• Stabilizing the laser if the laser has been idle, shut down, or recently
turned on

• Lowering the inner lid of the Typhoon instrument to hold the screen flat
against the glass platen

Note: To avoid the extra 5 minutes of initialization time used to stabilize

the lasers when the instrument has been in the Sleep state, click the Initialize
Scanner button in the Scanner Control window several minutes before you
plan to start the scan.

6.6.4 Canceling the scan

If you decide you need to cancel the scan, click Cancel Scan in the ImageQuant
Preview window. Scanner Control saves the data collected before you canceled
the scan.

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 Chapter 6 Scanning a storage phosphor screen

6.6.5 Monitoring the scan progress

After you start the scan, the ImageQuant Preview window appears (figure 6-9),
and the green Scan indicator light on the top of the instrument blinks. As
the Typhoon instrument scans the storage phosphor screen, Scanner Control
displays an image in the ImageQuant Preview window. In addition, Scanner
Control displays the number of data lines scanned and the total scan time
remaining (excluding initialization). Scanner messages can also appear as the
scan progresses.

Figure 6-9. The ImageQuant Preview window during a scan of a storage phosphor
screen that has one scan area defined.

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Part two Scanning in the storage phosphor mode

A More Info button appears in the ImageQuant Preview window when

the Typhoon instrument reports errors. Click the More Info button to view
the error message.

• If the error is a nonfatal error, the instrument continues to scan, and

Scanner Control saves the file when the scan is finished. You should
check the image in ImageQuant to make sure the data are not corrupted.

• If the error is a fatal error, the instrument aborts the scan, and Scanner
Control saves the data collected before the fatal error occurred. You
should check the image in ImageQuant. Depending on where the fatal
error occurred in the scan, you might be able to use the data. If you
cannot use the image for quantitation, you must repeat the exposure
and scan again.

If the instrument is scanning multiple scan areas, you see the Preview Sample
box at the top of the window, which lists the number of scan areas. To view
the progress of a different scan area, select the scan area from the list.

6.6.6 Viewing the preview image for saturated data

While the instrument is scanning, an image appears in the ImageQuant Preview
window. The image shows the part of the sample that has been scanned.
Saturated data appear in red in the image. If the data portions of the image
appear saturated, you will not be able to perform quantitative analysis on
the portions of the image that are saturated. Because saturation causes a total
loss of the ability to distinguish the signal intensity fluctuations, a saturated
image can be used only for viewing the shapes and positions of the spots on
the sample.

Because the scanning process destroys the signal on the storage phosphor
screen, you should finish the scan. If the image appears unusable, expose a
clean, erased storage phosphor screen to the original sample and expose the
screen for a shorter time. Alternatively, you can prepare a new sample and
expose a clean, erased storage phosphor screen to the new sample.

Important Before repeating the exposure and the scan, verify in ImageQuant that the image
is saturated and that you cannot perform accurate quantitation.

6.6.7 Completing the scan

Scanner Control saves the image using the file name you typed in the Save as or
Multiple Sample Naming window. The ImageQuant Preview window displays
a Complete message and then closes. The Scan indicator light on the Typhoon
instrument turns off.

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 Chapter 6 Scanning a storage phosphor screen

At the end of the scan, an image of the sample appears automatically in the
software you selected from the Image Analysis list. If you selected None, the
Scanner Control window remains active for more scanning.

6.7 Cleaning up after the scan

After the Typhoon instrument completes the scan, open the sample lid and
remove the storage phosphor screen. Avoid touching the white side of the
screen.

To lift a large mounted screen, pull up on the round tabs attached to the
metal plate, and then slide a finger under the edge of the metal backing. If
your screen does not have tabs or the tabs are damaged, you should replace
the tabs. Contact Technical Support. See Assistance in the preface for contact
information.

After each scan, you should—

• Remove the sample from the exposure cassette and dispose of the sample
using the established procedure in your laboratory.

• Check the storage phosphor screen for contamination (section 5.2.2).

• Clean the storage phosphor screen (section 5.2.3).

• Erase the storage phosphor screen (section 5.2.4).

• Check the Image Eraser for contamination and clean the eraser
(section 14.1).

• Check the glass platen and sample lid for contamination and clean the
glass platen and sample lid of the Typhoon instrument (section 6.1).

• Check the exposure cassette for contamination and clean the exposure
cassette (section 14.4).

6.8 Storing the storage phosphor screen

Before storing the storage phosphor screen, you should clean, decontaminate
(if necessary), and erase the screen. Then store the screen—

• At room temperature.

• Away from sources of radiation, such as strong beta or gamma emitters or

x-ray machines.

• In a protective box or in a clean exposure cassette. Damaged screens are

unusable and must be replaced.

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Part two Scanning in the storage phosphor mode

6.9 Analyzing or preprocessing the scanned image

You should display the image of the sample to determine the quality of
the scan. If you selected an image analysis software in the Scanner Control
window, the software starts and displays the image. For information about
how to use the selected software, see the Help within the software or the
software documentation.

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Part three

Scanning in the fluorescence mode

Chapter 7 About fluorescence
scanning

This chapter describes the theory behind fluorescence. The topics in this
chapter are—

• How fluorescence works (section 7.1)

• Advantages of direct fluorescence (section 7.2)
• Emission filters (section 7.3)
• Beamsplitters (section 7.4)
• Linking fluorescent scans (section 7.5)
• Multilabel (multichannel) experiments (section 7.6)
• Common fluorochromes (section 7.7)

7.1 How fluorescence works

The absorption of light energy by a fluorochrome boosts an electron to a
higher energy shell (excited state). The characteristic light absorption pattern
of a fluorochrome is shown by its absorption spectrum (figure 7-1).

The excited state has a very short half-life, on the order of a few nanoseconds.
During the brief lifetime of the excited state, the excited electron generally
decays toward a lower energy level within the excited state. When the electron
falls to the ground state, the fluorochrome emits light of specific wavelengths.
The distribution of fluorescent emissions among different wavelengths is
plotted in the emission spectrum (figure 7-1).

The bulk of the fluorescent emission spectrum always shifts toward a longer
wavelength (lower energy) relative to the excitation spectrum, and the small
tail of the emission spectrum sometimes overlaps the excitation spectrum.
The difference in wavelength between the maxima of the absorption and the
emission spectra is called the Stokes shift. Because of this shift, the Typhoon
instrument uses optical filtration to separate the excitation light from the
longer-wavelength emitted light. Because the leading edge of the emission
spectra overlaps with the tail of the excitation spectra for some dyes, the
Typhoon instrument can excite dyes, such as FAM with 532 nm, and
collect emitted light at 526 nm and below.

For more information on how fluorescence is generated, see the Amersham

Biosciences publication Fluorescence Imaging principles and methods.
(See appendix C for a list of references.)

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Part three Scanning in the fluorescence mode

(a) Cy3 (b) Cy5

550 650
532 570 633 667

300 400 500 600 700 800 300 400 500 600 700 800
Wavelength Wavelength

Figure 7-1. Absorption (---) and emission (— —) spectra of the fluorescent product of (a) Cy3 and of (b) Cy5.
The wavelength with maximum absorption or emission is shown above the curves. The vertical line shows the
excitation wavelength. (These curves are approximations based on data collected at Amersham Biosciences.)

7.2 Advantages of direct fluorescence

When you use the Typhoon system to scan samples labeled or stained with dyes
excitable by one or more of the laser wavelengths, the results appear in a digital
image format. These results can be analyzed qualitatively and quantitatively
using ImageQuant.

Scanning direct fluorescence on the Typhoon system offers several

advantages—

• Nucleic acid and protein gels can be analyzed shortly after electrophoresis.
Soak the gels in a dye solution and rinse away the excess dye as you would
for the well-known ethidium bromide and Coomassie™ protocols. You can
use some of these same gels for follow-on blot experiments.

• You can analyze fluorescently labeled samples that can be detected directly
and do not require staining.

• You can analyze nucleic acid and protein blots using fluorescently labeled
probes, such as Cy™5-labeled DNA probes or antibodies.

• Pixel-by-pixel fluorescent excitation eliminates fluorescent blooming, which

is caused by constant excitation in traditional systems, and provides better
resolution of closely spaced bands.

• Quantitation is simplified because, unlike instant film, the Typhoon system

provides a linear response to the fluorescent signal intensities.

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 Chapter 7 About fluorescence scanning

7.3 Emission filters

The Typhoon instrument contains a standard set of emission filters and can
accommodate a total of 14 emission filters. The instrument uses emission filters
to reject reflected and scattered excitation light and background fluorescence
while allowing the emitted light from the sample to pass through to the PMT.
Table 7-1 lists the standard set of emission filters used with fluorescence
scanning.

Table 7-1. Standard set of emission filters

Emission filter Description

520-nm band-pass filter Transmits light between 500 nm and 540 nm and has a transmission peak centered
(520 BP 40) at 520 nm. Use this filter with fluorochromes, such as Cy2 and ECL Plus™, or with
(Typhoon 9400 and fluorescein when scanning with the 488-nm wavelength of the blue laser.
9410 only)

555-nm band-pass filter Transmits light between 545 nm and 565 nm and has a transmission peak centered
(555 BP 20) at 555 nm. Use this filter with fluorochromes, such as R6G and HEX.

580-nm band-pass filter Transmits light between 565 nm and 595 nm and has a transmission peak centered
(580 BP 30) at 580 nm. Use this filter with fluorochromes, such as TAMRA and Cy3.

610-nm band-pass filter Transmits light between 595 nm and 625 nm and has a transmission peak centered
(610 BP 30) at 610 nm. Use this filter with fluorochromes, such as ROX, EtBr, SYPRO™ Red,
and SYPRO Ruby.

670-nm band-pass filter Transmits light between 655 nm and 685 nm and has a transmission peak centered
(670 BP 30) at 670 nm. Use this filter with fluorochromes, such as Cy5.

526-nm short-pass filter Transmits light below 526 nm. Use this filter with fluorochromes, such as fluorescein
when scanning with the green laser. Note: When using the blue laser, the 520 BP 40
might provide better results.

560-nm long-pass filter Transmits light above 560 nm. Use this filter with fluorochromes, such as TRITC.

390-nm band-pass filter This filter is used for storage phosphor scanning and is not normally used for
fluorescence scanning.

For more information on emission filters, see the Amersham Biosciences

publication Fluorescence Imaging principles and methods. (See appendix C
for the references.)

You use the Fluorescence Setup window in the Scanner Control software to
select the appropriate filter (section 9.3). Sections 13.4 and 13.5 describe how
to install and remove an emission (optical) filter.

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Part three Scanning in the fluorescence mode

7.4 Beamsplitters
The Typhoon instrument contains three standard beamsplitters and has a slot
for one additional custom beamsplitter. You can use the beamsplitters with
multilabel fluorescent samples to create multichannel images. Table 7-2 lists the
three standard beamsplitters.

Table 7-2. Standard beamsplitters

Beamsplitter Description
560-nm dichroic Reflects light of wavelengths shorter than 560 nm and passes
light longer than 560 nm.

580-nm dichroic Reflects light of wavelengths shorter than 580 nm and passes
light longer than 580 nm.

630-nm dichroic Reflects light of wavelengths shorter than 630 nm and passes
light longer than 630 nm.

7.5 Linking fluorescent scans

The instrument uses one beamsplitter and two emission filters when you link
two scans together in the Fluorescence Setup window in the Scanner Control
software (section 9.3.7). You link scans that contain similar scan parameters so
that you can acquire signals from two different fluorochromes during one scan.
This optimizes scanning of samples containing multiple fluorochromes by
reducing the scan time.

Similar to a long-pass emission filter, the beamsplitter separates the emissions

from the linked scans so that one PMT collects the longer wavelength
emissions while the other PMT collects the shorter wavelength emissions
(figure 7-2).

Emission filter
Mirror
PMT
Short wavelength

Emitted light
PMT
Long wavelength
Beamsplitter
Emission filter

Figure 7-2. How the beamsplitter separates short- and long-wavelength emissions.

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 Chapter 7 About fluorescence scanning

Scanner Control determines that two scans can be linked if—

• The scans use the same laser, or they combine the red laser with the
green laser.

• The scans use different emission filters or at least one uses no emission
filter.

• The scans use the same sensitivity parameter.

• The wavelength of one of the beamsplitters is between the wavelengths

of the two emission filters, and the wavelength of the beamsplitter is at
least 5 nm from each filter. The filter value is determined as the center
wavelength for a band-pass filter, or the cutoff wavelength for a short-pass
or a long-pass filter.

Based on the selected emission filters and laser(s), Scanner Control selects
the appropriate beamsplitter to use with the linked scans. The possible links
appear in the Fluorescence Setup window (figure 7-3). You select whether or
not to activate the link.

Figure 7-3. Fluorescence Setup window showing possible scans that can be linked.

You can link a red laser scan with the green laser scan. Linking the two
scans decreases the scan time because the scans are performed simultaneously.
However, the image sensitivity can degrade slightly because the second laser
can increase the background of the first sample. This degradation varies based
on the sample type and media, and you might see no degradation at all. After
you evaluate the needs of the experiment, you might need to make a trade-off
between scan time and sensitivity.

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Part three Scanning in the fluorescence mode

(Typhoon 9400 and 9410 only) You cannot link a blue laser scan with a green
or red laser scan. You cannot link the 457-nm wavelength and the 488-nm
wavelength of the blue laser.

7.6 Multilabel (multichannel) experiments

You can label the sample with multiple fluorescent dyes and then create a
multichannel image. A multichannel image is a set of images (channels) that
can be viewed individually or as a composite (overlaid). To provide accurate
detection and separation of the signals, you label the sample with two, three,
or four fluorochromes that can be collected and distinguished from each
other using the available filters. You include a spectral separation standard
for each fluorochrome in the sample to assist in reducing cross talk
(cross-contamination) between the fluorescent emissions.
After the scan, you use the FluorSep™ software to remove the cross talk and
create a new image for each fluorochrome in the sample. The multichannel
image can be viewed in ImageQuant. In ImageQuant, you can view the set
of images (channels) overlaid in different colors, or you can view the channels
side-by-side in gray scale. For information on removing cross talk using
FluorSep, see the FluorSep Help or user documentation. For information
on viewing images in ImageQuant, see the ImageQuant Help or user
documentation.

7.7 Common fluorochromes

Table 7-3 lists the absorption and emission maxima of some common
fluorochromes. The chemistry of the experiment can alter the absorption
and emission spectra slightly.
For more information on selecting fluorochromes and for additional
fluorochrome recommendations, see the Amersham Biosciences publication
Fluorescence Imaging principles and methods. (See appendix C for the
references.)

Table 7-3. Fluorochrome absorption and emission maxima*

Fluorochrome Absorption maximum (nm) Emission maximum (nm)

Acridine Orange-dsDNA 502 526

BODIPY™ 493/503 493 503

BODIPY FL 503 512

Cy2 489 506

Cy3 550 570

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 Chapter 7 About fluorescence scanning

Table 7-3. Fluorochrome absorption and emission maxima* (continued)

Fluorochrome Absorption maximum (nm) Emission maximum (nm)

Cy5 649 670

DDAO-Phosphate 646 660

ECF™ Substrate 440 560

ECL Plus 420 460

Ethidium Bromide (EtBr) 526 610

FAM 495 535

Fluorescein (FITC) 490 520

HEX 529 560

NanoOrange™ 485 590

Phycoerythrin (R) 480 578

PicoGreen™-dsDNA 480 520

Rhodamine-6-G (R6G) 546 560

RiboGreen™ 500 520

ROX 590 605

SYBR™ Green I-dsDNA 497 520

SYBR Green II 497 513

SYBR Gold 495 537

SYPRO Orange 472 570

SYPRO Red 530 625

SYPRO Ruby 450 610

TAMRA 555 580

TET 519 545

Texas Red™ 595 615

TOTO™-1-dsDNA 513 532

TRITC 547 572

Vistra Green™ 490 520

* Values listed are from the manufacturers’ catalogs or from data collected at Amersham
Biosciences.

Typhoon User’s Guide ● p7-7

Chapter 8 Setting up for
fluorescence scanning

This chapter describes how to prepare the sample for fluorescence scanning
and how to place the sample in the Typhoon instrument. The topics in this
chapter are—

• Preparing the sample (section 8.1)

• Cleaning the glass platen and sample lid (section 8.2)
• Determining how to position the sample (section 8.3)
• Placing a gel or membrane on the glass platen (section 8.4)
• Placing a sandwich gel on the glass platen (section 8.5)
• Placing the slide holder and microarray slides on the glass platen
(Typhoon 8610, 9210, and 9410 only) (section 8.6)
• Placing the gel alignment guide and multiple sandwich gels on the glass
platen (section 8.7)

8.1 Preparing the sample

The following sections provide guidelines to use when preparing samples for
fluorescence scanning.

8.1.1 General guidelines

Dust fluoresces and scatters light, which causes artifacts on images and can
interfere with quantitation. To avoid this—

• Wear powder-free gloves—Because most powder used in laboratory gloves

fluoresces, you should wear powder-free gloves. Always rinse the gloves
with distilled or tap water before handling the sample and before preparing
the reagent.

• Filter solutions—Remove dust particles by filtering all the stock solutions

used to prepare the sample, sample matrix, and buffers. Use clean, rinsed
containers. Some reagents, such as fluorescent labels, are supplied dust
free and require no further filtration. When diluting clean reagents to
working concentration, use distilled water collected in a rinsed container
so that you do not have to filter the solutions again.

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Part three Scanning in the fluorescence mode

• Avoid fluorescent indicator dyes—Many of the commonly used

electrophoresis tracking dyes fluoresce (such as bromophenol blue or
xylene cyanol). Whenever possible, put the tracking dye in a separate
lane. Alternatively, use a dye in the sample loading buffer that is either
nonfluorescent or does not enter the gel.

• Avoid excessive exposure to light—Fluorochromes differ greatly in their

sensitivity to light-induced degradation (photobleaching). When working
with sensitive fluorochromes and fluorescently labeled samples, use
low-light conditions.

8.1.2 Label guidelines

Use the following guidelines when selecting the label for the fluorescence
scanning:

• Green-excited fluorescence—Detects samples labeled with fluorochromes

that are excited at 532 nm.

• Red-excited fluorescence—Detects samples labeled with fluorochromes

that are excited at 633 nm.

• (Typhoon 9400 and 9410 only) Blue-excited fluorescence—Detects

samples labeled with fluorochromes that are excited at 457 or 488 nm.
Note: The laser power at 457 nm is much lower than the laser power
at 488 nm.

• Multilabel fluorescence—Detects samples labeled with two, three, or

four fluorochromes and creates a multichannel image. To minimize the
spectral overlap from the fluorochromes, the emission peaks should be
greater than 30 nm apart. Use one or more lasers and up to four different
emission filters to create the multichannel image. The multichannel image
contains one image for each fluorochrome. Using ImageQuant, you can
view these images separately or overlaid.

Note: The instrument contains a built-in filter for the red and green lasers.
The built-in filter blocks the laser light at 532 nm ±8 nm or 635 nm ±10 nm.
For the Typhoon 9400 and 9410 instruments, an additional built-in filter
blocks all laser light below 500 nm. The Typhoon system automatically selects
the appropriate built-in filter based on the color of the laser you selected. The
built-in filters cannot be used simultaneously.

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 Chapter 8 Setting up for fluorescence scanning

8.1.3 Low-fluorescence sample support guidelines

For fluorescent samples requiring high sensitivity or highly accurate
quantitation, the following material sources have been tested and found
to have low background.

Gels
Background fluorescence contributed by the gel matrix increases with gel
thickness. Always use the thinnest gel practical for your experiment, especially
for agarose gels.
• Agarose—FMC SeaKem™ Gold and LE have low background. If another
type of agarose has properties that are useful for your application, scan
a test gel to make sure the background is low enough for your purposes.
Make sure the agarose is completely dissolved and well-mixed before
pouring the gel. Also, avoid generating bubbles when mixing and pouring.
Uneven agarose concentration and bubbles affect light scatter and can
cause artifacts and interfere with quantitation. If you poured the gel into
a plastic tray, remove the gel from the tray before placing the gel on the
glass platen of the Typhoon instrument.
If the agarose gel containing the sample is more than 4-mm thick, scan
the sample using the +3 mm focal plane parameter in the Scanner Control
window (section 9.2.7). If the agarose gel is less than 4-mm thick, scan
the sample using the Platen focal plane parameter. Check the results in
ImageQuant to make sure the selected focal plane provides the best limit
of detection and spatial resolution.
• Polyacrylamide—Polyacrylamide gels are usually clear and thin (less than
1 mm). The background contribution from the gel material is generally
very low. Make sure your electrophoresis glass plates are absolutely clean
before you pour the gel. Grease and fingerprint oils from the plates can
stick to the gel surface and attract dust and fluorescent dyes.

Electrophoresis glass plates

When using electrophoresis glass plates with the Typhoon instrument, make
sure that—
• The glass has a low-fluorescence background
• The glass is clean before preparing a sandwich gel
• The sandwich gel does not leak
Important Make sure the electrophoresis glass plate you place on the glass platen is
3 mm thick. The +3 mm focal plane parameter is designed for 3-mm-thick
glass. Make sure both the electrophoresis glass plates of a sandwich gel
have a low-fluorescence background.

Typhoon User’s Guide ● p8-3

Part three Scanning in the fluorescence mode

Gel alignment guides

The gel alignment guides contain spacers that raise the gels 0.2 mm above
the glass platen, which prevents optical interference and eliminates the need
to use distilled water or buffer on the glass platen. When selecting the Scanner
Control parameters, make sure you select the +3 mm parameter for the focal
plane, the Press Sample check box, and the correct tray definition.

Membranes
Membranes that generate lower background fluorescence generally offer
more optimal imaging results. The background fluorescence of the membranes
depends on the experimental conditions. You should scan a test piece of each
membrane you plan to use and check that the background is low enough for
your purposes. Before scanning the membrane, treat the membrane using the
same procedure you will be using in the experiment.

Microarray slide and slide holder

(Typhoon 8610, 9210, and 9410 only)
Make sure you use the microarray slide holder when scanning microarray
slides. When selecting the Scanner Control parameters—

• Select MicroArray 2 Slides in the Tray list.

Note: If the MicroArray 2 Slides tray definition is not available and you
are scanning one slide, select A2 through D2 for the scan area. If you are
scanning two slides, select A2 through J2 for the scan area. If you want
to create two scan areas, see section 3.6 to create two scan areas—
A2 through D2 and F2 through J2.

• Select Fluorescence for the acquisition mode.

• Select +3 mm for the focal plane.

• Select 10 microns for the pixel size.

• Select ( ) for the orientation.

• Select the Press Sample check box.

p8-4 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

Microplates
Because the bottoms of the wells in most microplates raise the sample at least
2 mm above the glass platen, you should use the +3 mm focal plane parameter
in the Scanner Control window (section 9.2.7). You might want to scan a test
microplate and check the results in ImageQuant to make sure the selected focal
plane provides the best limit of detection and spatial resolution. In addition,
check the background fluorescence of the microplate to make sure it is within
an acceptable range. To prevent the microplate from moving during the scan,
make sure you select the Press Sample parameter in the Scanner Control
window.

Microplate strips
Scan a test microplate strip using the +3 mm focal plane parameter in the
Scanner Control window (section 9.2.7). Check the results in ImageQuant
to make sure the selected focal plane provides the best limit of detection and
spatial resolution. In addition, check the background fluorescence of the
microplate strip to make sure it is within an acceptable range.

Transparency support
To avoid contaminating the glass platen and sample lid, you can place
a sample, such as a membrane, in a plastic bag, between two pieces of
transparency material, or between sheet protectors (section 8.4). You should
check the background generated by the material to make sure it is low enough
for your purposes.

Solvents
Spectroscopic-grade solvents have the lowest autofluorescence.

8.2 Cleaning the glass platen and sample lid

You should clean the glass platen and sample lid before placing your sample
on the platen. In addition, you should protect the glass from scratches because
scratches interfere with data collection and quantitation.

Important If you use the Typhoon instrument for storage phosphor scanning, you should
periodically check the instrument for contamination from radioactive samples
(section 6.1.1).

8.2.1 Cleaning the glass platen

The glass platen of the Typhoon instrument should be kept free of sources
of fluorescent background (such as dust, dried buffer, and skin oils). It is good
practice to clean the glass platen before and after you scan each sample.

Typhoon User’s Guide ● p8-5

Part three Scanning in the fluorescence mode

Important To protect your hands from the ethanol and hydrogen peroxide used in this
procedure and to avoid transferring oils from your hands onto the glass platen,
you should wear powder-free gloves.

To clean the glass platen—

1. Push up on the lid release under the center front of the sample lid until the
lid opens (figure 8-1).

Push up on the
lid release.

Sample lid
(open)

Lid release

Sample lid

Figure 8-1. Opening the sample lid.

2. (Optional) If fluorescent material has come in direct contact with the

glass platen, moisten a lint-free cloth with 10% hydrogen peroxide and
wipe the glass several times.

3. Clean the glass with distilled water and a clean, lint-free cloth or paper.
If visible spots remain, clean the glass first with 75% ethanol and then
with distilled water.

Caution Because window cleaners contain ingredients that can fluoresce, do not use
window cleaners to clean the glass platen. In addition, the use of acetone or the
excessive use of ethanol can shorten the lifetime of the instrument. Protect the
glass from scratches. Scratches interfere with accurate imaging and quantitation.

p8-6 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

8.2.2 Cleaning the sample lid

The surface of the inner lid should be clean and free of fluorescent
contamination. If necessary, clean the surface with a damp (not saturated)
cloth moistened with a small amount of distilled water. Note: You should wear
powder-free gloves to protect your hands when cleaning the sample lid using
75% ethanol. If visible spots remain, clean the surface first with 75% ethanol
and then with distilled water. To prevent liquid from seeping inside the lid or
rolling down onto the glass, do not spray liquid on the lid.

8.3 Determining how to position the sample

Before you load the sample, you should determine how to position it on the
glass platen. Use the following guidelines to determine the sample orientation
and the sample placement.

8.3.1 Determining the sample orientation

Determine whether to place the sample face up or face down on the glass
platen. The Typhoon system illuminates the sample and collects data from
underneath the sample—

• For a one-sided, opaque sample, such as a membrane or TLC plate, place

the sample face down.

• For a sandwich gel, make sure you create the sandwich gel using a 3-mm
electrophoresis glass plate. Place the 3-mm electrophoresis glass plate on
the glass platen of the instrument.

• As a reference point for the sample orientation, you can cut a corner of the
gel or sample.

• If the sample is physically uneven on one side, such as an agarose gel, place
the flat side down. This allows the sample to lie flat on the glass platen.

• For a microplate or microplate strip, place the plate or strip on the glass
platen so that the edges of the plate or strip align with the grid markings
on the glass platen.

• For a microarray slide, place the slide or slides in the microarray slide
holder so that the spotted side is face down toward the glass platen.

• For multiple gels, use the gel loading guides to place up to two large gels
side-by-side or up to four smaller gels in a 2-by-2 grid.

Typhoon User’s Guide ● p8-7

Part three Scanning in the fluorescence mode

8.3.2 Determining the sample placement

Use the following guidelines and figure 8-2 to determine where on the glass
platen to place the sample:

• To minimize the scan time—

- Place the sample near the A1 corner of the grid. Each lettered or
numbered grid segment is marked by two dots.

- Position a rectangular sample so that the shortest edge is along the

numbered side of the glass platen as shown in figure 8-2. Because each
pass of the scan head moves the entire length of the glass platen (from
front to back), placing the longest edge of the sample along the scan
head path minimizes the scan time.

- (Typhoon 8610, 9210, and 9410 only) If you are scanning only one
microarray slide, position the slide in the first well.

• To minimize the image file size—

- Scan only the number of grid squares covered by the sample. If you do
not want to scan the entire sample, scan the squares that contain the
part of the sample you are interested in analyzing.

- (Typhoon 8610, 9210, and 9410 only) Use the 10-µm pixel size to scan
smaller samples and microarray slides. Because the 10-µm pixel size
creates a large file, you can scan approximately two-thirds of the total
scan area before you exceed the 1-GB file size limit for a single-channel
image or for each channel of an unlinked multichannel image. For
a linked multichannel image, each channel cannot exceed 400 MB.
Scanner Control warns you if you try to select a scan area that exceeds
the file size limit. If the scan area exceeds the limit, you can scan the
sample twice using two different scan areas.

• To record multiple samples during the same scan without using the gel
alignment guides, place the samples close together. Make sure the samples
are the same thickness. If the samples are not the same thickness, the
selected focal plane might not be optimal for each sample, which can result
in a bad scan, poor image, and poor quantitation results.

• Align the lanes and rows of the sample with the edges of the grid on the
glass platen so that the scanned image will be straight.

p8-8 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L Coordinates
K

J
K

J
of this grid
I

H
I

H
square, L10
G G

F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Coordinates of this
grid square, A1

Front of the Typhoon instrument

Figure 8-2. Sample placement on the glass platen of the Typhoon instrument.

8.4 Placing a gel or membrane on the glass platen

Caution If you place the sample directly on the glass platen, make sure you place the
sample in the correct position when you first set it down. Although unlikely, any
fluorescent material left on the glass after you move a sample can result in a
double image.

You can place the sample directly on the glass platen. However, for gels and
membranes, you can avoid contaminating the glass platen and possible double
images if you place the gel on a low-fluorescence electrophoresis glass plate
or place a membrane in a low-fluorescence plastic bag.

You place the sample on the glass platen so that the sample creates a smooth
surface on the glass platen. Avoid trapping air bubbles between the sample
and the glass platen. Air bubbles can appear on the scanned image. Before
placing a wet sample on the glass platen of the instrument, squirt a little
buffer or distilled water on the glass. The buffer or distilled water lessons
the chance of trapping air bubbles between the sample and the glass platen.

Typhoon User’s Guide ● p8-9

Part three Scanning in the fluorescence mode

Caution Make sure you wipe off the excess buffer or distilled water. Using too much liquid
can cause the sample to move on the glass platen during the scan, which could
affect the quality of the collected data.

To place a gel or membrane on the glass platen of the Typhoon instrument—

1. If the sample lid is not already open, push up on the lid release under the
center front of the lid until the lid opens (figure 8-1).

2. (Optional) For wet samples, squirt a little buffer or distilled water on the
glass platen.

3. Hold the sample by the edges or use a clean plastic spatula (for gels) or
forceps (for membranes) to handle the sample. Gently lower the sample
onto the glass platen starting at the A1 corner. Do not trap air bubbles
under the sample or scratch the glass. Cover a membrane with a glass plate
to keep it flat.

Important Do not touch the glass platen or the part of the sample that will be read by the
Typhoon instrument. Oil from fingerprints and powder from gloves, even thoroughly
washed gloves, might leave a print that can be detected.

4. Make a note of the grid square coordinates of the area you want to scan
(figure 8-2). You will use this information later in the Scanner Control
window (section 9.2.3).

5. Close the sample lid and press the lid down until the latch clicks. The
sample is ready to scan.

8.5 Placing a sandwich gel on the glass platen

Important Make sure the low-fluorescence electrophoresis glass plate that you place on
the glass platen is 3 mm thick. The +3 mm focal plane parameter is optimized
for 3-mm-thick glass.

You can use Kapton™ tape to help prevent an optical interaction between
the glass platen and the 3-mm electrophoresis glass plate. The Kapton tape
prevents the two pieces of glass from coming in contact with each other, which
can cause optical interference patterns or rings to appear on the image. Before
assembling the sandwich gel, place one strip of Kapton tape on each long
side of the 3-mm electrophoresis glass plate. Make sure each piece of Kapton
tape covers at least 75% of the long edge of the plate.

p8-10 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

To place a sandwich gel on the glass platen of the Typhoon instrument—

1. If the sample lid is not already open, push up on the lid release under the
center front of the lid until the lid opens (figure 8-1).

2. Hold the sandwich gel by the edges and make sure the 3-mm
electrophoresis glass plate edged with Kapton tape is on the bottom.

3. Place one edge of the sandwich gel on the glass platen of the instrument
(figure 8-3).

4. Squirt distilled water on the glass platen. The distilled water increases the
sensitivity of the scan by filling the space created by the Kapton tape with
water. In addition, the water helps provide a continuous interface for the
laser light to pass through on its way to the sample.

5. Lower the sandwich gel onto the glass platen. Make sure you do not trap
air bubbles as you lower the sandwich gel onto the glass platen.

Important Do not touch the glass platen or the part of the sandwich gel that will be read
by the Typhoon instrument. Oil from fingerprints and powder from gloves, even
thoroughly washed gloves, might leave a print that can be detected.

6. When you can no longer lower the sandwich gel using your fingers,
insert the Wonder Wedge™ tool between the glass platen and the 3-mm
electrophoresis glass plate.

7. Lower the sandwich gel onto the Wonder Wedge, and then slowly remove
the Wonder Wedge. Make sure you do not trap air bubbles between the
glass platen and the 3-mm electrophoresis glass plate. Make sure the
sandwich gel is aligned on the glass platen.

8. Make a note of the grid square coordinates that are covered by the area
of the sample you want to scan (figure 8-2). You will use this information
later in the Scanner Control window (section 9.2.3).

9. Close the sample lid and press the lid down until the latch clicks. The
sample is ready to scan.

Typhoon User’s Guide ● p8-11

Part three Scanning in the fluorescence mode

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q
Q
P P

O O

N N

M M

L L

K K

J J

I I

H H

G G

F Sandwich gel F

E E

D D

C Wonder Wedge C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 A

1 21
Front of the Typhoon instrument

Front view Top view

Sandwich gel Wonder Wedge

Sandwich gel
3-mm glass plate
Kapton tape
Squirt distilled water here

Glass platen Glass platen

Figure 8-3. Aligning a sandwich gel on the glass platen of the Typhoon instrument.

p8-12 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

8.6 Placing the slide holder and microarray slides

on the glass platen (Typhoon 8610, 9210,
and 9410 only)
To scan microarray slides on the Typhoon instrument, you should use the
Microarray Slide Holder Kit (optional accessory). For more information on
the kit, contact Technical Support. See Assistance in the preface for contact
information.

The slide holder allows you to scan one or two microarray slides. The slide
holder positions the slides at the proper height above the glass platen so
that the instrument can accurately collect data.

Caution To prevent anomalies in the image data, make sure the glass platen of the
Typhoon instrument, the microarray slide holder, and the slides are clean.
Remove any liquid marks, fingerprints, or dust particles from the back of
the slides before scanning.

To position the slide holder and microarray slides on the glass platen—

1. If the sample lid is not already open, push up on the lid release under
the center front of the lid until the lid opens (figure 8-1).

2. Moisten a lint-free cloth with distilled water and clean the slide holder.

3. Gently position the slide holder at the front left corner of the glass platen
as shown in figure 8-4.

Typhoon User’s Guide ● p8-13

Part three Scanning in the fluorescence mode

Microarray slide holder

L
K
J
I
H
G
F
E
D
C
B
A
2 3 4 5

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

I
J

I
Coordinates of this
H

G
H

G
grid square, J2
F F

E E

D D

C C

B B

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
A
Coordinates of this
grid square, A2

Front of the Typhoon instrument

Figure 8-4. Positioning the microarray slide holder on the glass platen.

p8-14 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

4. Holding the slide with the spotted side face down, carefully lower the
slide into the first well on the slide holder as figure 8-5 shows. (If you are
scanning only one slide, positioning the slide in the first well minimizes
the scan time.)

Note: Alternatively, you can place the slides in the slide holder first, and
then position the slide holder on the glass platen. However, this method
increases the risk of dropping the slides.

Hold the slide with the

spotted side face down.

Gently lower the slide onto

the slide holder.

Figure 8-5. Positioning the slides in the slide holder.

5. (Optional) If you are scanning two slides, repeat step 4 to position the slide
in the second well on the slide holder.

6. Make sure the slides are seated in the grooves of the slide holder and make
sure the slide holder is seated firmly against the front and left metal sides
of the platen area as shown in figures 8-4 and 8-5. The positions of the
slides and the slide holder keep the slides at the proper angle and location
for accurate scanning.

Typhoon User’s Guide ● p8-15

Part three Scanning in the fluorescence mode

7. Place a slide restraint over each slide as shown in figure 8-6. Make sure
each restraint is correctly positioned in the grooves on the slide holder.

8. Close the sample lid and press the lid down until the latch clicks. The
microarray slides are ready to scan.

Lower the
slide restraint
onto the slide.

Slide

Figure 8-6. Positioning the slide restraint on the slide holder.

p8-16 ● Typhoon User’s Guide

 Chapter 8 Setting up for fluorescence scanning

8.7 Placing the gel alignment guide and multiple

sandwich gels on the glass platen
To scan multiple sandwich gels on the Typhoon instrument, you should use
the gel alignment guides (optional accessory). For more information on the
guides, contact Technical Support. See Assistance in the preface for contact
information.

The gel alignment guides allows you to scan up to two large or four small
sandwich gels. The gel alignment guides position the sandwich gels at the
proper height above the glass platen so that the instrument can accurately
collect data.

Important Make sure the electrophoresis glass plate you use for the bottom of the sandwich
gel is 3 mm thick and has a low-fluorescence background.

Caution To prevent anomalies in the image data, wipe any excess liquid from the sandwich
gel with a lint-free cloth before scanning.

Warning When placing the sandwich gel on the gel alignment guide and glass platen,
make sure you hold the sandwich gel with one hand on the gripper and the other
hand on the edge of the sandwich gel. Holding the sandwich gel by the gripper
only can cause the sandwich gel to fall out of the gripper and onto the glass
platen, which could break the electrophoresis glass plates or the glass platen.

8.7.1 Loading one or two large sandwich gels

To scan one or two large sandwich gels, you use the Ettan DALT gel alignment
guide and two grippers (one for each sandwich gel). The large sandwich gels
can be up to 21 cm by 27.5 cm (8.2 in by 10.7 in).

Important You do not need to squirt distilled water or buffer on the glass platen when you use
the gel alignment guide. The spacers on the guide and grippers hold the sandwich
gel 0.2 mm above the glass platen, which prevents optical interference.

To position the Ettan DALT gel alignment guide and one or two large
sandwich gels on the glass platen—

1. If the Typhoon lid is not already open, push up on the lid release under the
center front of the lid until the lid opens (figure 8-1).

2. Moisten a lint-free cloth with distilled water and clean the Ettan DALT gel
alignment guide.

3. Place the guide along the front edge of the glass platen as shown in
figure 8-7.

Typhoon User’s Guide ● p8-17

Part three Scanning in the fluorescence mode

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

Gripper N N

M M

L L

K K

J J

I I

H H

G G

F F
Sandwich gel
E E

D D

C C

B B

A A
Ettan DALT gel
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
alignment guide

Front of the Typhoon instrument

Figure 8-7. Placing the Ettan DALT gel alignment guide and sandwich gel with attached gripper on the
glass platen.

4. Attach the gripper to one end of the prepared sandwich gel so that the
spacers are on the side of the sandwich gel that you will place on the
glass platen.

5. Holding the sandwich gel by the gripper and one edge, place the edge of
the sandwich gel without the gripper on the edge of the guide (figure 8-7).
Make sure the sandwich gel rests on the two spacers.

6. Lower the sandwich gel and gripper onto the glass platen.

7. (Optional) Repeat steps 4 through 6 for the second sandwich gel.

8. Close the Typhoon lid and press the lid down until the latch clicks. The
sandwich gels are ready to scan.

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 Chapter 8 Setting up for fluorescence scanning

8.7.2 Loading one through four small sandwich gels

To scan one through four small sandwich gels, you use the SE600 gel alignment
guide and four grippers (one for each sandwich gel). The small sandwich gels
can be up to 16 cm by 18 cm (6 in by 7 in).

Important You do not need to squirt distilled water or buffer on the glass platen when you use
the gel alignment guide. The spacers on the guide and grippers hold the sandwich
gel 0.2 mm above the glass platen, which prevents optical interference.

To position the SE600 gel alignment guide and up to four small sandwich gels
on the glass platen—

1. If the sample lid is not already open, push up on the lid release under the
center front of the lid until the lid opens (figure 8-1).

2. Moisten a lint-free cloth with distilled water and clean the three pieces of
the SE600 gel alignment guide.

3. Place the front SE600 guide along the front edge of the glass platen as
shown in figure 8-8.

4. Place the back SE600 guide along the back edge of the glass platen as
shown in figure 8-8.

5. Place one end of the center SE600 guide in the groove on the back SE600
guide, and place the other end in the groove on the front SE600 guide as
shown in figure 8-8.

Typhoon User’s Guide ● p8-19

Part three Scanning in the fluorescence mode

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Back SE600
Q

P
Q

P
gel alignment guide
O O

N N
Groove
M M

L L

K K

J J

I I
Center SE600
H H

G G
gel alignment guide
F F

E E

C
D

C
Groove
B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
Front SE600
gel alignment guide

Front of the Typhoon instrument

Figure 8-8. Placing the three pieces of the SE600 gel alignment guide on the glass platen.

6. Attach the gripper to one end of the prepared sandwich gel so that the
spacers are on the side of the sandwich gel that you will place on the
glass platen.

7. Holding the sandwich gel by the gripper and one edge, place the edge of the
sandwich gel without the gripper on the edge of the center gel alignment
guide (figure 8-9). Make sure the sandwich gel rests on the two spacers.

8. Lower the sandwich gel and gripper onto the glass platen.

9. (Optional) Repeat steps 6 through 8 for the remaining sandwich gels.

10. Close the sample lid and press the lid down until the latch clicks. The
sandwich gels are ready to scan.

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 Chapter 8 Setting up for fluorescence scanning

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

Gripper K
L L

J J

I I

H H

G G

F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Front of the Typhoon instrument

Figure 8-9. Placing a sandwich gel with attached gripper on the SE600 gel alignment guide.

Warning When placing the sandwich gel on the gel alignment guide and glass platen,
make sure you hold the sandwich gel with one hand on the gripper and the other
hand on the edge of the sandwich gel. Holding the sandwich gel by the gripper
only can cause the sandwich gel to fall out of the gripper and onto the glass
platen, which could break the electrophoresis glass plates or the glass platen.

Typhoon User’s Guide ● p8-21

Chapter 9 Scanning a fluorescent
sample

This chapter provides step-by-step instructions for scanning a fluorescent

sample. The topics in this chapter are—

• Checking the instrument state (section 9.1)

• Selecting the scan parameters in the Scanner Control window (section 9.2)
• Using the Setup window to select the fluorescence parameters (section 9.3)
• Starting a scan and checking the progress (section 9.4)
• Removing the sample from the Typhoon instrument (section 9.5)
• Cleaning the glass platen and sample lid (section 9.6)
• Analyzing or preprocessing the scanned image (section 9.7)

9.1 Checking the instrument state

If time is critical for your experiment, you can make sure the instrument is
ready to scan the fluorescent sample by checking the instrument state, which
is displayed at the top left of the Scanner Control window (figure 9-1). If the
instrument state is Ready, you can select the scan parameters for your scan,
place the sample on the glass platen, and start the scan.

If the instrument is in the Sleep state, click the Initialize Scanner button to
bring the instrument to the Ready state. The Instrument State area displays
a Warming Up message. The warm-up period takes approximately 5 minutes.
During the warm-up period, you can select the scan parameters in the
Scanner Control window.

If time is not critical for your experiment, you can select the scan parameters,
place the sample on the glass platen, and start the scan while the instrument
is in the Sleep state. The instrument takes approximately 4 minutes during
initialization to stabilize the lasers and system components before starting
the scan. The instrument takes approximately 1 additional minute to position
the scan head, select the correct emission filter or filters, and lower the sample
lid (if selected).

For more information on instrument states, see section 3.4.

Typhoon User’s Guide ● p9-1

Part three Scanning in the fluorescence mode

Instrument State area

Figure 9-1. The Scanner Control window set for a fluorescence scan.

9.2 Selecting the scan parameters in the

Scanner Control window
You use the Scanner Control window (figure 9-1) to select the scan parameters
you want to use when you scan the fluorescent sample. If the Scanner Control
window is not open, see section 3.3.

9.2.1 Selecting a template

If a template exists with the parameters you want to use, you can select the
template, review the parameters, add user comments (section 9.2.9), and
then start the scan (section 9.4). For more information on creating and using
templates, see section 3.7.
To select a template, choose Load from the Templates menu and then select
the template name from the list.
If a template does not exist, select the parameters using the instructions in
sections 9.2.2 through 9.3.8.

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9.2.2 Selecting the fluorescence scan acquisition mode

Make sure Fluorescence is the selected acquisition mode. If it is not,
select Fluorescence from the Acquisition Mode list. The parameters for the
fluorescence scan acquisition mode appear in the Scanner Control window
(figure 9-1) and in the additional Fluorescence Setup window.

9.2.3 Selecting the scan area

The grid in the Scanner Control window allows you to select the area to
scan. The letter and number markings correspond to the markings on the glass
platen of the Typhoon instrument. The white rectangle on the grid designates
the area you want to scan. You can either use the current scan area, select a
predefined scan area from the Tray list, or select a new scan area using the grid.

If you are selecting a predefined scan area from the Tray list, select the tray
definition that matches how you are placing the samples on the glass platen.
The grid changes to the parameters for the tray definition you selected. If
you are scanning fewer samples than defined in the tray definition, select the
number in the Tray number list that corresponds to the number of samples you
are scanning. The grid changes to reflect the number of scan areas you selected.

Important In the Tray area, the User Select parameter allows you to select the scan area
using the procedure below. The 1 parameter indicates that you have selected
only one scan area. However, if you are scanning multiple samples, you can
customize the scan area using the Tray Editor to define a separate scan area
for each sample (section 3.6).

To select a new scan area using the grid—

1. In the Tray list, choose User Select.

2. Place the pointer in the grid square that corresponds to the lowest lettered
and numbered grid square of the area you want to scan (figure 9-2). For
example, grid square A1 is the lowest lettered and numbered grid square
on the glass platen.

3. Drag the pointer to the grid square that corresponds to the highest lettered
and numbered grid square of the area you want to scan. For example, R22
is the highest lettered and numbered grid square on the glass platen.

4. Release the mouse button. The scan area you selected appears in white.
The Scanning Information area displays the image file size, the approximate
scan time, and the number of lines per channel.

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Part three Scanning in the fluorescence mode

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

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F F

D
Top E

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A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

Figure 9-2. Selecting the scan area.

9.2.4 Selecting the sample orientation

You select the sample orientation from the Setup area in the Scanner Control
window (figure 9-1). The orientation buttons allow you to change how the
scanned image will be displayed in ImageQuant. To do this, select the icon
that represents how you aligned the upper left corner of the sample with
the grid markings on the glass platen or the gel alignment guide. Figure 9-3
describes each sample orientation parameter.

If you placed the sample on the glass platen so that the top of the sample was
aligned with the numbered rows, you can use the orientation buttons to display
the top of the sample at the top of the Image window in ImageQuant.

If you placed the sample on a gel alignment guide, use the gel orientation
guide (in the Gel Alignment Guide Kit) to help you determine the orientation.
Hold the gel orientation guide over the gel making sure that the IEF strip
and molecular weight orientation of the guide match that of the gel. The
appearance of the letter “R” as seen from the front of the Typhoon instrument
shows which letter “R” to select in the Scanner Control software. Selecting
the matching letter “R” orients the image correctly for viewing in ImageQuant.

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Orientation buttons

Sample placement on the For face-up sample, For face-down sample,

glass platen— select— select—

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

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P P

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Top
F F

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D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

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A1 corner

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

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Top
F F

E E

D D

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

Figure 9-3. Determining which orientation button to use.

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Part three Scanning in the fluorescence mode

To display the orientation buttons, place the pointer on the button next
to Orientation in the Options area and hold down the mouse button. The
orientation buttons appear. Move the pointer to the button that represents
how you aligned the sample on the glass platen and release the mouse
button. During the scan, the software maps the pixels to permit display
of the sample image face up and top-end up in ImageQuant.

9.2.5 Selecting the Press Sample parameter

If you are scanning a sample, such as a dry membrane or filter paper, that
does not lie flat against the glass platen of the instrument, you should select
the Press Sample check box. When you scan the sample, the inner lid of the
Typhoon instrument lowers to press the sample flat. If you do not select
Press Sample, the inner lid remains retracted during the scan.
Caution Do not select Press Sample if you are scanning wet membranes, wet gels, or
soft samples. Pressing wet or soft samples can damage the instrument. In addition,
pressing a soft sample can distort the sample and the image.

9.2.6 Selecting the pixel size

Pixel size refers to the size of each individual picture element that is recorded
and, together with the thousands of other pixels, forms the image. You select
the pixel size from the Pixel Size list in the Setup area of the Scanner Control
window (figure 9-1). After you change the pixel size, Scanner Control updates
the image size, the scan time, and the number of data lines per channel in
the Scanning Information area.
You should choose the largest pixel size that provides the best resolution
for your sample. Using the smaller pixel sizes increases the scan time
and the image file size.
You can use the 1 000- and 500-µm pixel sizes to perform a quick prescan
of the sample to make sure the experiment was successful or to check the
PMT voltage parameters to make sure the data is not saturated.
Table 9-1 lists the pixel sizes.

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Table 9-1. Pixel sizes

Pixel Size Description

1 000 µm For a very quick scan of the sample, select 1 000 microns.
The 1 000-µm pixel size produces 10 data points per
centimeter and 20 data lines per grid square.
(Note: The 1 000-µm pixel size produces very rough data
that is good for a quick prescan, but is not recommended
for quantitative analysis.)

500 µm For a quick scan of the sample, select 500 microns. The
500-µm pixel size produces 20 data points per centimeter
and 40 data lines per grid square.

200 µm For most samples, select 200 microns. The 200-micron

pixel size produces 50 data points per centimeter and
100 data lines per grid square.

100 µm For samples that require high resolution, select

100 microns. The 100-µm pixel size produces 100 data
points per centimeter and 200 data lines per grid square.

50 µm For samples that require a higher resolution, select

50 microns. The 50-µm pixel size produces 200 data
points per centimeter and 400 data lines per grid square.

25 µm For samples that require an even higher resolution, select

25 microns. The 25-µm pixel size produces 400 data points
per centimeter and 800 data lines per grid square.

10 µm For samples that require the highest resolution, select

(Typhoon 8610, 9210, 10 microns. The 10-µm pixel size produces 1 000 data
and 9410 only) points per centimeter and 2 000 data lines per grid square.

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9.2.7 Selecting the focal plane

The Focal Plane area allows you to adjust the focal point of the laser and
collection optics. Two parameters are available—

• Platen—Use this parameter if you placed a thin (less than 3 mm) or surface
sample, such as a gel or membrane, directly on the glass platen of the
Typhoon instrument. Scanner Control adjusts the focal point of the laser
beam and collection optics to the area just above the glass platen of the
Typhoon instrument.

• +3 mm—Use this parameter if you placed a microplate or a sandwich gel

on the glass platen of the Typhoon instrument. Scanner Control adjusts the
focal point of the laser beam and collection optics 3 mm higher than the
glass platen of the Typhoon instrument. If you used different thicknesses of
electrophoresis glass plates, make sure you place the 3-mm electrophoresis
glass plate of the sandwich gel on the glass platen.

9.2.8 Selecting the image analysis software

If you want to analyze the image after you finish scanning, you can select the
image analysis software you want to use from the Image Analysis list in the
Setup area of the Scanner Control window (figure 9-1). After the instrument
finishes scanning, the selected software starts and displays the image.

If you select None from the Image Analysis list, the Scanner Control window
remains active so that you can perform another scan.

9.2.9 Entering user comments (optional)

Important The user comments are not saved as part of a template. If you want to include
comments, you must type the comments each time you scan.

In the User Comment box, type any comments you want to save with the image
(approximately 4 000 characters, including spaces). The comments are for
reference only and do not affect the scan. After the scan, you can view, but
not change, the comments in ImageQuant.

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9.3 Using the Setup window to select the

fluorescence parameters
You use the Fluorescence Setup window to select the fluorescence parameters
to use with the sample. You can select from one through four sets of
parameters to perform one through four scans. The following sections
describe how to use the Fluorescence Setup window (figure 9-4).

Figure 9-4. The Fluorescence Setup window with Image 1 active.

9.3.1 Displaying the Fluorescence Setup window

To display the Fluorescence Setup window, make sure Fluorescence is the
selected acquisition mode, and then click the Setup button in the Acquisition
Mode area in the Scanner Control window (figure 9-1).

9.3.2 Selecting the number of scans

The Fluorescence Setup window displays the fluorescence parameters for all
four scans. As a default, Scanner Control activates the parameters for Image 1
only, as shown in figure 9-4. If your sample contains two or more labels, you
can set up scan parameters for all the labels in your sample (up to 4). See
section 7.6 for more information on multilabel experiments.

To activate the parameters for Images 2, 3, and then 4, click the Use check
box for Images 2, 3, and then 4, respectively.

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9.3.3 Selecting the emission filter

You select an emission filter from the Emission Filter list for each scan
you want to perform. Each list displays the filters that are installed on the
Typhoon instrument. If you do not want to use an emission filter, select None
from the list. For a description of the emission filters, see section 7.3. When
you select a filter, Scanner Control automatically suggests the laser you should
use with the emission filter you selected. However, if desired, you can select
a different laser.

Important The laser and emission filter combinations listed in the Fluorescence Setup
window are based on the excitation and emission maxima of the selected
fluorochrome. For most gel microplate and array samples, these combinations
provide the best scanning results. However, for membrane samples, selecting
a laser and emission filter combination that is close to the excitation and
emission maxima might not provide the best results because of the high
background interference. For the best results, you should test the membrane
samples with different laser and emission filter combinations to determine the
optimal combination.

9.3.4 Setting the PMT voltage

For fluorescent samples, you can alter the PMT voltage to improve the
signal collection capabilities of the Typhoon instrument.

Guidelines for changing the PMT voltage

For accurate quantitation of high-intensity samples, the pixel intensities
in your scanned image should be within a specific range. To determine
the correct PMT voltage, scan a test sample or scan the real sample using
the 1 000- or 500-µm pixel size, and then display the image in ImageQuant.
Use the Gray/Color Adjust feature to display the intensity values of the image.
For more information, see the ImageQuant User’s Guide or Help within
the software.

• If the pixel values are more than 1 count and less than 100 000 counts,
all spots in your image are within the dynamic range of the instrument.

• If some of the pixel values are equal to or greater than 100 000 counts,
part of your image is at or near saturation. Lower the PMT voltage, rescan,
and confirm that the image is not saturated.

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If your experiment includes only very weak samples or only very intense
samples, you can adjust the voltage to extend the limit of detection.

• For weak samples, increase the PMT voltage. If you increase the PMT
voltage, the image might lose quantitation accuracy at the upper end of
the signal range. If the sample background is very low, a PMT voltage
above 900 V might increase the PMT noise and cause a loss in sensitivity.
Note that the maximum PMT voltage is 1 000 V.

• For high-intensity samples that saturate the system, decrease the

PMT voltage to bring high-intensity signals into the linear range of the
instrument. Otherwise the image might lose the sensitivity and quantitation
accuracy at the lower end of the signal range. If you decrease the voltage
below 400 V, the image might lose linearity.

Important For the best sensitivity, use the High sensitivity parameter with a medium PMT
voltage (600–800 V).

If you change your sample matrix, you should test the PMT values between
400 V and 1 000 V to determine which voltage provides an acceptable
background. As a suggested starting point, use 600 V.

Procedure for changing the PMT voltage

To set the voltage in the PMT Voltage box—

• Click the box to select it, and then type the value you want. The maximum
value is 1 000 V.

• Use the up or down arrows to change the value in 5-V increments. To

approximately double the signal intensity, increase the PMT voltage
by 50 V.

Because different labels, lasers, and emission filters affect the signal intensity,
you need to select an appropriate PMT voltage for each scan of a multilabel
experiment.

9.3.5 Selecting the laser

Based on the emission filter you select, Scanner Control selects the laser you
should use for the scan. You can change the laser displayed in the Laser list
to the other nonoptimal parameter. The parameters are the Green (532) or
Red (633) laser.

(Typhoon 9400 and 9410 only) Two additional laser parameters appear in the
list: Blue (488) and Blue (457). Note: The laser power of the 457 wavelength
is much lower than the laser power of the 488 wavelength. You might need
to adjust the PMT voltage accordingly.

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9.3.6 Selecting the sensitivity (limit of detection)

You use the sensitivity parameters to help improve the limit of detection
of the Typhoon instrument. The sensitivity parameter controls how long
the Typhoon instrument collects data from each pixel. The Sensitivity
parameters are—

• Normal (default)—Collects data from each pixel once. In general, you

should use the Normal parameter.

• Medium—Collects data from each pixel four times and averages the
results. Using the Medium parameter to detect weak signals improves
the sensitivity by reducing the background noise. Selecting Medium
will increase the scanning time but does not increase the size of the
image file. Check the Scanning Information area in the Scanner Control
window for the time required to complete the scan.

(Typhoon 8610, 9210, and 9410 only) For the 10-µm pixel size, the
system collects data from each pixel twice and then averages the values.)

• High—Collects data from each pixel eight times and averages the results.
Using the High parameter to detect weak signals improves the sensitivity
by reducing the background noise. Selecting High will increase the scanning
time but does not increase the size of the image file. Check the Scanning
Information area in the Scanner Control window for the time required
to complete the scan. Note: This parameter is not available for the
10- and 25-µm pixel sizes.

If you are performing multiple scans, you set sensitivity parameters for
each scan.

9.3.7 Linking scans

You link scans that contain similar parameters so that you can acquire
signals from two different fluorochromes during one scan. This optimizes
the scanning of samples containing multiple fluorochromes by reducing the
scan time. The beamsplitter separates the emissions from the linked scans
so that one PMT collects the longer wavelength emissions while the other
PMT collects the shorter wavelength emissions. For a description of the
beamsplitters in the Typhoon instrument, see section 7.4. For information
on how scans are linked, see section 7.5.

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Determining if scans can be linked

Scans can be linked if they meet the following criteria:

• The scans use the same laser, or they combine the red laser with the green
laser. Make sure you select the Speed mode if you combine the red and
green laser.

(Typhoon 9400 and 9410 only) The 457 and 488 wavelengths of the
blue laser are not considered to be the same laser and cannot be linked.

• The scans use different emission filters or at least one uses no emission
filter.

• The scans use the same sensitivity parameter.

• The wavelength of one of the beamsplitters is between the wavelengths

of the two emission filters, and the wavelength of the beamsplitter is
at least 5 nm from each filter.

If Scanner Control determines that scans can be linked, the Link With area
becomes active. Scan number buttons appear in the Link With area for the
scans that can be linked (figure 9-5), and the Auto-Link button becomes active.
After you link two scans, the Unlink All button becomes active so that you
can remove the links if you do not want to use them.

Scanner Control selects the optimal link by determining which scans provide
the best limit of detection and the best spectral separation. The Link With
area displays the scans that can be linked and uses colored dots above the
scan numbers to show the optimal link for each scan. The color of the dot
represents the selected laser, and the number represents the scan that will be
linked if you click the Auto-Link button.

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Part three Scanning in the fluorescence mode

(a) Before linking

(b) After linking

Bracket indicates
linked scans

Figure 9-5. The Fluorescence Setup window. (a) The example shows the scans that can be linked.
(b) The example shows that the first and second scans and the third and fourth scans have been linked.

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Automatically linking scans

The Fluorescence Setup window allows you to link scans automatically. After
you select the scans you want to perform and select the parameters for each
scan, Scanner Control determines which scans can be linked, activates the
Link With area, and displays colored dots above the scan numbers to show
the optimal links.

For optimal linking, Scanner Control requires more than 5 nm between

the peak of a band-pass filter and the edge of the beamsplitter, or more than
5 nm between the edge of a short-pass or long-pass filter and the edge of the
beamsplitter.
If you select emission filters that are separated by less than 15 nm, Scanner
Control disables the Auto-Link button. If you select None for any of the filters,
Scanner Control disables the Auto-Link feature. To activate the Auto-Link
button, change the emission filters to more optimal pairs.
If you link scans, you need to select an auto-link mode. The parameters are—
• Sensitivity—Select Sensitivity if you want to avoid cross talk between
the fluorochromes that are excited by the different lasers. The Sensitivity
parameter only allows auto-linking of fluorochromes that use the same
laser. The scans requiring different lasers are not linked and are performed
sequentially. Selecting Sensitivity improves the signal-to-noise ratio by as
much as 20% for the red laser.

• Speed—Select Speed if you want to decrease the total scan time by linking
scans that use different lasers. For example, you can link the Cy3 dye
using the green laser with the Cy5 dye using the red laser. Both the red
and green lasers excite the sample simultaneously. Scanning with two lasers
simultaneously can cause the emission light from one dye to appear in the
other channel for some fluorochromes. The resulting cross talk can reduce
the sensitivity for some fluorochromes. However, for some samples, the
Speed mode does not reduce the sensitivity.

Depending on the sample, you should experiment using both modes so that
you can make a reasonable trade-off between scan time and sensitivity. If you
are unsure and need the best results for your multilabel experiment, you should
use the Sensitivity parameter.

After you click the Auto-Link button, Scanner Control links the scans that
display the colored dots. Brackets appear connecting the Use check boxes, and
the Image numbers change to indicate which scans Scanner Control combined
into one scan (figure 9-5).

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Manually linking scans

If you do not want to use the Auto-Link feature, you can manually link two
scans using the link buttons in the Link With area. For each scan that can
be linked, link buttons ( ) appear in the Link With area. An
optimal link displays a colored dot above the link button. Nonoptimal links do
not display a colored dot. You can create both optimal and nonoptimal links.

In the Link With area for one of the scans you want to combine, click the
link button that corresponds to the scan you want to combine with this scan.
After you click the link button, brackets appear connecting the Use check
boxes for the linked scans.

For example, figure 9-5(a) shows Image 1 can be linked to either Image 2, 3,
or 4. The colored dot above the link button for Image 2 shows that Image 2
is the optimal link for Image 1. To manually link Image 1 and Image 2, you
click one of the link buttons that has a colored dot. Figure 9-5(b) shows the
Fluorescence Setup window after the scans have been linked. Note that both
scans now display a 1 as the image number.

Scanner Control selects the beamsplitter you should use for the linked scan.
You can change to any beamsplitter displayed in the Beamsplitter list. Scanner
Control warns you that you selected a nonoptimal beamsplitter when you close
the Fluorescence Setup window.

Figure 9-5(a) also shows that you could link Image 1 with Image 3 or Image 4,
but these links are not the optimal links.

To link Image 1 with Image 3, click the Image 1 link button in the Link With
area for Image 3. After you click the link button, brackets appear connecting
the Use check boxes for the original Image 1 and Image 3. In addition, the
Image numbers change to indicate which scans you combined into one scan.
After you link nonoptimal scans and click OK, Scanner Control warns you that
your selection is not optimal, saves the parameters, and closes the Fluorescence
Setup window.

If you do not want Scanner Control to warn you that you selected nonoptimal
links, click the Disable link warning check box. Otherwise, after you click OK
to save the parameters and close the Fluorescence Setup window, Scanner
Control will display a message warning you of the nonoptimal links.

Unlinking scans
If you want to make changes to the scan parameters, you must unlink the scan
first. To unlink the linked scans, click the Unlink All button. Scanner Control
removes all the links. You no longer see the brackets connecting the Use check
boxes, and the Image numbers return to their original numbers.

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9.3.8 Closing the Fluorescence Setup window

After you finish selecting the fluorescence parameters, click OK to save the
parameters and close the Fluorescence Setup window. Scanner Control warns
you if you have selected a nonoptimal link, laser, or beamsplitter.

If you do not want to save the parameters, click Cancel to return to the
Scanner Control window.

The Scanning Information area in the Scanner Control window displays the
parameters you selected in the Fluorescence Setup window, including the
linking information.

Important In the Scanner Control window, the scans are labeled by channel number, not
scan number. If you linked scans, the channel numbers might not match the order
of the Image number in the Fluorescence Setup window. Scanner Control reorders
the scans so that linked scans appear as contiguous channel numbers. For
example, if you linked Images 1 and 3, they become channels 1 and 2 in the
Scanning Information area. In addition, the scans are arranged so that the scan
with the longest wavelength is listed first in the channel order. ImageQuant uses
the channel number to display multichannel images. For more information, see the
ImageQuant User’s Guide or Help within the software.

9.4 Starting a scan and checking the progress

Warning Do not attempt to defeat the safety interlocks on the sample lid. These interlocks
are designed to protect you from laser light exposure.

Caution Never turn off the Typhoon instrument or disconnect the Ethernet cable while
scanning. You can damage the internal mechanism of the instrument.

Important Keep the sample lid closed during the scan. Opening the lid causes the
instrument to close the laser shutter and block the laser light. Then Scanner
Control aborts the scan and saves the data already collected.

During the scanning process, light illuminates each position on the sample
only while the corresponding pixel is being recorded. The position is minimally
exposed during the rest of the scan.

Scanner Control creates a single image file or a set of files and automatically
adds the correct file extensions. The image file extensions are—

• Data File (.gel)—A single image file. If you are scanning the sample once
using one laser or you selected the DIGE File Naming Format check box,
Scanner Control adds this extension.

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Part three Scanning in the fluorescence mode

• Dataset File (.ds)—The image file required for viewing a multichannel

image. If you linked scans or are scanning the sample more than once
by selecting more than one scan in the Fluorescence Setup window,
Scanner Control adds this extension.

If you select Dataset File (.ds), Scanner Control creates a Directory folder
(.dir) in the Data folder (or the location you selected) and names the
.dir folder using the same name as the .ds file. The .dir folder contains a
backup .ds file and one .gel file for each channel of the multichannel image
(up to four channels).

Note: If you select or type the wrong file extension, Scanner Control changes
the file type back to the correct extension.

9.4.1 Starting a single-channel scan of a single sample or

single scan area
If you are scanning a single sample or included multiple samples in a single
scan area, you create one image file.
To start the scan—
1. Make sure that the sample is in place, the sample lid is shut, and all the
parameters are correct in the Scanner Control and Fluorescence Setup
windows.
2. In the Scanner Control window, click the Scan button. The Save as window
appears (figure 9-6).

Figure 9-6. The Save as window.

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3. In the Save As window, type a name in the File name box.

Caution If you type a name that is already used, a message appears and asks you if you
want to replace the existing file. Before you click Yes, make sure you do not want
to keep the existing image file. Clicking Yes deletes the existing image and all the
associated auxiliary files. If you have analyzed the image using ImageQuant, all
the data will be deleted.

4. (Optional) Select a different folder. Otherwise, the software saves the image
in the Data folder.

Caution Using a network to save the scanned data to a folder located on a remote computer
can slow or delay the scan. For the best results, select a folder on the local hard
drive. After you scan the sample, move the image files to the remote computer.

5. To start the scan, click Save.

If you selected Press Sample in section 9.2.5, the inner lid of the Typhoon
instrument lowers to hold the sample flat against the glass platen of the
instrument.

9.4.2 Starting a multichannel (non-DIGE) scan of multiple

samples and multiple scan areas
If you are scanning multiple (non-DIGE) samples and you created separate
scan areas for each sample, you can create a separate multichannel dataset file
for each scan area.

To start the scan—

1. Make sure that the sample or samples are in place, the sample lid is shut,
and all the parameters are correct in the Scanner Control and Fluorescence
Setup windows.

Important Make sure the tray definition and number of samples in the Tray area match the
positions of the samples on the glass platen.

2. In the Scanner Control window, click the Scan button. The Multiple Sample
Naming window appears (figure 9-7).

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Part three Scanning in the fluorescence mode

Figure 9-7. The Multiple Sample Naming window.

3. In the Use Common Setting for All Samples area, click Browse and locate
an existing folder from the Browse for Folder window. Click OK to close
the window and return to the Multiple Sample Naming window. Click Set.

Caution Using a network to save the scanned data to a folder located on a remote computer
can slow or delay the scan. For the best results, select a folder on the local hard
drive. After you scan the sample, move the image files to the remote computer.
For dataset image files, make sure you move both the .ds file and the .dir folder.

4. To name—

• Each dataset file individually—In the File Name list, click the file
name that you want to change and then click Edit Sample File Name.
The Save As window appears. Type the name you want to use in the
File Name box, and click Save to close the window and return to the
Multiple Sample Naming window. Click the next file name that you
want to change and repeat the steps in this bullet.

• Each dataset file using the same base file name—In the Use Common
Setting for All Samples area, type a name in the Base File Name
box, and click Set. The software displays the base file name in the
File Name list.

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 Chapter 9 Scanning a fluorescent sample

• Each dataset file using an existing base file name—In the Use Common
Setting for All Samples Area, click Browse, and locate the file name
you want to use in the Name File window. Click OK to close the
window, and then click Set in the Multiple Sample Naming window.

5. Click Scan to start the scan.

After the scan, the software saves each dataset in the folder you selected.

• If you used unique names, the folder contains a dataset file (.ds) and dataset
folder (.dir) for each scan area.

• If you used a base file name, the software appends a number to each dataset
file (.ds) and dataset folder (.dir) to make the names unique. For example,
the file name for sample one will be basefilename1, where basefilename
is the name you entered in the Base File Name box and 1 is the number
appended to the name to indicate the first sample.

9.4.3 Starting a multichannel (DIGE) scan of multiple samples

and multiple scan areas
If you are scanning samples that you want to save in the DIGE file naming
format, you can create a separate image file for each channel in each scan area.

To start the scan—

1. Make sure that the samples are in place, the sample lid is shut, and all
the parameters are correct in the Scanner Control and Fluorescence Setup
windows.

Important Make sure the tray definition and number of samples in the Tray area match the
positions of the samples on the glass platen.

2. Make sure the DIGE File Naming Format check box is selected.

3. In the Scanner Control window, click the Scan button. The Multiple Sample
Naming window appears (figure 9-7). Default file names appear for each
sample.

4. In the Use Common Setting for All Samples area, click Browse and locate
an existing folder from the Browse for Folder window. Click OK to close
the window and return to the Multiple Sample Naming window. Click Set.

Caution Using a network to save the scanned data to a folder located on a remote computer
can slow or delay the scan. For the best results, select a folder on the local hard
drive. After you scan the sample, move the image files to the remote computer.

Typhoon User’s Guide ● p9-21

Part three Scanning in the fluorescence mode

5. To name the files from the Multiple Sample window, either—

• In the Use Common Setting for All Samples area, type a name in the
Base File Name box, and click Set. The software displays the base file
name in the File Name list.

• In the Use Common Setting for All Samples Area, click Browse, and
locate an existing file name you want to use in the Name File window.
Click OK to close the window, and then click Set in the Multiple
Sample Naming window.

To uniquely identify each dataset, the software appends a number to each

base file name.

6. (Optional) If you want to change the dataset name or the individual file
names for a sample, click the file name that you want to change and then
click the Edit Sample File Names button. The DIGE File Naming Format
window appears and displays the default names for each image of the
multichannel image (figure 9-8).

Figure 9-8. The DIGE File Naming Format window.

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 Chapter 9 Scanning a fluorescent sample

You can—

• Change the dataset name—Click the Edit button and type a new name
in the dataset name box. After you click OK, the name appears in the
Dataset Name box and in each image box.

• Change each image name—Delete the default image name and then
type a new image name.

• Identify the image to use as the standard—Click the Standard button

to the right of the image that you want to use as a standard. If you do
not want to identify an image as the standard, click None.

After you make all the changes, click OK to close the DIGE File Naming
Format window and return to the Multiple Sample Naming window.

Important After you type unique file names in the DIGE File Naming Format window and close
the window, do not type a name in the Base File Name box in the Multiple Sample
Naming window. Doing so causes the unique file names to be overwritten.

7. (Optional) If you want to change the file name for another sample,
repeat step 6.

8. Click Scan to start the scan.

After the scan, the software saves each dataset in the folder you selected.

• If you used unique names, the folder contains a datset file (.ds) and dataset
folder (.dir) for each scan area. The dataset folder contains the uniquely
named image files (.gel).

• If you used a base file name, the software appends a number to each
dataset file (.ds) and dataset folder (.dir) to make each multichannel dataset
name unique. The dataset folder contains the image files (.gel). To make
each image file name unique the software appends the fluorescent label
associated with the emission filter used to collect the image to the file
name. For example, the file name for the first scan of sample one will
be basefilename1dye, where basefilename is the name you entered in the
Base File Name box, 1 is the number appended to the name to indicate
the first sample, and dye is the fluorescent label.

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Part three Scanning in the fluorescence mode

9.4.4 The initialization process

Before the Typhoon instrument begins the scan, an initialization process
occurs. Depending on the state of the instrument and the scan parameters you
selected in Scanner Control, the initialization can take as long as 5 minutes.
A timer displays the time estimated for initialization. The timer counts down
as the initialization proceeds.

The initialization procedures include—

• Moving the scan head into position

• Changing the filters to match the scan parameters

• Stabilizing the laser if the laser has been idle, shut down, or recently
turned on

• Lowering the inner lid of the Typhoon instrument to hold the sample flat
against the glass platen (if selected)

Note: To avoid the extra 5 minutes of initialization time used to stabilize

the lasers when the instrument has been in the Sleep state, click the Initialize
Scanner button in the Scanner Control window several minutes before you
plan to start the scan.

9.4.5 Canceling the scan

If you decide you need to cancel the scan, click Cancel Scan in the ImageQuant
Preview window. Scanner Control saves the data collected before you canceled
the scan.

9.4.6 Monitoring the scan progress

After you start the scan, the ImageQuant Preview window appears (figure 9-9),
and the green Scan indicator light on the top of the instrument blinks. As the
Typhoon instrument scans the sample, Scanner Control displays the image in
the ImageQuant Preview window. In addition, Scanner Control displays the
number of data lines scanned and the total scan time remaining (excluding
initialization). Scanner messages can also appear as the scan progresses.

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 Chapter 9 Scanning a fluorescent sample

Figure 9-9. The ImageQuant Preview window during a scan set up for multiple
scan areas.

A More Info button appears in the ImageQuant Preview window when

the Typhoon instrument reports errors. Click the More Info button to view
the error message.

• If the error is a nonfatal error, the instrument continues to scan, and

Scanner Control saves the file when the scan is finished. You should
check the image in ImageQuant to make sure the data are not corrupted.

• If the error is a fatal error, the instrument aborts the scan, and Scanner
Control saves the data collected before the fatal error occurred. You
should check the image in ImageQuant. Depending on where the fatal
error occurred in the scan, you might be able to use the data. If you
cannot use the image for quantitation, you must scan again.

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Part three Scanning in the fluorescence mode

If you are performing a multichannel scan, the ImageQuant Preview window

displays the current scan. For example, if you selected parameters for four
unlinked scans in the Fluorescence Setup window, the instrument scans the
sample four times. You see an image in the ImageQuant Preview window for
each scan, one at a time.

If you used the link feature to combine two scans, you see one channel image
that was created using one emission filter, and you see one channel image that
was created using the second emission filter (figure 9-9).

If you create a multichannel image from both linked and unlinked scans, you
see two channel images for the linked scan, and you see one channel image
for the unlinked scans. Only the active scan image is shown in the ImageQuant
Preview window.

If the instrument is scanning multiple scan areas, you see the Preview Sample
box at the top of the window, which lists the number of scan areas. To view
the progress of a different scan area, select the scan area from the list.

9.4.7 Viewing the preview image for saturated data

While the instrument is scanning, an image appears in the ImageQuant Preview
window that shows the part of the sample that has been scanned. Saturated
data appear in red in the image. If the data portions of the image appear
saturated, you will not be able to perform quantitative analysis on the image.
Because saturation causes a total loss of the ability to distinguish the signal
intensity fluctuations, a saturated image can be used for viewing only the
shapes and positions of the spots on the sample.

To avoid saturation of the data, lower the PMT voltage you selected in the
Fluorescence Setup window (section 9.3.4). Note: Do not select a PMT voltage
below 500 V.

Important Before repeating the scan, verify in ImageQuant that the image is saturated
(100 000 rfu) and that you cannot perform accurate quantitation.

9.4.8 Completing the scan

Scanner Control saves the image or images using the file name you typed in
the Save As or Multiple Sample Naming window. The ImageQuant Preview
window displays a Complete message, and then closes. The Scan indicator light
on the Typhoon instrument turns off.

At the end of the scan, an image of the sample appears automatically in the
software you selected from the Image Analysis list. If you selected None, the
Scanner Control window remains active for more scanning.

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 Chapter 9 Scanning a fluorescent sample

9.5 Removing the sample from the Typhoon

instrument
After you finish scanning, you should remove the sample from the Typhoon
instrument and dispose of the sample using the established procedures in your
laboratory. Make sure the Scan indicator light turns off before you open the
sample lid and remove the sample.

9.6 Cleaning the glass platen and sample lid

To remove fluorescent contamination, you should clean the glass platen and
sample lid after you finish each scan. See section 8.2 for details.

9.7 Analyzing or preprocessing the scanned image

You should display the image of the sample to determine the quality of
the scan. If you selected an image analysis software in the Scanner Control
window, the software starts and displays the image. For detailed information,
see the user documentation or Help for the selected software.

If you created a multichannel image, the channel numbers displayed in the

Scanning Information area of the Scanner Control window are the same as
the channel numbers displayed in ImageQuant.

Typhoon User’s Guide ● p9-27

Part four

Scanning in the
chemiluminescence mode
Chapter 10 About
chemiluminescence
scanning

This chapter describes the theory behind chemiluminescence. The topics in

this chapter are—

• How chemiluminescence works (section 10.1)

• Advantages of chemiluminescence (section 10.2)
• How to optimize the chemiluminescent experiment (section 10.3)
• Beamsplitters (section 10.4)

10.1 How chemiluminescence works

Chemiluminescence is the release of light energy from a chemical reaction.
Chemiluminescent reactions used in biological assays typically emit visible
light from the enzymatic conversion of a synthetic substrate.

Most common chemiluminescent substrates react with enzymes, such as

peroxidase, alkaline phosphatase, or galactosidase. Each enzyme can initiate
multiple chemiluminescent reactions.

Depending on the system you use, the reaction kinetics and the wavelength
of the emitted light will vary. To assure saturation kinetics, you use an
excessive amount of the substrate. In addition, environmental influences,
such as temperature, affect the efficiencies of some chemiluminescent reactions.
See the manufacturer’s documentation for information about how the
environment affects the chemistry you are using.

You can detect the light emission from a chemiluminescent reaction using
film autoradiography or using a light-sensitive instrument, such as the
Typhoon system.

10.2 Advantages of chemiluminescence

Chemiluminescence is a popular and convenient alternative to radioactive,
fluorescent, and colorimetric detection methods. Unlike colorimetric or
fluorescent measurements, chemiluminescent samples contribute very little
native background because an exogenous light source (illumination or
excitation) is not required for detection. The lack of inherent background

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Part four Scanning in the chemiluminescence mode

and an extended output of the light signal (caused by enzyme catalysis)

contribute to sensitive detection over a wide dynamic range.

A variety of chemiluminescent substrates are commercially available for

different enzymes. The substrates are optimized for either solution or
solid-phase assays.

You can use the Typhoon system for membrane-based chemiluminescent

detection of protein and nucleic acid blots. In addition, you can use the
Typhoon system to scan microplate assays.

10.3 How to optimize the chemiluminescent

experiment
When you design the chemiluminescent experiment, you need to evaluate
how to prepare the sample so that the image you create using the Typhoon
instrument can be used for quantitation. Several factors affect the quality
of the experiment.

For accurate quantitation and limit of detection, time is a critical factor in

the chemiluminescent experiment. You should make sure you understand the
effects the following have on the quality of the scan:

• Substrate—You should test several substrates and evaluate which substrate

emits light for the length of time required for the Typhoon instrument
to scan the sample. If the signal intensity of the substrate diminishes
significantly before the instrument completes the scan, you might not
be able to perform accurate quantitation on the last part of the sample
scanned by the instrument (figure 10-1).

Substrate 2
Signal Intensity Substrate 1

Time (hr)

Figure 10-1. How signal intensity of a substrate and time affect the scan.

p10-2 ● Typhoon User’s Guide

 Chapter 10 About chemiluminescence scanning

• Scanner Control parameters—The parameters you select in Scanner

Control affect how long the instrument needs to scan the sample. The
parameters that can increase the scan time are sensitivity (section 12.3.2),
which sets the limit of detection, and pixel size (section 12.2.6).

• Sample size and position—The size of the scan area and the position of
the sample on the glass platen also affect the amount of time the Typhoon
instrument needs to scan the sample (section 11.3).

• Instrument state—An instrument in the Sleep state requires approximately

4 minutes to warm up before entering the Ready state. You can reduce the
time required to scan a sample by 4 minutes if you bring the instrument
to the Ready state before starting the scan (section 3.4).

When selecting the parameters in the Scanner Control window and the
Chemiluminescence Setup window, note the time change in the Scanning
Information area at the bottom of the Scanner Control window. If the signal
intensity of the sample diminishes significantly before the instrument finishes
the scan, the accuracy of the collected data can be affected.

10.4 Beamsplitters
The Typhoon instrument contains three standard beamsplitters and has a slot
for one additional custom beamsplitter. You can use the beamsplitters with
chemiluminescent detection to collect light emitted at different wavelengths.
Table 10-1 lists the three standard beamsplitters.

Table 10-1. Standard beamsplitters

Beamsplitter Description
560-nm dichroic Reflects light of wavelengths shorter than 560 nm and
passes light longer than 560 nm.

580-nm dichroic Reflects light of wavelengths shorter than 580 nm and

passes light longer than 580 nm.

630-nm dichroic Reflects light of wavelengths shorter than 630 nm and

passes light longer than 630 nm.

The instrument uses the beamsplitter you select in the Chemiluminescence

Setup window of the Scanner Control software (section 12.3.3) to create
two images from a single scan. This optimizes scanning of samples containing
two chemiluminescent substrates by reducing the scan time. The beamsplitter
separates the emissions from the substrates so that one PMT collects the longer
wavelength emissions while the other PMT collects the shorter wavelength
emissions (figure 10-2).

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Part four Scanning in the chemiluminescence mode

Emission filter

Mirror
PMT
Short wavelength

Emitted light
PMT
Long wavelength
Beamsplitter
Emission filter

Figure 10-2. How the beamsplitter separates short- and long-wavelength emissions.

p10-4 ● Typhoon User’s Guide

 Chapter 11 Setting up for
chemiluminescence
scanning

This chapter describes how to prepare a sample for chemiluminescence

scanning and how to place the sample in the Typhoon instrument. The topics
in this chapter are—

• Preparing the sample (section 11.1)

• Cleaning the glass platen and sample lid (section 11.2)
• Loading the sample (section 11.3)

11.1 Preparing the sample

You should follow the manufacturer’s guidelines for preparing membranes or
microplates for chemiluminescence scanning.

To avoid compromising the chemistry on the membrane, place the membrane

between two pieces of transparency material or between sheet protectors.
Alternatively, you can place the membrane in a plastic bag to keep the sample
wet and surrounded by substrate.

11.2 Cleaning the glass platen and sample lid

You should clean the glass platen and sample lid before placing the sample
on the platen. In addition, you should protect the glass from scratches because
scratches interfere with accurate imaging and quantitation.

Important If you use the Typhoon instrument for storage phosphor scanning, you should
periodically check the instrument for contamination from radioactive samples
(section 6.1.1).

11.2.1 Cleaning the glass platen

The glass platen of the Typhoon instrument should be kept free of sources of
contamination (such as substrate). It is good practice to clean the glass platen
before and after you scan each sample.

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Part four Scanning in the chemiluminescence mode

Important To protect your hands from the ethanol and hydrogen peroxide used in this
procedure and to avoid transferring oils from your hands onto the glass platen,
you should wear gloves. If you use the Typhoon instrument for fluorescence
scanning, make sure the gloves are powder free.

To clean the glass—

1. Push up on the lid release under the center front of the sample lid until the
lid opens (figure 11-1).

Push up on the
lid release.

Sample lid
(open)

Lid release

Sample lid

Figure 11-1. Releasing and opening the sample lid.

2. (Optional) If you use the instrument for fluorescent scanning and

fluorescent material has come in direct contact with the glass platen,
moisten a lint-free cloth with 10% hydrogen peroxide and wipe the
glass several times.

3. Clean the glass with distilled water and a clean, lint-free cloth or paper.
If visible spots remain, clean the glass first with 75% ethanol and then
with distilled water.

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 Chapter 11 Setting up for chemiluminescence scanning

Caution Because window cleaners contain ingredients that can fluoresce, do not use
window cleaners to clean the glass platen. In addition, the use of acetone or the
excessive use of ethanol can shorten the lifetime of the instrument. Protect the
glass from scratches. Scratches interfere with accurate imaging and quantitation.

11.2.2 Cleaning the sample lid

The surface of the inner lid should be clean and free of chemiluminescent
contamination. If necessary, clean the surface with a damp (not saturated)
cloth moistened with a small amount of distilled water. Note: You should wear
powder-free gloves to protect your hands when cleaning the sample lid using
75% ethanol. If visible spots remain, clean the surface first with 75% ethanol
and then with distilled water. To prevent liquid from getting inside the lid or
rolling down onto the glass, do not spray liquid on the lid.

11.3 Loading the sample

Important If time is a critical factor for scanning the sample, you should set up the scan
parameters using the procedures in chapter 12 before you place the sample on the
glass platen.

Before you load the sample, determine how to position the sample on the glass
platen of the instrument.

11.3.1 Determining the sample orientation

The Typhoon instrument collects data from underneath the sample. Use the
following guidelines when determining the sample orientation:

• Membranes—Place the sample face down on the glass platen.

• Microplate—Place the microplate on the glass platen so that the edges of

the plate are aligned with the grid markings on the glass platen.

Note: Make a note of the grid square coordinates covered by the sample. You
will use this information in the Scanner Control window (section 12.2.4).

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Part four Scanning in the chemiluminescence mode

11.3.2 Determining the sample placement

Use the following guidelines and figure 11-2 to determine where on the glass
platen to place the sample:

• To minimize the scan time—

- Place the sample near the A1 corner of the grid. Each lettered or
numbered grid segment is marked by two dots.

- Position a rectangular sample so that the shortest edge is along the

numbered side of the glass platen as shown in figure 11-2. Because each
pass of the scan head moves the entire length of the glass platen (from
front to back), placing the longest edge of the sample along the scan
head path minimizes the scan time.

• To minimize the size of the image file—

- Scan only the number of grid squares covered by the sample. If you do
not want to scan the entire sample, scan the squares that contain the
part of the sample you are interested in analyzing.

- (Typhoon 8610, 9210, and 9410 only) Use the 10-µm pixel size to scan
smaller samples only. Because the 10-µm pixel size creates a large file,
you can scan approximately two-thirds of the total scan area before
you exceed the 1-GB file size limit for a single-channel image. For
a linked multichannel image, each channel cannot exceed 400 MB.
Scanner Control warns you if you try to select a scan area that exceeds
the two-thirds limit.

• To record multiple samples during the same scan, place the samples close
together. Make sure the samples are the same thickness. If the samples
are not the same thickness, the selected focal plane might not be optimal
for each sample, which can result in a bad scan, poor image, and poor
quantitation results.

• Align the lanes and rows of the sample with the edges of the grid on the
glass platen so that the scanned image will be straight.

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 Chapter 11 Setting up for chemiluminescence scanning

Top view Back of the Typhoon instrument

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L Coordinates
K

J
K

J
of this grid
I

H
I

H
square, L10
G G

F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Coordinates of this
grid square, A1
Front of the Typhoon instrument

Figure 11-2. Sample placement on the glass platen of the Typhoon instrument.

11.3.3 Placing a sample on the glass platen

You can place the sample directly on the glass platen. If you are scanning a
membrane, place the membrane inside transparency material, sheet protectors,
or a plastic bag, and then place this on the glass platen.

You place the sample on the glass platen so that the sample creates a smooth
surface on the glass. Avoid trapping air bubbles between the sample and the
glass platen. Air bubbles can appear on the scanned image.

Before placing a wet sample on the glass platen of the instrument, squirt a little
buffer or distilled water on the glass platen. The buffer or distilled water lowers
the chance of trapping air bubbles between the sample and the glass platen.

Important Make sure you wipe up the excess buffer or distilled water. Using too much
liquid can cause the sample to move on the glass platen during the scan,
which could affect the quality of the collected data.

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Part four Scanning in the chemiluminescence mode

To place a sample on the glass platen of the Typhoon instrument—

1. If the sample lid is not already open, push up on the lid release under the
center front of the lid until the lid opens (figure 11-1).

2. (Optional) For a wet sample, squirt a little buffer or distilled water on the
glass platen.

3. Hold the sample by the edges or use forceps to handle the sample. Gently
lower the sample onto the glass platen starting at one edge. Do not trap air
bubbles under the sample or scratch the glass.

Important Do not touch the glass platen or the part of the sample that will be read by the
Typhoon instrument. Oil from fingerprints and powder from gloves, even thoroughly
washed gloves, can leave a mark that affects the quality of the image.

4. Make a note of the grid square coordinates of the area you want to scan
(figure 11-2). You will use this information later in the Scanner Control
window (section 12.2.3).

5. Close the sample lid and press the lid down until the latch clicks. The
sample is ready to scan.

p11-6 ● Typhoon User’s Guide

Chapter 12 Scanning a
chemiluminescent
sample

This chapter provides step-by-step instructions for scanning a

chemiluminescent sample. The topics in this chapter are—

• Checking the instrument state (section 12.1)

• Selecting the scan parameters in the Scanner Control window (section 12.2)
• Using the Setup window to select the chemiluminescence parameters
(section 12.3)
• Starting a scan and checking the progress (section 12.4)
• Removing the sample from the Typhoon instrument (section 12.5)
• Cleaning the glass platen and sample lid (section 12.6)
• Analyzing or preprocessing the scanned image (section 12.7)

12.1 Checking the instrument state

If time is critical for your experiment, you can make sure the instrument is
ready to scan the chemiluminescent sample by checking the instrument state,
which is displayed at the top left of the Scanner Control window (figure 12-1).
If the instrument state is Ready, you can select the scan parameters for your
scan, place the sample on the glass platen, and start the scan.

If the instrument is in the Sleep state, click the Initialize Scanner button to
bring the instrument to the Ready state. The Instrument State area displays
a Warming Up message. The warm-up period takes approximately 5 minutes.
During the warm-up period, you can prepare the sample and select the scan
parameters in the Scanner Control window.

If time is not critical for your experiment, you can select the scan parameters,
place the sample on the glass platen, and start the scan while the instrument
is in the Sleep state. The instrument takes 4 minutes during initialization
to stabilize the lasers and system components before starting the scan. The
instrument takes approximately 1 additional minute to position the scan
head, select the correct beamsplitter, and lower the sample lid (if selected).

For more information on instrument states, see section 3.4.

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Part four Scanning in the chemiluminescence mode

Instrument State area

Figure 12-1. The Scanner Control window set for a chemiluminescence scan.

12.2 Selecting the scan parameters in the

Scanner Control window
You use the Scanner Control window (figure 12-1) to select the parameters
you want to use when you scan the chemiluminescent sample. If the Scanner
Control window is not open, see section 3.3.

12.2.1 Selecting a template

If a template exists with the parameters you want to use, you can select the
template, review the parameters, add user comments (section 12.2.9), and
then start the scan (section 12.4). For more information on creating and using
templates, see section 3.7.
To select a template, choose Load from the Templates menu and then select
the template name from the list.
If a template does not exist, select the parameters using the instructions in
sections 12.2.2 through 12.3.4.

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 Chapter 12 Scanning a chemiluminescent sample

12.2.2 Selecting the chemiluminescence scan acquisition

mode
Make sure Chemiluminescence is the selected scan acquisition mode. If it is
not, select Chemiluminescence from the Acquisition Mode list. The selections
for the chemiluminescence scan acquisition mode appear in the Scanner
Control window (figure 12-1) and in the additional Chemiluminescence Setup
window.

12.2.3 Selecting the scan area

The grid in the Scanner Control window allows you to select the area to
scan. The letter and number markings correspond to the markings on the glass
platen of the Typhoon instrument. The white rectangle on the grid designates
the area you want to scan. You can either use the current scan area, select a
predefined scan area from the Tray list, or select a new scan area using the grid.

If you are selecting a predefined scan area from the Tray list, select the tray
definition that matches how you are placing the samples on the glass platen.
The grid changes to the parameters for the tray definition you selected. If
you are scanning fewer samples than defined in the tray definition, select the
number in the Tray number list that corresponds to the number of samples you
are scanning. The grid changes to reflect the number of scan areas you selected.

Important In the Tray area, the User Select parameter allows you to select the scan area
using the procedure below. The 1 parameter indicates that you have selected only
one scan area. However, if you are scanning multiple samples, you can customize
the scan area using the Tray Editor to define a separate scan area for each sample
(section 3.6).

To select a new scan area using the grid—

1. Place the pointer in the grid square that corresponds to the lowest lettered
and numbered grid square of the area you want to scan (figure 12-2). For
example, grid square A1 is the lowest lettered and numbered grid square on
the glass platen.

2. Drag the pointer to the grid square that corresponds to the highest lettered
and numbered grid square of the area you want to scan. For example, R22
is the highest lettered and numbered grid square on the glass platen.

3. Release the mouse button. The scan area you selected appears in white. The
Scanning Information area displays the image file size, the approximate
scan time, and the number of lines per channel.

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Part four Scanning in the chemiluminescence mode

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

J J

I I

H H

G G

F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

Figure 12-2. Selecting the scan area.

12.2.4 Selecting the sample orientation

You select the sample orientation from the Setup area in the Scanner Control
window (figure 12-1). The orientation buttons allow you to change how the
scanned image will be displayed in ImageQuant. To select an orientation, select
the icon that represents how you aligned the upper left corner of the sample
with the grid markings on the glass platen. Figure 12-3 describes each
orientation parameter.

Note: If you placed the sample on the glass platen so that the top of the sample
was aligned with the numbered rows, you can use the orientation buttons to
display the top of the sample at the top of the Image window in ImageQuant.

To display the orientation buttons, place the pointer on the button next
to Orientation in the Options area and hold down the mouse button. The
orientation buttons appear. Move the pointer to the button that represents
how you aligned the sample on the glass platen and release the mouse button.
During the scan, the software maps the pixels to display the image of your
sample face up and top-end up.

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 Chapter 12 Scanning a chemiluminescent sample

Orientation buttons

Sample placement on the For face-up sample, For face-down sample,

glass platen— select— select—

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

J J

I I

H H

G G

Top
F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

J J

I I

F
Top H

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

J J

I I

H H

G G

D
Top F

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

Q Q

P P

O O

N N

M M

L L

K K

J J

I I

H H

G G

Top
F F

E E

D D

C C

B B

A A

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

A1 corner

Figure 12-3. Determining which orientation button to use.

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Part four Scanning in the chemiluminescence mode

12.2.5 Selecting the Press Sample parameter

If you are scanning a dry membrane that does not lie flat against the glass
platen of the instrument, you can select the Press Sample check box. When you
scan the sample, the inner lid of the Typhoon instrument lowers to press the
sample flat. Alternatively, lay an electrophoresis glass plate over the sample
after you place the sample on the glass platen of the instrument.

If you do not select Press Sample, the inner lid remains retracted during
the scan.

Caution Do not select Press Sample if you are scanning wet membranes. Pressing wet
membranes that are not in a plastic bag can damage the instrument.

12.2.6 Selecting the pixel size

Pixel size refers to the size of each individual picture element that is recorded
and, together with the thousands of other pixels, forms the image. You select
the pixel size from the Pixel Size list in the Setup area of the Scanner Control
window (figure 12-1). After you change the pixel size, Scanner Control updates
the image size, the scan time, and the number of data lines per channel in the
Scanning Information area.

The pixel size you select affects the amount of time required to scan the
sample. Because chemiluminescent samples decay over time, the signal intensity
collected at the beginning of the scan is stronger than at the end of the scan.
Make sure you select a pixel size that causes the least amount of signal intensity
degradation for your scan; for example, use the 500-µm pixel size. For
more information on optimizing your chemiluminescent experiment, see
section 10.3.

Table 12-1 lists the pixel sizes.

Table 12-1. Pixel sizes

Pixel Size Description

1 000 µm For a very quick scan of the chemiluminescent sample, select
1 000 microns. The 1 000-µm pixel size produces 10 data points
per centimeter and 20 data lines per grid square. Note: If you
use the 1 000-µm pixel size, place your sample toward the
center of the scan area along the J row. The 1 000-µm pixel
size provides very rough data and is not recommended for
quantitative analysis.

500 µm For a quick scan of the chemiluminescent sample, select

500 microns. The 500-µm pixel size produces 20 data points
per centimeter and 40 data lines per grid square.

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 Chapter 12 Scanning a chemiluminescent sample

Table 12-1. Pixel sizes (continued)

Pixel Size Description

200 µm For most samples, select 200 microns. The 200-µm pixel size
produces 50 data points per centimeter and 100 data lines
per grid square.

100 µm For small samples that require high resolution, select

100 microns. The 100-µm pixel size produces 100 data
points per centimeter and 200 data lines per grid square.

50 µm The 50-µm pixel size produces 200 data points per centimeter
and 400 data lines per grid square.
Note: The amount of time required to scan using this pixel
size could exceed the signal intensity of the chemiluminescent
sample.

25 µm The 25-µm pixel size produces 400 data points per centimeter
and 800 data lines per grid square.
Note: The amount of time required to scan using this pixel
size could exceed the signal intensity of the chemiluminescent
sample.

10 µm The 10-µm pixel size produces 1 000 data points per centimeter
(Typhoon 8610, and 2 000 data lines per grid square.
9210, and 9410 Note: The amount of time required to scan using this pixel
only) size could exceed the signal intensity of the chemiluminescent
sample.

12.2.7 Selecting the focal plane

The Focal Plane area allows you to adjust the focal point of the collection
optics. Two parameters are available—

• Platen—Use this parameter if you placed a thin (less than 3 mm) membrane
on the glass platen of the Typhoon instrument. Scanner Control adjusts
the focal point of the collection optics to the area just above the glass platen
of the Typhoon instrument.

• +3 mm—Use this parameter if you are scanning a microplate or you

want to place the membrane on a piece of 3-mm electrophoresis glass plate
before setting the membrane on the glass platen of the Typhoon instrument.
Scanner Control adjusts the focal point of the collection optics 3 mm higher
than the glass platen to accommodate the height of the electrophoresis
glass plate used to support the membrane.

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Part four Scanning in the chemiluminescence mode

12.2.8 Selecting the image analysis software

If you want to analyze the image after you finish scanning, you can select the
image analysis software you want to use from the Image Analysis list in the
Setup area of the Scanner Control window (figure 12-1). After the instrument
finishes scanning, the selected software starts and displays the image.

If you select None from the Image Analysis list, the Scanner Control window
remains active so that you can perform another scan.

12.2.9 Entering user comments (optional)

Important The user comments are not saved as part of a template. If you want to include
comments, you must type the comments each time you scan.

In the User Comment box, type any comments you want to save with the image
(approximately 4 000 characters, including spaces). The comments are for
reference only and do not affect the scan. After the scan, you can view, but
not change, the comments in ImageQuant.

12.3 Using the Setup window to select the

chemiluminescence parameters
You use the Chemiluminescence Setup window to select the chemiluminescence
parameters to use with the sample. The following sections describe how to
use the Chemiluminescence Setup window (figure 12-4).

Figure 12-4. The Chemiluminescence Setup window contains parameters for

scanning a chemiluminescent sample.

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 Chapter 12 Scanning a chemiluminescent sample

12.3.1 Displaying the Chemiluminescence Setup window

To display the Chemiluminescence Setup window, make sure
Chemiluminescence is the selected acquisition mode, and then click the
Setup button in the Acquisition Mode area in the Scanner Control window
(figure 12-1).

12.3.2 Selecting the sensitivity (limit of detection)

You use the sensitivity parameters to help improve the limit of detection of the
Typhoon instrument. The sensitivity parameter controls how long the Typhoon
instrument collects data from each pixel. The Sensitivity parameters are—

• Normal (default)—Collects data from each pixel once. In general, you

should use the Normal parameter.

• Medium—Collects data from each pixel four times and averages the
results. Using the Medium parameter to detect weak signals improves the
sensitivity by reducing the background noise. Selecting Medium increases
the scanning time but does not increase the size of the image file. Check the
Scanning Information area in the Scanner Control window for the time
required to complete the scan.

(Typhoon 8610, 9210, and 9410 only) For the 10-µm pixel size, the system
collects data from each pixel twice and then averages the values.)

• High—Collects data from each pixel eight times and averages the results.
Using the High parameter to detect weak signals improves the sensitivity
by reducing the background noise. Selecting High will increase the scanning
time but does not increase the size of the image file. Check the Scanning
Information area in the Scanner Control window for the time required
to complete the scan. Note: This parameter is not available for the 10- and
25-µm pixel sizes.

12.3.3 Selecting a beamsplitter for a multichannel scan

The Typhoon instrument contains three standard beamsplitters and has a
slot for one additional custom beamsplitter. Table 10-1 lists the three standard
beamsplitters.

If you want to scan the chemiluminescent sample and create a multichannel

image, you must select a beamsplitter from the Beamsplitter list. The default
selection is None, which is the correct parameter for a single-channel
chemiluminescent scan.

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Part four Scanning in the chemiluminescence mode

12.3.4 Setting the PMT voltage

For chemiluminescent samples, you can alter the PMT voltage to improve the
signal collection capabilities of the Typhoon instrument.

Guidelines for changing the PMT voltage

For accurate quantitation of high-intensity samples, the pixel intensities in
your scanned image should be within a specific range. To determine the correct
PMT voltage, scan a test sample and display the image in ImageQuant. Use
the Gray/Color Adjust feature to display the intensity values of the image.
For more information, see the ImageQuant User’s Guide or Help within the
software.

• If the pixel values are more than 1 count and less than 100 000 counts, all
spots in your image are within the dynamic range of the instrument.

• If some of the pixel values are equal to or greater than 100 000 counts, part
of your image is at or near saturation. Lower the PMT voltage, rescan, and
confirm that the image is not saturated.

• For high-intensity samples that saturate the system, decrease the PMT
voltage. This brings high-intensity signals into the linear range of the
instrument. The image might lose the sensitivity and quantitation accuracy
at the lower end of the signal range. If you decrease the PMT voltage below
400 V, the image might lose linearity.

Important Increasing the PMT voltage can cause the signal-to-noise ratio to deteriorate and
lower the sensitivity. For the best sensitivity, use the High sensitivity parameter
with a lower PMT voltage.

If you change your sample matrix, you should test the PMT values between
400 V and 1 000 V to determine which voltage provides an acceptable
background. As a suggested starting point, use 600 V.

Procedure for changing the PMT voltage

To set the voltage in the PMT Voltage box—

• Click the box to select it, and then type the value you want. The maximum
value is 1 000 V.

• Use the up or down arrows to change the value in 5-V increments. To

approximately double the signal intensity, increase the PMT voltage
by 50 V.

If you are using a beamsplitter to perform a multichannel scan, you can select
a PMT voltage for each scan.

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 Chapter 12 Scanning a chemiluminescent sample

12.3.5 Closing the Chemiluminescence Setup window

After you finish selecting the chemiluminescence parameters, click OK to save
the parameters and close the Chemiluminescence Setup window. If you do not
want to save the parameters, click Cancel to return to the Scanner Control
window.

The Scanning Information area in the Scanner Control window displays the
parameters you selected in the Chemiluminescence Setup window.

12.4 Starting a scan and checking the progress

Warning Do not attempt to defeat the safety interlocks on the sample lid. These interlocks
are designed to protect you from laser light exposure.

Caution Never turn off the Typhoon instrument or disconnect the Ethernet cable while
scanning. You can damage the internal mechanism of the instrument.

Important Keep the sample lid closed during the scan. Opening the lid causes Scanner
Control to abort the scan and save the data already collected.

During the scanning process, the chemiluminescent sample emits light, which is
collected by either one or two PMTs.

Scanner Control creates a single image file or a set of files and automatically
adds the correct file extensions. The image file extensions are—

• Data File (.gel)—A single image file.

• Dataset File (.ds)—The image file required for viewing a multichannel

image. If you are scanning the sample using a beamsplitter, Scanner Control
adds this extension.

If you select Dataset File (.ds), Scanner Control creates a Directory folder
(.dir) in the Data folder (or the location you selected) and names the .dir
folder using the same name as the .ds file. The .dir folder contains a backup
.ds file and one .gel file for each channel of the multichannel image.

Note: If you select or type the wrong file extension, Scanner Control changes
the file type back to the correct extension.

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Part four Scanning in the chemiluminescence mode

12.4.1 Starting a single-channel scan of a single sample or

scan area
If you are scanning a single sample or included multiple samples in a single
scan area, you create one image file.

To start a scan—

1. Make sure that the sample is in place, the sample lid is shut, and all the
parameters are correct in the Scanner Control and Chemiluminescence
Setup windows.

2. In the Scanner Control window, click the Scan button. The Save as window
appears (figure 12-5).

Figure 12-5. The Save as window.

3. In the Save as window, type a name in the File name box.

Caution If you type a name that is already used, a message appears and asks you if you
want to replace the existing file. Before you click Yes, make sure you want to
replace the existing image file. Clicking Yes deletes the existing image and all the
associated auxiliary files. If you have analyzed the image using ImageQuant, all
the data will be deleted.

4. (Optional) Select a different folder. Otherwise, the software saves the

image in the Data folder.

Caution Using a network to save the scanned data to a folder located on a remote
computer can slow or delay the scan. For the best results, select a folder on the
local hard drive. After you scan the sample, move the image files to the remote
computer. For dataset image files, make sure you move both the .ds file and
the .dir folder.

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 Chapter 12 Scanning a chemiluminescent sample

5. To start the scan, click Save.

If you selected Press Sample in section 12.2.5, the inner lid of the Typhoon
instrument lowers to hold the sample flat against the glass platen of the
instrument.

12.4.2 Starting a multichannel (non-DIGE) scan of multiple

samples and scan areas
If you are scanning multiple samples and you created separate scan areas
for each sample, you can create a separate multichannel dataset file for each
scan area.

To start the scan—

1. Make sure that the sample or samples are in place, the sample lid is
shut, and all the parameters are correct in the Scanner Control and
Chemiluminescence Setup windows.

Important Make sure the tray definition and number of samples in the Tray area match the
positions of the samples on the glass platen.

2. In the Scanner Control window, click the Scan button. The Multiple Sample
Naming window appears (figure 12-6). Default file names appear for
each sample.

Figure 12-6. The Multiple Sample Naming window.

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Part four Scanning in the chemiluminescence mode

3. In the Use Common Setting for All Samples area, click Browse and locate
an existing folder from the Browse for Folder window. Click OK to close
the window and return to the Multiple Sample Naming window. Click Set.

Caution Using a network to save the scanned data to a folder on a remote computer can
slow or delay the scan. For the best results, select a folder on the local hard drive.
After you scan the screen, move the image file to the remote computer.

4. To name—

• Each dataset file individually—In the File Name list, click the file
name that you want to change and then click Edit Sample File Name.
The Save As window appears. Type the name you want to use in the
File Name box, and click Save to close the window and return to the
Multiple Sample Naming window. Click the next file name that you
want to change and repeat the steps in this bullet.

• Each dataset file using the same base file name—In the Use Common
Setting for All Samples area, type a name in the Base File Name
box, and click Set. The software displays the base file name in the
File Name list.

• Each dataset file using an existing base file name—In the Use Common
Setting for All Samples Area, click Browse, and locate the file name
you want to use in the Name File window. Click OK to close the
window, and then click Set in the Multiple Sample Naming window.
The software displays the base file name in the File Name list.

5. Click Scan to start the scan.

After the scan, the software saves each dataset in the folder you selected.

• If you used unique names, the folder contains a dataset file (.ds) and dataset
folder (.dir) for each scan area.

• If you used a base file name, the software appends a number to each dataset
file (.ds) and dataset folder (.dir) to make the names unique. For example,
the file name for sample one will be basefilename1, where basefilename
is the name you entered in the Base File Name box and 1 is the number
appended to the name to indicate the first sample.

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 Chapter 12 Scanning a chemiluminescent sample

12.4.3 Starting a multichannel (DIGE) scan of multiple

samples and multiple scan areas
If you are scanning samples that you want to save in the DIGE file naming
format, and you are creating a dataset, you can specify the file name for each
gel file within the dataset.

To start the scan—

1. Make sure that the samples are in place, the sample lid is shut, and all
the parameters are correct in the Scanner Control and Fluorescence Setup
windows.

Important Make sure the tray definition and number of samples in the Tray area match the
positions of the samples on the glass platen.

2. Make sure the DIGE File Naming Format check box is selected.

3. In the Scanner Control window, click the Scan button. The Multiple
Sample Naming window appears (figure 12-6). Default file names appear
for each sample.

4. In the Use Common Setting for All Samples area, click Browse and locate
an existing folder from the Browse for Folder window. Click OK to close
the window and return to the Multiple Sample Naming window. Click Set.

Caution Using a network to save the scanned data to a folder located on a remote computer
can slow or delay the scan. For the best results, select a folder on the local hard
drive. After you scan the sample, move the image files to the remote computer.

5. To name the files from the Multiple Sample window, either—

• In the Use Common Setting for All Samples area, type a name in the
Base File Name box, and click Set. The software displays the base file
name in the File Name list.

• In the Use Common Setting for All Samples Area, click Browse, and
locate an existing file name you want to use in the Name File window.
Click OK to close the window, and then click Set in the Multiple
Sample Naming window.

To uniquely identify each dataset file, the software appends a number to

the file name.

6. (Optional) If you want to change the dataset name or the individual file
names, click the file name that you want to change and then click the
Edit Sample File Names button. The DIGE File Naming Format window
appears and displays the default names for each image of the multichannel
image (figure 12-7).

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Part four Scanning in the chemiluminescence mode

Figure 12-7. The DIGE File Naming Format window.

You can—

• Change the dataset name—Click the Edit button and type a new name
in the dataset name box. After you click OK, the name appears in the
Dataset Name box and in each image box.

• Change each image name—Double-click to highlight the default image

name and then type a new image name.

• Identify the image to use as the standard—Click the Standard button to

the right of the image that you want to use as a standard. If you do not
want to identify an image as the standard, click None.

After you make all the changes, click OK to close the DIGE File Naming
Format window and return to the Multiple Sample Naming window.

Important After you type unique file names in the DIGE File Naming Format window and close
the window, do not type a name in the Base File Name box in the Multiple Sample
Naming window. Doing so causes the unique file names to be overwritten.

7. (Optional) If you want to change the file name for another sample,
repeat step 6.

8. Click Scan to start the scan.

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 Chapter 12 Scanning a chemiluminescent sample

After the scan, the software saves each dataset in the folder you selected.

• If you used unique names, the folder contains a dataset file (.ds) and dataset
folder (.dir) for each scan area. The dataset folder contains the uniquely
named image files (.gel).

• If you used a base file name, the software appends a number to each dataset
file (.ds) and dataset folder (.dir) to make the names unique. For example,
the file name for the first scan of sample one will be basefilename 1, where
basefilename is the name you entered in the Base File Name box and 1 is
the number appended to indicate the first sample.

12.4.4 The initialization process

Before the Typhoon instrument begins the scan, an initialization process
occurs. Depending on the state of the instrument and the scan parameters you
selected in Scanner Control, the initialization can take as long as 5 minutes.
A timer displays the amount of time estimated to be used during initialization.
The timer counts down as the initialization proceeds.

The initialization procedures include—

• Moving the scan head into position

• Changing the filters to match the scan parameters

• Stabilizing the PMT cooler if it has been idle, shut down, or recently
turned on

• Lowering the inner lid of the Typhoon instrument to hold the sample flat
against the glass platen (if selected)

Note: To avoid delays in initialization caused by the instrument warm-up time,

click the Initialize Scanner button several minutes before you plan to start
the scan.

12.4.5 Canceling the scan

If you decide you need to cancel the scan, click Cancel Scan in the ImageQuant
Preview window. Scanner Control saves the data collected before you canceled
the scan.

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Part four Scanning in the chemiluminescence mode

12.4.6 Monitoring the scan progress

After you start the scan, the ImageQuant Preview window appears
(figure 12-8), and the green Scan indicator light on the top of the instrument
blinks. As the Typhoon instrument scans the sample, Scanner Control displays
the image in the ImageQuant Preview window. In addition, Scanner Control
displays the number of data lines scanned and the total scan time remaining
(excluding initialization). Scanner messages can also appear as the scan
progresses.

Figure 12-8. The ImageQuant Preview window, showing a single-channel scan

of a chemiluminescent sample.

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 Chapter 12 Scanning a chemiluminescent sample

A More Info button appears in the ImageQuant Preview window when

the Typhoon instrument reports errors. Click the More Info button to view
the error message.

• If the error is a nonfatal error, the instrument continues to scan, and

Scanner Control saves the file when the scan is finished. You should
check the image in ImageQuant to make sure the data are not corrupted.

• If the error is a fatal error, the instrument aborts the scan, and Scanner
Control saves the data collected before the fatal error occurred. You
should check the image in ImageQuant. Depending on where the fatal error
occurred in the scan, you might be able to use the data. If you cannot use
the image for quantitation, you must scan again.

If you are scanning a sample using a beamsplitter, the ImageQuant Preview

window displays two images.

If the instrument is scanning multiple scan areas, you see the Preview Sample
box at the top of the window, which lists the number of scan areas. To view
the progress of a different scan area, select the scan area from the list.

12.4.7 Viewing the preview image for saturated data

While the instrument is scanning, an image appears in the ImageQuant Preview
window that shows the part of the sample that has been scanned. Saturated
data appear in red in the image. If the data portions of the image appear
saturated, you will not be able to perform quantitative analysis on the image.
Because saturation causes a total loss of the ability to distinguish the signal
intensity fluctuations, a saturated image can be used for viewing only the
shapes and positions of the spots on the sample.

To avoid saturation of the data, lower the PMT voltage you selected in the
Chemiluminescence Setup window (section 12.3.4), prepare a new sample,
and scan again.

Important Before repeating the experiment, verify in ImageQuant that the image is saturated
(100 000 rfu) and that you cannot perform accurate quantitation.

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Part four Scanning in the chemiluminescence mode

12.4.8 Completing the scan

Scanner Control saves the image or images using the file name you typed in
the Save as or Multiple Sample Naming window. The ImageQuant Preview
window displays a Complete message and then closes. The Scan indicator light
on the Typhoon instrument turns off.

At the end of the scan, an image of the sample appears automatically in the
software you selected from the Image Analysis list. If you selected None, the
Scanner Control window remains active for more scanning.

12.5 Removing the sample from the Typhoon

instrument
After you finish scanning, you should remove the sample from the Typhoon
instrument and dispose of the sample using the established procedures in your
laboratory. Make sure the Scan indicator light turns off before you open the
sample lid and remove the sample.

12.6 Cleaning the glass platen and sample lid

To remove chemiluminescent contamination, you should clean the glass platen
and sample lid after you finish each scan. See section 11.2 for details.

12.7 Analyzing or preprocessing the scanned image

You should display the image of the sample to determine the quality of the
scan. If you selected an image analysis software in the Scanner Control
window, the software starts and displays the image. For detailed information,
see the user documentation or Help for the selected software.

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Part five

Maintaining the Typhoon system

hardware
 Chapter 13 Maintaining the Typhoon
instrument

This chapter provides information about maintaining the Typhoon instrument.

The topics in this chapter are—

• Starting the Typhoon Direct Instrument Access software (section 13.1)

• Selecting a laser shut-off time (section 13.2)
• Changing the TCP/IP address (section 13.3)
• Installing an optical filter (section 13.4)
• Removing an optical filter (section 13.5)
• Changing the definition of an optical filter (section 13.6)
• Changing the fuses (section 13.7)
• Moving the Typhoon instrument (section 13.8)

13.1 Starting the Typhoon Direct Instrument Access

software
Several maintenance procedures use the Typhoon Direct Instrument Access
software to control the instrument or change parameters that affect the
instrument.

To use the Typhoon Direct Instrument Access software, you must have the
Internet Explorer browser software installed on the computer controlling the
Typhoon instrument.

Important If you use a proxy server to access the Internet, you must modify the Internet
options to exclude the address [Link] (or the IP number assigned to the
Typhoon instrument) from the proxy server. For more information on proxy servers,
see your browser software documentation, or the following Web site:
[Link].

To start the Typhoon Direct Instrument Access software—

1. Close the Scanner Control software.

Caution Before using the Typhoon Direct Instrument Access software, make sure you close
the Scanner Control software. Leaving Scanner Control running while you use the
window might cause problems in Scanner Control.

2. Start the Internet Explorer browser software.

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Part five Maintaining the Typhoon system hardware

3. Type the following in the Address box:

[Link]

Alternatively, type the IP address of the Typhoon instrument if the address

has been changed (section 13.3).

4. Click Go. The Typhoon Direct Instrument Access window appears in the
browser window (figure 13-1).

The Typhoon Direct Instrument Access window lists the maintenance

procedures. If you want to—

• Select a new laser shut off time, see section 13.2.

• Change the Typhoon IP address and subnet mask, see section 13.3.

• Install a new optical filter, see section 13.4.

• Remove an optical filter, see section 13.5.

• Prepare the instrument for moving or shipping, see section 13.8.

Figure 13-1. The Typhoon Direct Instrument Access window.

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13.2 Selecting a laser shut-off time

Shutting down the lasers after the instrument has been idle helps to prolong
the life of the lasers. You can use the Typhoon Direct Instrument Access
software to select the amount of time you want the instrument to remain idle
before the software shuts off the lasers. The lasers turn on automatically when
you turn on the instrument, when you start a scan, or when you click the
Initialize Scanner button in the Scanner Control window.

Caution Before using the Typhoon Direct Instrument Access software, make sure you close
the Scanner Control software. Leaving Scanner Control running while you use the
window might cause problems in Scanner Control.

To select a shut-off time for the lasers—

1. In the Typhoon Direct Instrument Access window, click Select A Laser Shut
Off Time. The Select A Laser Shut Off Time window appears (figure 13-2).

Figure 13-2. The Select A Laser Shut Off Time window.

2. In the Minutes box, type the number of minutes you want the instrument
to remain idle before the lasers shut off. The minimum value is 60 minutes.

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Part five Maintaining the Typhoon system hardware

3. Click Done to set the shut-off time and return to the Typhoon Direct
Instrument Access window.

4. Close the Typhoon Direct Instrument Access software.

Whenever the Typhoon instrument is idle for the time period you specified,
the lasers shut off. To reactivate the lasers, you can click the Initialize Scanner
button in the Scanner Control window, start a scan, or turn the instrument
off and then turn the instrument back on.

13.3 Changing the TCP/IP address

Caution Before using the Typhoon Direct Instrument Access software, make sure you
close the Scanner Control software. Leaving Scanner Control running while you
use the window might cause problems in Scanner Control.

When you received the Typhoon instrument, the default IP address was
[Link] and the default subnet mask was [Link].

To change the default TCP/IP address of the Typhoon instrument—

1. Consult the administrator for your laboratory network to determine an

appropriate new TCP/IP address and subnet mask for the instrument.

Important The IP address must be dedicated to the Typhoon instrument only.

2. In the Typhoon Direct Instrument Access window, click Change the

Typhoon TCP/IP Address. The Change Instrument IP Address window
appears (figure 13-3a).

3. Click Change IP Address. The Enter New IP Address window appears

(figure 13-3b).

4. In the IP address box, type the IP address that you received from the
administrator of the laboratory network.

5. Click Done. A message appears listing the old IP address and the new
IP address. Make sure the new address is correct. Do not restart the
instrument at this time.

Important Write down the new address here.

New IP address _______________________________________________________

6. Click the Back button once to return to the Change Typhoon Instrument
IP Address window (figure 13-3c).

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 Chapter 13 Maintaining the Typhoon instrument

(a)

(b)

(c)

Figure 13-3. Changing the IP address and subnet mask using (a) the Change Instrument IP Address window,
(b) the Enter New IP Address window, and (c) the Enter New IP Subnet Mask window.

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Part five Maintaining the Typhoon system hardware

7. Click Change IP Subnet Mask. The Enter New IP Subnet Mask window
appears.

8. In the Subnet Mask box, type the subnet mask that you received from the
administrator of the laboratory network.

9. Click Done. A message appears and lists the old subnet mask and the new
subnet mask. Make sure the new subnet mask is correct.

Important Write down the new subnet mask here.

New subnet mask _____________________________________________________

10. Close the Typhoon Direct Instrument Access software.

11. Restart the Typhoon instrument to reestablish the communication between

the instrument and the computer.

13.4 Installing an optical filter

Warning You must leave the Typhoon instrument turned on when you change the optical
filter selection. After you remove the front cover of the Typhoon instrument
and open the access and filter doors, make sure you follow the procedures in
this section to avoid injury.

When you receive the Typhoon instrument, the instrument contains a

standard set of optical (emission) filters that you use for fluorescence scanning
(section 7.3), one additional filter for storage phosphor scanning, and one
blank filter for multichannel experiments. The filter changer in the Typhoon
instrument can contain a maximum of 14 filters. To purchase additional filter
holders and for a list of possible filter vendors, contact Technical Support. See
Assistance in the preface for contact information.

The Typhoon instrument uses a bar code to identify each optical filter
installed in the filter changer. Bar codes 1 through 20 are reserved for optical
filters defined by Amersham Biosciences. Bar codes 21 through 62 can be used
for optical filters that you define. If you purchase custom optical filters from
another source and you do not have a sheet of bar code labels, contact
Technical Support.

You use the Typhoon Direct Instrument Access software to install an optical
filter. To start the software, see section 13.1.

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13.4.1 Moving the filter changer to the access door

The filter changer, which is attached to the slow stage of the Typhoon
instrument, is stored at the left side of the Typhoon instrument. The access
door for changing the filters is at the right side of the instrument. Before you
can install an optical filter, you must move the filter changer to the access door.
The following procedure moves the slow stage and positions the filter changer
at the access door so that you can add an optical filter.
Caution Before using the Typhoon Direct Instrument Access software, make sure you close
the Scanner Control software. Leaving Scanner Control running while you use the
window might cause problems in Scanner Control.
1. Start the Typhoon Direct Instrument Access software (section 13.1).
2. In the Typhoon Direct Instrument Access window (figure 13-1), click the
Insert or Eject Optical Filters option. The Filter Changer Maintenance Page
window appears (figure 13-4).

Figure 13-4. The Filter Changer Maintenance Page window.

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Part five Maintaining the Typhoon system hardware

3. Make sure the sample lid is closed, and then click Install a New Optical
Filter. The Insert a New Optical Filter into the Filter Changer window
appears (figure 13-5).

4. Click Access Filter Rod.

The slow stage begins to move from the left to the right side of the instrument,
and the Scan indicator light blinks red. When the Scan indicator light stops
blinking, the slow stage is in position to access the filter changer.

Figure 13-5. The Insert a New Optical Filter into the Filter Changer window.

13.4.2 Accessing the filter changer

Warning You must leave the Typhoon instrument turned on when you change the optical
filter selection. After you remove the front cover of the Typhoon instrument and
open the access and filter doors, make sure you follow the procedures in this
section to avoid injury.
To access the filter changer, you remove the front cover of the Typhoon
instrument and open the access and filter doors.
1. Make sure the slow stage has stopped moving, and the Scan indicator
light is no longer blinking.

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2. Use a 9/64-inch hex wrench to loosen the two socket-head screws on the
bottom of the front panel (figure 13-6). Turn the screws several times, but
do not remove them. Pull off the front cover.

Typhoon instrument
(a) Removing the front door

Access door

Screw

Screw

Front cover

(b) Opening the access door

Screw

(c) Opening the filter door Slide the filter holder

Fingernut all the way to the left.

Access door (open) Filter door Access door (open) Prongs Filter door (open)

Figure 13-6. Removing the front cover and opening the access and filter doors.

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Part five Maintaining the Typhoon system hardware

3. Use a 9/64-inch hex wrench to loosen the screw on the access door and
open the access door.

4. Loosen the fingernut on the filter door and open the filter door.

If the slow stage has not moved the filter changer into position, call Technical
Support. See Assistance in the preface for contact information.

13.4.3 Inserting a new optical filter

Warning You must leave the Typhoon instrument turned on when you change the optical
filter selection. After you remove the front cover of the Typhoon instrument and
open the access and filter doors, make sure you follow the procedures in this
section to avoid injury.

Before you insert the optical filter into the filter changer make sure the filter
is clean. If the filter is not clean—

• Remove dust using puffs from a dust-free blower.

• Remove water spots using a soft cloth.

• Remove fingerprints using a lens tissue and a few drops of spectroscopic

grade isopropyl alcohol.

Caution Before using the Typhoon Direct Instrument Access software, make sure you close
the Scanner Control software. Leaving Scanner Control running while you use the
window might cause problems in Scanner Control.

You use the Insert a New Optical Filter into the Filter Changer window to
insert a new filter.

1. Make sure a bar-code label is attached squarely to the top of the filter
holder as shown in figure 13-7.

2. Write down the bar code and the wavelength of the filter you are installing.
After you install the filter, you will need this information to register the
filter in the Scanner Control software (section 13.4.5).

3. Make sure the filter changer is in position.

4. Hold the optical filter so that the bar code is facing up and the metal notch
on the holder is on the left (figure 13-7).

5. Align the holes in the filter holder with the prongs on the filter changer
(figure 13-6).

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Bar code

Notch

Tab

Figure 13-7. The optical filter and holder with the bar-code label attached to the
top of the holder and the metal notch to the left.

6. Slide the filter holder all the way to the left. Make sure the bar code is on
the top and the metal notch is on the left.

Important Insert one filter at a time.

7. In the Insert a New Optical Filter into the Filter Changer window
(figure 13-5), click Insert Filter. The filter changer moves back inside the
Typhoon instrument. The instrument scans the bar code and moves the
filter holder to a slot farther back in the changer.

Messages appear for the following:

• If the instrument cannot insert the filter

• If you inserted the filter holder backwards

• If you did not push the filter holder all the way to the left

• If the filter holder does not have a bar-code label

• If you clicked Insert Filter before you inserted the filter

• If the instrument locates another filter that uses the same bar code as
the one you are installing

8. (Optional) To install additional filters, click Access Filter Rod, and then
repeat steps 1 through 7.

9. Click Done. The Typhoon instrument scans the bar codes of all the installed
filters and records the changes. After a minute, you see a list of all the filters
installed in the Typhoon instrument. Make sure the ID code for the filter(s)
you installed appears in the list.

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Part five Maintaining the Typhoon system hardware

10. Click OK to close the window and return to the Typhoon Direct Instrument
Access window.

11. Close the Typhoon Direct Instrument Access software.

13.4.4 Closing the doors and replacing the front cover

Warning You must leave the Typhoon instrument turned on when you change the optical
filter selection. After you remove the front cover of the Typhoon instrument and
open the access and filter doors, make sure you follow the procedures in this
section to avoid injury.

Use the following procedure and figure 13-6 to close the access doors and
replace the front cover.

1. Close the filter door and tighten the fingernut.

Important Make sure you tighten the fingernut. The Typhoon instrument will not scan if the
fingernut is loose.

2. Close the access door and use a 9/64-inch hex wrench to tighten the screw.

3. Align the pins on the instrument frame with the holes on the front cover
and gently push the cover back into place.

4. Use a 9/64-inch hex wrench to tighten the two socket-head screws at the
bottom of the front cover.

13.4.5 Registering a new optical filter in Scanner Control

Every time you start the Scanner Control software, Scanner Control checks the
current optical (emission) filters installed in the instrument. If Scanner Control
detects a filter with a new bar code, Scanner Control displays the Define the
Filter window so that you can define the filter.

1. Start the Scanner Control software. The Define the Filter window appears
(figure 13-8).

Important If you installed more than one filter, make sure you enter the correct filter
information for the bar code number displayed in the window.

2. In the Type list, select the filter type that you installed. The filter types are
Long Pass, Short Pass, and Band Pass.

3. In the Name box, type a name for the filter. For example, use the name of
a fluorescent dye that you will scan using this filter.

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Important If you will be using the DIGE file naming format, you should use the fluorescent dye
as the filter name. The software appends the filter name to the individual image
files created using the DIGE file naming format. For more information on the DIGE
file naming format, see section 9.4.3.

Figure 13-8. The Define the Filter window.

4. In the Peak WL box, type the wavelength of the filter. For example, type
555 for a 555-nm filter.

5. If the filter type you selected in step 2 is band pass, the BW box is active.
Type the bandwidth of the band-pass filter. For example, type 20 if the
bandwidth is 20 nm.

6. Click Register Filter. (If you click Don’t Register Now, you can use the
Typhoon instrument for scanning, but you will not be able to use the
new filter.)

7. (Optional) If you installed more than one filter, the Define the Filter
window appears again and displays the bar code number for the next filter
you inserted. Repeat steps 1 through 6 to register the additional filter(s).

You can now use the new optical filter(s) for scanning.

13.5 Removing an optical filter

Warning You must leave the Typhoon instrument turned on when you change the optical
filter selection. After you remove the front cover of the Typhoon instrument and
open the access and filter doors, make sure you follow the procedures in this
section to avoid injury.

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Part five Maintaining the Typhoon system hardware

You can remove an optical filter you no longer want to use. Make sure that
this filter is not used in any active templates created using the Scanner Control
software (section 3.7). If the filter is used in a template, you should modify or
delete the template. If you do not, Scanner Control removes the template from
the template list, and you cannot use it.

The following procedure moves the slow stage and positions the filter changer
at the access door so that you can remove an optical filter.

Caution Before using the Typhoon Direct Instrument Access window, make sure you close
the Scanner Control software. Leaving Scanner Control running while you use the
window might cause problems in Scanner Control.

1. In the Typhoon Direct Instrument Access window (figure 13-1), click the
Insert or Eject Optical Filters option. The Filter Changer Maintenance Page
window appears (figure 13-4).

2. Make sure the sample lid is closed, and then click Remove an Optical Filter.
The Remove an Optical Filter from the Filter Changer window appears
(figure 13-9).

Figure 13-9. The Remove an Optical Filter from the Filter Changer window.

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3. Click Eject Filter. The Select Filter ID to Eject window appears and displays
a list of the bar codes for the installed filters (figure 13-10).

Figure 13-10. The Select Filter ID to Eject window.

4. In the Filter box, type the bar code for the filter you want to remove.
(If you do not know the bar code, click Display Filter Descriptions to view
a list of the installed filters. Click Back to return to the Select Filter ID to
Eject window and type the bar code.)

5. In the Select Filter ID to Eject window, click Done to return to the Remove
an Optical Filter from the Filter Changer window. The slow stage begins
to move from the left to the right side of the instrument, and the Scan
indicator light blinks red. You can lift the sample lid and watch the slow
stage move into position.

6. After the slow stage stops moving and the Scan indicator light stops
blinking, use the procedure in section 13.4.2 to remove the front cover
and open the access and filter doors.

7. Slide the filter holder all the way to the right and remove the filter. Make
sure you do not touch the glass filter.

8. Store the filter in a lint-free box.

9. (Optional) To remove additional filters, click Eject Filter, type the bar code
for the next filter you want to remove, and then repeat steps 7 and 8.

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Part five Maintaining the Typhoon system hardware

10. In the Remove an Optical Filter from the Filter Changer window, click
Done. The instrument scans all the bar codes and displays a list of the
installed filters.

11. Click OK to close the window and return to the Typhoon Direct
Instrument Access window.

12. Close the Typhoon Direct Instrument Access software.

13. Use the procedure in section 13.4.4 to replace the front cover.

13.6 Changing the definition of an optical filter

After you install an optical (emission) filter in the Typhoon instrument and
define the filter in Scanner Control, you can change the definitions for the filter.
To do this—

1. In the Scanner Control window, select Fluorescence as the scan acquisition

mode and then click the Setup button. The Fluorescence Setup window
appears.

2. Select the emission filter you want to redefine from the Emission Filter list.

3. To display the Define the Filter window, right-click the selected emission
filter in the Emission Filter list. The Define the Filter window appears
and displays the current definition of the filter you selected in step 2
(figure 13-11).

4. Modify any of the following:

• Select a new filter type from the Type list.

• Type a new filter name in the Name box.

Important If you will be using the DIGE file naming format, you should use the fluorescent dye
as the filter name. The software appends the filter name to the individual image
files created using the DIGE file naming format. For more information on the DIGE
file naming format, see section 9.4.3.

• Type a new peak wavelength in the Peak WL box.

• If the filter is a band-pass filter, type a new bandwidth in the BW box.

5. Click Register Filter to redefine the filter and close the window. (If you
do not want to redefine the filter, click Don’t Register Now to close the
window.)

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Figure 13-11. The Define the Filter window.

13.7 Changing the fuses

Warning If fuses must be replaced repeatedly, the Typhoon instrument could have an
electrical problem. Do not use the instrument. Contact Technical Support. See
Assistance in the preface for contact information.

You can use the Typhoon instrument with either a 220–240 V (230V) power
source or a 100–120 V (115V) power source. The power supply in the
instrument switches to the correct voltage automatically. The fuse box is
located to the right of the power switch (figure 13-12).

The Typhoon instrument takes two 5A, 250V ( , T5A, 250V) slow-acting
fuses. The fuse holder is designed to accept both 0.25-in by 1.25-in English
fuses (designated 3AG fuses) and 5-mm by 20-mm metric fuses.

Front Back

Fuse box

Figure 13-12. Right side view of the Typhoon instrument.

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Part five Maintaining the Typhoon system hardware

(Typhoon 9400 and 9410 only) Note: You cannot change the fuses in the
blue laser module. If the blue laser module does not power on, contact
Technical Support. See Assistance in the preface for contact information.

To change a fuse—

1. Turn off the Typhoon instrument (section 3.9) and disconnect the
power cord.

2. Place the end of a small flathead screwdriver into the groove to the right
of the fuse box and pry open the fuse box (figure 13-13).

3. Place the screwdriver in the groove on the side of the fuse holder and pry
out the fuse holder. When the holder is loose, pull it out of the fuse box.

4. One or both fuses may be blown. Replace each blown fuse with a new fuse
of the same type and rating. Fuse specifications are listed at the beginning
of this section and on the serial number and fuse labels located on either
side of the fuse box.

5. Insert the fuse holder into the fuse box.

6. Snap the cover of the fuse box back into place.

7. Reconnect the power cord and turn on the Typhoon instrument

(section 3.1).

Fuse cover
Groove

Pry here to open

the fuse cover.

Pry here to remove

the fuse holder.
V511
V032

SPST

Fuse holder
Fuse cover open

Figure 13-13. Opening the fuse box.

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13.8 Moving the Typhoon instrument

If you need to move the instrument, contact Technical Support. See Assistance
in the preface for contact information. Use this section to determine a new
location for the instrument and to prepare for the move.

Warnings The Typhoon instrument weighs approximately 160 kg (350 lb). Only authorized
Technical Support representatives should move the instrument using the proper
lifting equipment. Injury to personnel and damage to the instrument can result
from attempting to lift the instrument without authorized personnel and proper
equipment.

If you use unauthorized personnel to move the Typhoon instrument, Amersham

Biosciences is not responsible for damage to the instrument or injury to personnel.
Damaging the instrument can void the warranty and can affect the accuracy of
the collected data.

(Typhoon 9400 and 9410 only) The blue laser module weighs approximately
29.5 kg (65 lb). Only authorized Service Support engineers should move the
module using the proper lifting equipment. Injury to personnel and damage
to the blue laser module can result from attempting to lift the module without
authorized personnel and proper equipment.

(Typhoon 9400 and 9410 only) To protect you from laser light exposure, only
authorized Service Support engineers can connect and disconnect the fiber-optic
cable from the blue laser power unit to the Typhoon instrument.

13.8.1 Determining a new location for the instrument

If you need to move the Typhoon instrument, make sure the new location for
the instrument is away from strong air currents, such as near an air vent. The
airflow can carry dust or dirt particles into sensitive parts of the instrument.
In addition, you should place the instrument away from direct sunlight or
other very bright light. Bright light can cause excessive heat or compromise
the light-tight operation of the instrument.

Make sure the instrument has at least 5 cm (2 in) of clearance on both

sides and behind it. Make sure you have 1.2 m (4 ft) of clearance above the
instrument. If the temperature of the room containing the instrument exceeds
30 °C (86 °F), increase the clearance on all sides by 2.5 cm (1 in).

Caution Blocking the airflow to the instrument can cause the instrument to overheat,
which can impact the instrument’s performance.

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(Typhoon 9400 and 9410 only) Make sure the blue laser module has at least
7.5 cm (3 in) of clearance behind it and 20 cm (8 in) of clearance on both sides.
If the blue laser module is located under a laboratory bench, you must provide
30 cm (12 in) of clearance on both sides of the module. If the temperature in
the room exceeds 30 °C (86 °F), you should use an external fan to vent the
exhaust out of the room.

Caution (Typhoon 9400 and 9410 only) If you do not use an external exhaust fan, the top of
the blue laser module can get very warm. Do not place any temperature-sensitive
materials on top of the blue laser module.

13.8.2 Preparing to move the Typhoon instrument

To prepare the Typhoon instrument for moving, you use the Typhoon Direct
Instrument Access software to park the scanner.

Caution If you do not park the scanner, the optical system of the Typhoon instrument can be
damaged during the move.

To park the scanner—

1. Start the Typhoon Direct Instrument Access software (section 13.1).

2. In the Typhoon Direct Instrument Access window, click Park Scanner for
Shipping. The Park Scanner for Shipping window appears (figure 13-14).

3. Click Park Scanner Now. The scan head moves to a secure position in the
Typhoon instrument.

4. Close the Typhoon Direct Instrument Access software.

5. Use the procedures in sections 3.9 and 3.10 to turn off the instrument and
computer.

Warning Do not disconnect the cables with the power on.

6. Disconnect the power cords and the Ethernet connections.

7. Wait for authorized Technical Support representatives to move the

instrument to the new location.

Warning (Typhoon 9400 and 9410 only) Do not disconnect the fiber-optic cable connecting
the blue laser module to the Typhoon instrument. Wait for the authorized Support
Service engineer.

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Figure 13-14. The Park Scanner for Shipping window.

13.8.3 Completing the installation after the move

If you connect the Typhoon instrument to a different computer than the
one used previously, you must make sure that the computer has a dedicated
Ethernet card to communicate with the Typhoon instrument. If you use
an Ethernet connection for your local area network (LAN), you will need two
Ethernet cards: one for communicating with the Typhoon instrument and one
for communicating with your building network. See the following Web site for
the Approved Computer list: [Link]. For the Ethernet
configuration procedure, see the same Web site and the instructions provided
with the Ethernet cards. In addition, you must make sure the computer is
running the Microsoft Windows operating system and that the Internet
Explorer browser software is installed on the computer.

After the instrument and computer have been moved to the new location,
you should—

1. Reconnect the instrument and computer.

2. Make sure you plug the instrument and computer into a surge protector,
which is plugged into a properly grounded outlet.

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3. Use the procedures in sections 3.1 and 3.2 to turn on the instrument and
computer.

4. Use the procedure in section 3.3 to start the Scanner Control software.

Scan a test sample to make sure the instrument is working properly. If

the instrument is not working properly, contact Technical Support. See
Assistance in the preface for contact information.

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 Chapter 14 Maintaining the
Typhoon system
accessories

This chapter provides information on the care and maintenance of the

Typhoon system accessories. The topics in this chapter are—

• Cleaning the Image Eraser (section 14.1)

• Changing the bulbs in the Image Eraser (section 14.2)
• Changing the fuses in the Image Eraser (section 14.3)
• Cleaning and protecting the exposure cassettes (section 14.4)
• Cleaning and protecting the microarray slide holder (Typhoon 8610, 9210,
and 9410 only) (section 14.5)
• Cleaning and protecting the gel alignment guides (section 14.6)

14.1 Cleaning the Image Eraser

Important To protect your hands from the ethanol used in this procedure, you should
wear gloves.

The surface of the Image Eraser must be clean and free of contamination from
radioactive samples when you erase screens. Otherwise, the screens will be
exposed to radioactive contamination during the erasure process.

Warning Because the Image Eraser uses high voltage, always turn off and unplug the eraser
before cleaning the surface. Do not allow liquid to seep into the Image Eraser. Use
a damp cloth only. Do not pour or spray liquid over the surface. Make sure the
eraser is totally dry before you reconnect the power cord.

1. Turn off the Image Eraser and disconnect the power cord (figure 14-1).

2. Clean the surface of the eraser with a damp cloth moistened with a small
amount of distilled water. If visible spots remain, clean the surface first with
75% ethanol and then with distilled water.

Caution Do not use powdered detergents. Any undissolved particles can scratch the
surface of the eraser.

3. Verify that the eraser surface is free of contamination from radioactive

samples.

4. Reconnect the power cord and turn on the Image Eraser.

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Part five Maintaining the Typhoon system hardware

Front view Side view

Image Eraser

Time Erase

Fuse window
Power switch

Figure 14-1. The Image Eraser.

14.2 Changing the bulbs in the Image Eraser

The Image Eraser contains four warm-white compact fluorescent bulbs. When
one of the bulbs fails, replace all four bulbs to provide uniform light intensity
across the screen. To order replacement bulbs, contact Technical Support or
your local service office (see the manufacturer part number on the bulb). See
Assistance in the preface for contact information.

To replace the bulbs—

1. Turn off the Image Eraser and disconnect the power cord (figure 14-1).

2. Remove the two screws that hold the clip support and diffuser screen
in place.

3. Lift off the clip support and diffuser screen.

4. Unscrew the bulb and fixture from the receptacle and replace the bulb and
fixture with a new bulb and fixture (figure 14-2).

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 Chapter 14 Maintaining the Typhoon system accessories

Screws

Image Eraser
Clip support

Grasp here and unscrew.

Time Erase
On/off switch

Figure 14-2. Removing a bulb from the Image Eraser.

5. Repeat step 4 to replace the three remaining bulbs and fixtures.

6. Replace the front diffuser screen and clip support, and reinsert the two
screws.

7. Reconnect the power cord and turn on the Image Eraser (figure 14-1).

14.3 Changing the fuses in the Image Eraser

Warning If the fuses must be replaced repeatedly, the Image Eraser could have an electrical
problem. Do not use the Image Eraser. Contact Technical Support. See Assistance
in the preface for contact information.

You can use the Image Eraser with either a 220–240 V (230 V) power source
or a 100–120 V (115 V) power source. The selected operating voltage of the
Image Eraser appears in the fuse window on the lower right side of the eraser,
next to the power switch (figure 14-1).

The fuse holder of the Image Eraser takes two 1.5A, 250V ( , T1.5A, 250V)
slow-acting fuses. The fuse holder accepts both 0.25- × 1.25-in English fuses
(designated 3AG fuses) and 5- × 20-mm metric fuses.

Typhoon User’s Guide ● p14-3

Part five Maintaining the Typhoon system hardware

To change a fuse—

1. Turn off the Image Eraser and disconnect the power cord (figure 14-1).

2. Note the voltage (115V or 230V) showing in the fuse window

(figure 14-3).

3. Look for the small groove above the fuse window.

4. Place the end of a small flathead screwdriver in the groove and pry open
the fuse box (figure 14-3).

5. Place the screwdriver in the groove on the upper edge of the fuse holder
and pry out the fuse holder. When the holder is loose, pull it out of the
fuse box.

6. One or both fuses may be blown. Replace each blown fuse with a new
fuse of the same type and rating. Fuse specifications are listed on the
serial number label located to the left of the fuse box.

7. Insert the fuse holder into the fuse box, making sure the correct voltage
rating for your power supply is right side up.

Pry here Pry here

to open the to remove the
fuse cover. fuse holder.
Groove

Fuse window Fuse holder

SPST

115V 115V 115V

230V

Fuse cover

Fuse cover open

Figure 14-3. Opening the fuse box.

p14-4 ● Typhoon User’s Guide

 Chapter 14 Maintaining the Typhoon system accessories

8. Snap the cover of the fuse box back into place. Check that the correct
voltage rating for your power source appears in the voltage window.
If the voltage is incorrect for your power source, remove the fuse holder,
rotate the holder 180° so that the correct voltage rating is right side up,
and reinsert the fuse holder.

Caution Before you turn on the Image Eraser after you change the fuse, make sure
that the correct operating voltage appears in the fuse window. Selecting the
wrong voltage can severely damage the eraser.

9. Reconnect the power cord and turn on the Image Eraser (figure 14-1).

14.4 Cleaning and protecting the exposure

cassettes
To protect the exposure cassettes from contamination and damage, observe
the following precautions and cleaning procedure:

• Do not place uncovered wet gels in the exposure cassette. Wet gels can
permanently contaminate the cassette. For information on using wet gels,
see section 5.1.2.

• Do not place sharp or heavy objects inside the cassette. A crease or dent
in the cassette lining causes uneven pressure on the sample.

• Keep the foam inside the cassette dry.

Important To protect your hands from the ethanol used to clean the exposure cassette, you
should wear gloves.

• Immediately before placing the sample in the cassette, clean the grid
surface of the cassette with a damp cloth moistened with a small amount
of distilled water. If visible spots still remain, clean the surface first with
75% ethanol and then with distilled water.

Caution Do not allow liquid to seep into the exposure cassette. Use a damp cloth only. Do
not pour or spray liquid in the cassette.

Typhoon User’s Guide ● p14-5

Part five Maintaining the Typhoon system hardware

14.5 Cleaning and protecting the microarray slide

holder (Typhoon 8610, 9210, and 9410 only)
To protect the microarray slide holder from contamination and damage,
observe the following precautions and cleaning procedure:

• After each use, clean the microarray slide holder and slide restraints with
a lint-free cloth moistened with distilled water.

• Store the microarray slide holder and slide restraints in a box or drawer
lined with a lint-free cloth.

14.6 Cleaning and protecting the gel alignment

guides
Caution Exposing the gel alignment guides to high heat can damage the guides. For
example, do not use an autoclave to clean the guides.

To protect the gel alignment guides from contamination and damage, observe
the following precautions and cleaning procedure:

• After each use, clean the gel alignment guides with a lint-free cloth
moistened with distilled water.

• Store the gel alignment guides in the gel alignment guides storage box.

p14-6 ● Typhoon User’s Guide

Part six

Appendixes
Appendix A Troubleshooting

If you are having problems with the Typhoon instrument or the Scanner
Control software, use the troubleshooting sections below to locate the
description that matches your problem. If you cannot find a solution, call
Technical Support. See Assistance in the preface for contact information.

Problems, in bold print, are followed by possible causes and solutions. The
topics in this appendix are—

• Power and communication (section A.1)

• Scanning (section A.2)
• Image (section A.3)

A.1 Power and communication

The power indicator light on the Typhoon instrument will not turn on.
• The instrument could be unplugged, or the surge protector switch could
be turned off. Plug in the instrument or turn on the surge protector.

• The wall outlet could be faulty. Test the outlet or try another one.

• The fuse(s) could have blown. To change the fuse(s), see section 13.7.

The Typhoon instrument is on but cannot communicate with the computer.

• You could be using the wrong type of Ethernet cable, or the cable could be
bad. The Typhoon instrument requires a crossover Ethernet cable. If you
are using the cable, make sure you are using the red Ethernet cable supplied
with the instrument.

• The Ethernet cable might not be properly plugged into the computer or the
instrument. Check the connections to make sure they are plugged in and
are securely fastened (figure A-1).

• If the New TCP IP Address window appears when you open Scanner
Control, the IP address has changed. Type the correct address in the
IP Address box and click OK. If you do not know the IP address, check
with your network administrator.

• If the problem still occurs, contact Technical Support. See Assistance in

the preface for contact information.

Typhoon User’s Guide ● A-1

Part six Appendixes

Typhoon 9200 and 9210 only

Computer
(Rear view)
Typhoon instrument
(right side view)

Red Ethernet cable

To site network

Typhoon 9400 and 9410 only

Computer
(Rear view)
Typhoon instrument
(right side view)

Red Ethernet cable

To site network
Laser control Fiber-optic
cable cable
Cables to blue laser module

Figure A-1. Ethernet connections on the Typhoon instrument and computer.

A-2 ● Typhoon User’s Guide

 Appendix A Troubleshooting

(Typhoon 9400 and 9410 only) The Typhoon instrument is on, but the
external blue laser module does not come on or the Connection light on
the instrument is not lit.
• The laser communication cable is not connected between the instrument
and the blue laser module. Alternatively, the cable might be the wrong
type. You must use the blue Ethernet cable that was included with the
instrument.

• The blue laser module is not plugged in or the wall outlet is faulty.

• If the problem still occurs, contact Technical Support. See Assistance in

the preface for contact information.

(Typhoon 9400 and 9410 only) The Laser On light on the blue laser
module is not lit.
• After you turn on the instrument or click the Initialize Scanner button,
approximately 30 seconds elapse before the light turns on. If the Laser On
light is not on after 30 seconds, contact Technical Support. See Assistance
in the preface for contact information.

• Check the instrument state in the Scanner Control window. If it is in the

Sleep state, click Initialize Scanner to turn on the laser.

• If the problem still occurs, contact Technical Support. See Assistance in

the preface for contact information.

(Typhoon 9400 and 9410 only) The blue laser module does not turn off
when you turn off the instrument.
The blue laser module continues to run for several minutes after you turn off
the instrument. After cooling the laser, the module should turn off. However, if
the blue laser module does not turn off after several minutes, contact Technical
Support. See Assistance in the preface for contact information.

A.2 Scanning
The instrument will not scan, and a warning message tells you that the
sample lid is up.
The sample lid might not be completely closed. Make sure you press the lid all
the way down until the latch clicks.

Typhoon User’s Guide ● A-3

Part six Appendixes

You start a scan, the ImageQuant Preview window remains unchanged

for at least 3 minutes, and the pointer no longer responds when you move
the mouse.
The computer has stopped functioning. Restart the computer using the
manufacturer’s instructions. Then start the Scanner Control software, reselect
the scanner parameters, and start the scan again.

You start a scan, and the software aborts the scan and displays the
following message: “Scan aborted—hardware error, please try to scan
again.”
The first time this happens, start the scan again. If the scan aborts again,
turn off the power switch on the right side of the Typhoon instrument, wait
a few seconds, and then turn the instrument back on. If the error happens
repeatedly, contact Technical Support. See Assistance in the preface for contact
information.

You start a scan, the software aborts the scan, and either—
• The software displays a message that does not give instructions for
resolving the problem (note the number of the message).

• The red Scan indicator light blinks.

Restart the scan as follows:

1. Close the Scanner Control window. Leave the computer on.

2. Turn off the power switch on the right side of the Typhoon instrument.
Wait a few seconds and turn it on again.

3. Start the Scanner Control software, reselect the parameters, and rescan.

If the problem occurs repeatedly, contact Technical Support. See Assistance

in the preface for contact information.

(Typhoon 9400 and 9410 only) The instrument will not scan using the
blue laser.
Make sure the blue laser module is plugged in, and the cables are connected to
the instrument. If the instrument state is Ready or the instrument is scanning,
all three lights on the front of the module are lit.

If the instrument still will not scan using the blue laser, contact Technical
Support. See Assistance in the preface for contact information.

A-4 ● Typhoon User’s Guide

 Appendix A Troubleshooting

A.3 Image
The image has a high background or inaccurate readings.
• The instrument might not have been warmed up before the sample was
scanned. If the Typhoon instrument has been turned off, allow 30 minutes
to warm up the instrument.

• The instrument could be damaged and no longer light tight. If so, do not
continue to use the instrument. Contact Technical Support to arrange for
repair. See Assistance in the preface for contact information.

• Dust, fingerprints, or other dirt could be on the screen, sample, or glass

platen. Clean the glass platen. If necessary, for fluorescence scans, filter
the liquid samples, reagents, and components used to make the gels.
For more information on removing contaminants, see sections 5.2
(storage phosphor), 8.2 (fluorescence), or 11.2 (chemiluminescence).

• The storage phosphor screen might not have been erased immediately
before you exposed it to the sample, or the residual image from an
intense sample might not have been erased completely.

• The sample support could have high autofluorescence. Use a low-

fluorescence material (section 8.1.3).

• The wrong emission filters could have been used for a fluorescent sample
(section 9.3.3).

The image is incomplete.

• The selected scan area in the Scanner Control window could be incorrect.
See sections 6.5.3 (storage phosphor), 9.2.3 (fluorescence), or 12.2.3
(chemiluminescence).

• The signal emitted by a chemiluminescent sample could have diminished

before the instrument finished scanning.

• The scan was aborted before it was complete, or an error occurred during
the scan.

The edges of the image created from a storage phosphor screen show
a loss of signal.
A light leak could have occurred during exposure. Make sure you expose
screens in the exposure cassette (or, with wet gels or thick samples, in a
light-tight drawer or other light-tight place). Check that your exposure
cassette closes properly.

Typhoon User’s Guide ● A-5

Part six Appendixes

The image created from a storage phosphor screen shows a loss of

resolution.
The sample might not be placed directly against the screen. Use the exposure
cassette whenever possible. Do not expose wet gels or thick samples in
exposure cassettes. Cover a wet gel with plastic wrap or polyester film to
protect the general-purpose (GP) screen.

The image created from either a storage phosphor screen or

fluorescent sample contains streaks or other artifacts.
• The instrument might not have been warmed up before the sample was
scanned. If the Typhoon instrument has been turned off, allow 30 minutes
to warm up the instrument.
• Diagonal streaks could indicate a light leak during scanning. Check
for damaged panels on the instrument. Contact Technical Support. See
Assistance in the preface for contact information.
• The glass platen could be scratched. If possible, scan the sample on another
portion of the glass. Contact Technical Support to order replacement glass
platen and arrange for a service call. See Assistance in the preface for
contact information.
• The storage phosphor screen could be contaminated. See section 5.2.3 for
details.

The image created from a storage phosphor screen contains streaks or

other artifacts.
• Static electricity could have accumulated on the screen. Clean the GP and
LE screens with an intensifying screen cleaner. Do not attempt to clean the
tritium (TR) screen.

• The screen could be contaminated with radioactive material. The source

of this contamination could be the surfaces of the eraser or the exposure
cassette. Clean the GP or LE screen, exposure cassette, and eraser surfaces
(section 5.2).

• The screen could have been exposed to too much light between the time
you removed it from the exposure cassette and the time you put it in the
instrument for scanning. Keep the screen face down in subdued light until
you place it in the instrument.

• The screen might not have been erased immediately before exposure.
Cosmic radiation will generate a background signal on screens left unused
for long periods of time.

• The screen might not have been completely erased. Select a higher setting
and erase again (section 5.2.4).

A-6 ● Typhoon User’s Guide

 Appendix A Troubleshooting

• The screen could be scratched. If possible, expose the sample on another

portion of the screen. For large samples, you will need to use a different
screen.

• Fingerprints could be on the screen. Clean the GP and LE screens with an

intensifying screen cleaner. Do not clean the TR screen. Instead, use a new
TR screen.

The image created from a fluorescent sample contains streaks or other

artifacts.
• Fingerprints appear in the scan. Clean the glass platen. If the fingerprints
are on the gel, rinse the gel briefly in 0.1% Tween™ or SDS. Rinse the gel
in distilled water and then scan again. If the fingerprints persist, you might
need to prepare a new gel and handle the new gel more carefully.

• Dust specks appear on the scan. Rinse wet gels in filtered distilled water
to remove surface dust prior to scanning. Filter liquid reagents used in
gels and buffers. Make sure you dissolve agarose completely before pouring
the gel. Clean the glass platen of the Typhoon instrument with a damp,
lint-free cloth.

• The tracking dye is fluorescing. Place the tracking dye in only one well,
or dilute the tracking dye with sample buffer.

• The sample could have stained unevenly. Make sure you mix staining
solutions thoroughly, use a large excess of staining solution, and
rock or shake the gels during staining, if possible.

The image created from a chemiluminescent sample contains streaks

or other artifacts.
• Make sure the sample is flat on the glass platen of the Typhoon instrument
and no air bubbles are trapped under the sample.

• Refer to the manufacturer’s documentation for any advice about sample

preparation.

The image created from a storage phosphor screen contains a double

image.
• The screen could have moved after the initial placement in the exposure
cassette. Always position the screen correctly on the first try and do
not readjust the placement. If readjustment is absolutely necessary, make
sure you erase the screen completely before placing it in the exposure
cassette again.

• The sample could have moved when the screen was inserted into the
cassette. Erase the screen and re-expose it to the sample. Do not tip the
cassette upright during exposure.

Typhoon User’s Guide ● A-7

Part six Appendixes

The image created from a fluorescent sample contains a double image.

• The sample could have moved after the initial placement on the glass platen
of the instrument. If fluorescent material has come off onto the glass platen,
carefully remove the sample and clean the glass. Then place the sample
on the glass platen again and do not readjust the placement.

• Remove excess liquid from gels so that the gels do not move on the
glass platen.

The image created from a chemiluminescent sample contains a

double image.
The sample could have moved after the initial placement on the glass platen
of the instrument. If chemiluminescent material has come off onto the glass
platen, carefully remove the sample and clean the glass. Then place the sample
on the glass platen again and do not readjust the placement.

The image created using the blue laser shows major fluctuations, or
the signal disappears in the middle of the scan.
The blue laser could be overheating. Make sure you have adequate room on
all sides of the blue laser module for ventilation (section 2.1).

A-8 ● Typhoon User’s Guide

Appendix B Quick reference for
menus and windows

The following is a quick reference for the Scanner Control software. The
topics in this appendix are—

• Menus (section B.1)

• Windows (section B.2)

B.1 Menus
The following menus and commands are used in the Scanner Control software:

File menu

Command Description
Name Dataset Displays the Save as window so that you can type a name
for the image you are about to create.

Exit Closes the Scanner Control software.

Templates menu

Command Description
Load Displays a list of all the templates for the Typhoon
instrument. After you select a template from the list,
the parameters for that template appear in the Scanner
Control window and, if the template is a fluorescence or
chemiluminescence template, in the Setup window.

Set Default/Load Displays a list of all the templates. After you select a
template from the list, the parameters for that template
become the default and appear when you open the
Scanner Control software.

Save As Template Displays the Save As Template window so that you can
type a name for the template and save the parameters.

Delete Template Displays the Delete Template(s) window, which lists all the
templates, except the template displayed in the Scanner
Control window and the Setup window (fluorescence and
chemiluminescence only). Allows you to select and
delete a template or templates.

Typhoon User’s Guide ● B-1

Part six Appendixes

Tray menu

Command Description
Tray Editor Displays the Tray Editor window, which allows you to
define multiple scan areas for a scan and save the
layout as a tray definition.

Help menu

Command Description
User’s Guide Displays an electronic version (in PDF format) of the
Typhoon User’s Guide.

Quickstart Displays an electronic version (in PDF format) of the

Typhoon Instrument QuickStart card.

About Displays the About Typhoon Scanner Control window,

which contains the copyright, version number of the
Scanner Control software, and contact information.

B.2 Windows
The following windows and window parameters are used in the Scanner
Control software:

Scanner Control window

Parameter Description
Scanner Information area Displays the model number, IP address, and serial
number of the Typhoon instrument.

Instrument State area Displays the current state of the instrument. The
states are Ready, Warming Up, Sleep, Initialization,
and Scanning. If Service appears, call Technical
Support for service. See Assistance in the preface
for contact information.

Instrument State area: Allows you to begin warming up the instrument before
Initialize Scanner button starting the scan. Resets the sleep time.

Template name Displays the template name for the parameters

displayed in the Scanner Control window and Setup
window (fluorescence and chemiluminescence only).
If no template is selected, the default parameters
appear in the windows.

B-2 ● Typhoon User’s Guide

 Appendix B Quick reference for menus and windows

Parameter Description
Scan area (grid) If User Select is selected in the Tray area, displays the
selected scan area (in white) and allows you to change
the selected area by redrawing the white rectangle.
If other than User Select is selected in the Tray area,
displays the multiple scan areas for the selected tray
definition.

Setup area: Displays the current user name.

User Name

Setup area: Allows you to select the scan acquisition mode. The
Acquisition Mode list choices are Storage Phosphor, Fluorescence, and
Chemiluminescence.

Setup area: Allows you to select a tray definition containing multiple

Tray area scan areas. Allows you to select which predefined areas
to scan.

Setup area: Available in the storage phosphor mode only. Allows

Phosphor Mode area: you to use full laser power to achieve the best
Best Sensitivity button sensitivity.

Setup area: Available in the storage phosphor mode only. Allows

Phosphor Mode area: you to lower the laser power to achieve greater
Best Resolution button resolution.

Setup area: Available in the fluorescence and chemiluminescence

Setup button modes. Depending on the selected acquisition mode,
displays the Setup window for fluorescence or
chemiluminescence.

Setup area: Click to display the eight sample orientation

Options area: parameters. Allows you to select the parameter that
Orientation button matches how you placed the sample on the glass
platen of the instrument or on the storage phosphor
screen.

Setup area: Available in the fluorescence and chemiluminescence

Options area: modes. Allows you to select that you want the sample
Press Sample check box pressed during scanning. (Pressing is automatic in the
storage phosphor mode.)

Setup area: Displays a list of pixel size parameters. The selections

Options area: are 1 000 microns, 500 microns, 200 microns,
Pixel Size list 100 microns, 50 microns, and 25 microns.
(Typhoon 8610, 9210, and 9410 only) The 10 microns
parameter is also available.

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Part six Appendixes

Parameter Description
Focal Plane area Available in the fluorescence and chemiluminescence
modes. Allows you to change the focal plane of the
laser and collection optics to match the sample type.
You can select either Platen (sample is on glass platen)
or +3 mm (sample is 3 mm higher than glass platen).

Setup area: Allows you to save comments (maximum 4 000

User Comment box characters) with the image file.

Setup area: Allows you to select the image analysis software to open
Image Analysis list after scanning. Select None to leave Scanner Control
active.

Setup area: Allows you to use the DIGE file naming format for image
DIGE File Naming Format file names.

Setup area: Click to start the scan. If you have not provided a name
Scan button for the scanned image, you are prompted to provide
one before the scan begins.

Scanning Information area Displays the parameters selected for the scan and the
approximate scan time and image file size required
for the scan.

Fluorescence Setup window

Parameter Description
Use check box Allows you to select the number of scans to perform.
Also displays scans that are linked.

Image box Displays the order in which the scans will be performed
by the Typhoon instrument.

Emission Filter list Allows you to select the emission filters to use for
each scan. After you select the emission filter, Scanner
Control determines the most appropriate laser to use
with the selected filter.

PMT Voltage list Allows you to select the PMT voltage to use for each
scan. Values range from 0 to 1 000 and are in 5-V
increments.

B-4 ● Typhoon User’s Guide

 Appendix B Quick reference for menus and windows

Parameter Description
Laser list Allows you to change the laser that Scanner Control
selected as the most appropriate laser to use with
the emission filter. You select either Green (532) or
Red (633).
(Typhoon 9400 and 9410 only) Two additional
laser parameters appear in the list: Blue (457) and
Blue (488).

Sensitivity list Allows you to select the sensitivity (limit of detection) to

use for each scan. Normal collects one data point from
each pixel. Medium collects four data points from each
pixel and averages the results. High collects eight data
points from each pixel and averages the results.

Beamsplitters list After you link the scans, displays the beamsplitter you
should use for the linked scan. Allows you to change
the selected beamsplitter.

Link With area: Allows you to select the scans you want to link. Scanner
Scan buttons Control displays brackets that connect the Use boxes
of the linked scans.

Link With area: Allows you to link the scans automatically. Scanner
Auto-Link button Control links the optimal scans, displays brackets
connecting the Use check boxes of the scans, and
renumbers the Image boxes.

Link With area: Allows you to remove the selected links. Scanner
UnLink All button Control removes the brackets connecting the Use
check boxes of the scans and renumbers the Image
boxes.

Link With area: Allows you to decrease the cross talk between
Auto Link Mode: fluorochromes for linked scans.
Sensitivity

Link With area: Allows you to decrease the total scan time for the
Auto Link Mode: linked scans.
Speed

Disable Link Warning Allows you to turn off the warning message that
check box appears if you select nonoptimal links.

Cancel button Closes the Fluorescence Setup window without saving

any changes.

OK button Saves the changes and closes the Fluorescence Setup

window.

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Part six Appendixes

Chemiluminescence Setup window

Parameter Description
Sensitivity list Allows you to select the sensitivity (limit of detection)
to use for each scan. Normal collects one data point
from each pixel. Medium collects four data points from
each pixel and averages the results. High collects eight
data points from each pixel and averages the results.

Beamsplitters list Allows you to select a beamsplitter if you want to

perform a multichannel scan. If you are performing
a single scan, leave the parameter at None.

PMT Voltage list Allows you to select the PMT voltage to use. Values
range from 0 to 1 000 and are in 5-V increments. If
you selected None in the Beamsplitter list, you see one
PMT Voltage list box. If you selected a beamsplitter, you
see two PMT Voltage list boxes.

Cancel button Closes the Chemiluminescence Setup window without

saving any changes.

OK button Saves the changes and closes the Chemiluminescence

Setup window.

B-6 ● Typhoon User’s Guide

 Appendix B Quick reference for menus and windows

Tray Editor window

Parameter Description
Tray area: Displays the list of tray definitions and number of
Tray definition list sample scan areas.

Tray area: Displays the New Tray window, which allows you to
New Tray button type a name for a new tray definition.

Tray area: Displays the Copy Tray window, which allows you to
Copy Tray button create a new tray definition from an existing one.

Tray area: Allows you to delete the selected tray definition from
Delete Tray button the Tray area.

Sample area: Displays the sample scan areas for the selected tray
Sample definition list definition.

Sample area: Displays the New Sample window, which allows you to
New Sample button select the scan area for each sample.

Sample area: Displays the Edit Sample window, which allows you to
Edit Sample button modify the scan area for the selected sample.

Sample area: Allows you to delete the selected sample scan area.
Delete Sample

Sample area: Allows you to hide the selected tray definition from the
Disable (Hide in Scanner Tray list.
Control) check box

Preview button Displays the Preview Sample Tray window, which allows
you to view the sample scan areas using the scan grid.

Save Current Tray button Allows you to save the tray definition.

Close button Closes the Tray Editor window.

Typhoon User’s Guide ● B-7

Part six Appendixes

Multiple Sample Naming window

Parameter Description
Sample file name list Displays a list of the sample file names and the
file sizes.

Edit Sample File Name Displays the Save As window or the DIGE File Naming
Format window, which allows you to type a new
name for the selected file name.

Use Common Setting Displays the name of the folder you selected for storing
for All Samples: the new image files.
Folder box

Use Common Setting Displays the Save folder to window, which allows you
for All Samples: to select the folder in which you want to store the new
Folder Browse button image files.

Use Common Setting Allows you to save the selected folder as the storage
for All Samples: location for the new image files.
Folder Set button

Use Common Setting Allows you to type a base file name to use for the new
for All Samples: image files. The software appends a number to the
Base File Name box base file name to make each file unique.

Use Common Setting Displays a window, which allows you to select an

for All Samples: existing file name to use as the base file name. The
Base File Name Browse software appends a number to the base file name to
button make each file unique.

Use Common Setting Allows you to save the base file name for the new
for All Samples: image files.
Base File Name Set button

Cancel button Closes the Multiple Sample Naming window without

saving the changes or starting the scan.

Scan button Saves the changes, closes the Muliple Sample Naming
window, and starts the scan.

B-8 ● Typhoon User’s Guide

 Appendix B Quick reference for menus and windows

DIGE File Naming Format window

Parameter Description
Dataset Name box Displays the path and dataset name that will be used
for the image files.

Edit button Displays a window that allows you to type a new

dataset name. The new dataset name appears in
the Dataset Name box and all the Image boxes.

Image 1 box Allows you to type a new file name for Image 1.

Image 2 box Allows you to type a new file name for Image 2.

Image 3 box Allows you to type a new file name for Image 3.

Image 4 box Allows you to type a new file name for Image 4.

Standard button Allows you to select one image to use as a standard.

NONE button Allows you to select no image as a standard.

OK button Saves the changes and closes the DIGE File Naming
window.

Cancel button Closes the DIGE File Naming window without saving
any changes.

Typhoon User’s Guide ● B-9

Appendix C Literature references

The following references are cited in this manual:

Fluorescence Imaging principles and methods. Amersham Biosciences

Technical Manual #63-0035-28.

Sonada, M., M. Takano, J. Mayahara, H. Kato. 1983. Computed radiography

utilizing scanning laser stimulated luminescence. Radiology 148:833-838.

Typhoon User’s Guide ● C-1

Glossary

.dir—the folder that contains the individual image files for a multichannel
dataset. The name of the .dir folder is the same as the .ds file name.

.ds—the file extension for a multichannel dataset.

.gel—the file extension of a single-channel image.

absorption—the energy transfer from a photon of light to a dye molecule.

acquisition mode—the type of scan. Choices are storage phosphor,

fluorescence, and chemiluminescence.

band-pass filter—an optical filter that allows light of wavelengths between two
specified wavelength cutoffs to pass through. The filter rejects most of the light
with wavelengths shorter than the first cutoff or longer than the second cutoff.

channel—one image in a set of images that make up a multichannel image.

For a chemiluminescent sample, two channels are created using a beamsplitter.
For a fluorescent sample, two, three, or four channels are created using a
combination of fluorescent dyes, emission filters, and beamsplitters.

chemiluminescence—the emission of light by a dye molecule as a result of

a chemical reaction.

cross talk—the interference from one signal collected by the Typhoon

instrument on another signal collected by the instrument when scanning
a multilabel fluorescent image. Also referred to as cross contamination.

dataset—the files and folders that make up a multichannel image.

default template—the template and parameters that appear in the Scanner

Control window when the software is first opened.

electrophoresis glass plate—a 3-mm-thick, low-fluorescence piece of glass used

to create sandwich gels.

emission—the release of light from a dye molecule when an electron falls from
an excited to a lower energy state.

emission spectrum—a plot of emitted light wavelength versus relative intensity

of emitted light.

excitation—the absorption of light energy by a molecule so that an electron is

boosted to a higher-level energy state.

Typhoon User’s Guide ● Glossary-1

Glossary

excitation spectrum—a plot of incident light wavelength versus relative

intensity of emitted light.

fluorescence—the emission of light by a dye molecule as a result of absorption

of laser light.

GP screen—general-purpose storage phosphor screen.

glass platen—the area of the Typhoon instrument on which you set the sample
or storage phosphor screen.

grid coordinates—the markings on the exposure cassette and glass platen of the
instrument that allow you to position the sample. The coordinates correspond
to markings in the Scanner Control window.

LE screen—low-energy storage phosphor screen.

link—the process of creating two images with one scan. Uses emission filters
and beamsplitters to separate and collect light of two different wavelengths.

long-pass filter—an optical filter that allows light of wavelengths longer than
a specified cutoff to pass through. The filter rejects most of the light with
wavelengths shorter than the cutoff.

multichannel image—a set of images that can be viewed as a composite

(overlaid) or viewed as individual images (side by side). A chemiluminescent
sample can be used to create a multichannel image consisting of two images.
A fluorescent sample can be used to create multichannel images consisting
of two, three, or four images. Each image is called a channel. Also referred
to as a multilabel image.

photomultiplier tube (PMT)—an electro-optic device in the Typhoon

instrument that converts light energy into electrical current and amplifies
the current.

pixel size—the size of each individual picture element that is recorded and,
together with the thousands of other pixels, forms the image.

quantitation—the process in which signal intensities of the sample and other

values are calculated.

sample lid—the underside of the cover of the Typhoon instrument.

short-pass filter—an optical filter that allows light of wavelengths shorter

than a specified cutoff to pass through. The filter rejects most of the light with
wavelengths longer than the cutoff.

spectral separation—the software process that removes the unwanted signals

present in each channel of a multichannel image.

Glossary-2 ● Typhoon User’s Guide

 Glossary

Stokes shift—the difference, in wavelength, between the apex of the excitation

spectrum (shorter wavelength, higher energy) and the apex of the emission
spectrum (longer wavelength, lower energy).

storage phosphor screen autoradiography—the emission of light by a

radioactive molecule, which is collected on a phosphor-coated screen instead
of on film.

template—scan parameters that are saved in Scanner Control using a

unique name. Templates can be saved for storage phosphor, fluorescence,
and chemiluminescence.

TR screen—tritium storage phosphor screen.

Typhoon User’s Guide ● Glossary-3

Index

A
abort scan 6-20, 9-25, 12-19
absorption
fluorescence 7-1 to 7-2
storage phosphor 4-1 to 4-2
access door 13-7
accessories for Typhoon system 1-3
acetic acid 5-2
agarose 8-3
alkaline gels 5-2
artifacts, image 8-1
assistance xvi
assumptions xiv
Auto-Link button in Fluorescence Setup window 9-13

B
background
chemiluminescence 11-1, 12-10
cosmic radiation 5-5
fluorescence 8-3, 8-5, 8-7, 9-11
storage phosphor screen 5-5, 5-9, 6-2
troubleshooting A-5
band-pass emission filter 7-3
bar code, optical filter 13-6
Beamsplitter list
Chemiluminescence Setup window 12-9
Fluorescence Setup window 9-12
beamsplitters
chemiluminescence 10-3
fluorescence 7-4
blue laser module
electrical safety 2-6
high-voltage hazard 2-9
indicator lights 3-3
label locations 2-5
laser safety precautions 2-13
serial number 2-2
turning off 3-20
turning on 3-3

Typhoon User’s Guide ● Index-1

Index

blue-excited fluorescence contamination

choosing laser 9-11 checking for 5-4
description 1-6 chemiluminescent 11-1, 11-3
label guidelines 8-2 cross talk 7-6
bulb, changing 14-2 to 14-3 dust 5-4, 6-2, 8-1, 8-5, 8-7, 11-1, 11-3
fingerprint oil 5-4, 6-2, 8-5, 8-7, 11-1, 11-3
C fluorescent 8-5, 8-7
cancel scan 6-18, 9-24, 12-17 glass platen 6-1
caution statement, defined xiv powder 8-1
CE declaration xiv radioactive sample 5-4, 6-1, 6-3
Change Instrument IP Addess window 13-5 storage phosphor screen 5-4
chemiluminescence Typhoon instrument 6-1
advantages 10-1 coordinates
beamsplitters 10-3 exposure cassette 5-8
contamination 11-1, 11-3 glass platen 8-9, 11-5
optimizing experiment 10-2 in tray definition 3-12
overview 10-1 Scanner Control window 6-8, 9-3, 12-3
preparing sample 11-1 counts, Typhoon system 5-3
removing sample 12-20 cross talk in multichannel experiments 7-6
saturated data 12-19
scan acquisition mode 1-6, 12-3 D
selecting a template 12-2 data file (.gel) 6-15, 9-17, 12-11
workflow 3-8 dataset file (.ds) 9-18, 12-11
Chemiluminescence Setup window Define the Filter window 13-13, 13-17
closing 12-11 Delete Template(s) window 3-20
displaying 12-9 detergent, powdered 5-4, 14-1
PMT Voltage box 12-10 DIGE File Naming Format check box 9-21, 12-15
quick reference B-6 DIGE File Naming Format window
selecting beamsplitter 12-9 description 9-22, 12-16
Sensitivity setting 12-9 quick reference B-9
cleaning documentation xiii
glass platen 6-2, 8-5, 11-1 double image 5-9, 8-9
Image Eraser 14-1 dust 5-4, 6-2, 8-1, 8-5, 11-1
sample lid 6-3, 8-7, 11-3
computer E
connecting new 13-21 Edit Sample Tray window 3-12
troubleshooting A-1 electrophoresis glass plate 8-3
turning off 3-21 emission
turning on 3-3 chemiluminescence 10-2
condensation on storage phosphor screen 5-9 fluorescence 7-1 to 7-2
storage phosphor 4-1 to 4-2

Index-2 ● Typhoon User’s Guide

 Index

emission filter filter changer

see also optical filter accessing 13-8
description 7-3 moving 13-7
overview 1-5 Filter Changer Maintenance Page window 13-7
selecting for fluorescence scanning 9-10 filter, see emission filter, optical filter
enhancers 2-14, 5-2 fingerprint oil 5-4, 6-2, 8-5, 11-1
Enter New IP Address window 13-5 fluorescence
Enter New IP Subnet Mask window 13-5 advantages of 7-2
erase time 5-5 beamsplitters 7-4
Ethernet 1-1, 13-21, A-1 blue-excited description 1-6
Ettan DALT gel alignment guide 8-17 contamination 8-5, 8-7
excitation description 7-1
description 7-1 green-excited description 1-6
fluorescence labeling 8-2 labeling 8-2
exposure multilabel-excited description 1-6
determining time 4-2 overview 7-1
guidelines for storage phosphor screen 5-6 red-excited description 1-6
temperature 5-9 saturated data 9-26
time for storage phosphor screen 5-12 scan acquisition mode 1-6, 9-3
exposure cassette selecting a template 9-2
closing 5-11 workflow 3-7
coordinates 5-7 Fluorescence Setup window
guidelines for placing sample 5-7 Auto-Link button 9-13
large and small sizes 5-8 closing 9-17
opening 6-4 description 9-9
placing mounted screen 5-9 to 5-10 disable link warning 9-16
placing sample 5-8 emission filter list 9-10
placing unmounted screen 5-11 to 5-12 laser list 9-11
types 4-3 Link With area 9-13
using with wet gel 5-2 linking scans 9-12 to 9-14
PMT Voltage box 9-10
F quick reference B-4
fatal scan errors 6-20, 9-25, 12-19 selecting beamsplitter 9-12
File menu B-1 selecting number of scans 9-9
file type Sensitivity parameter 9-12
data file (.gel) 6-15, 9-17, 12-11 Unlink All button 9-13
dataset file (.ds) 9-18, 12-11 fluorescent indicator dyes 8-2
fluorochrome 7-6
FluorSep 7-6
focal plane 9-8, 12-7

Typhoon User’s Guide ● Index-3

Index

fuse storage phosphor exposure cassette 5-7

Image Eraser storage phosphor sample preparation 5-1 to 5-3
changing 14-3 to 14-5 storage phosphor screen exposure 5-6
location 14-2
type 2-7 H
repeated replacement 2-8 hardware components 1-1
safety 2-7 hazardous materials, safety 2-14
Typhoon instrument Help menu B-2
changing 13-17 to 13-18 high-voltage hazard 2-8 to 2-11
type 2-7
I
G
image
gel
double 8-9
handling 8-10
sample orientation 6-10, 9-4, 12-4
placing on glass platen 8-9
saturation 9-10, 12-10
using 8-3
troubleshooting A-5
gel alignment guides
Image Analysis Software box 6-14, 9-8, 12-8
cleaning and protecting 14-6
Image Eraser
Ettan DALT 8-17
caution 2-8, 2-9, 2-10
guidelines 8-4
changing bulb 14-2 to 14-3
placing on glass platen 8-17 to 8-21
changing fuse 14-3 to 14-4
SE600 8-19
cleaning 14-1
glass platen
electrical safety 2-6
cleaning 6-2, 8-5, 11-1
fuse location 14-2
contamination 6-1
fuse type 2-7
placing multiple samples 8-8, 11-4
high-voltage hazard 2-8, 2-10
placing sample on 8-7, 11-3
label locations 2-6
solvents 6-2, 8-6, 11-2
operating voltage 2-7
gloves 8-1
power switch 14-2
GP screen
serial number and label 2-3
cleaning 5-4
ImageQuant Preview window 6-19, 9-24, 12-18
description 4-4
important statement, defined xiv
using plastic wrap 5-2
Initialize Scanner button 3-4, 6-6, 9-1, 12-1
green-excited fluorescence
Insert New Optical Filter into Filter Changer
choosing laser 9-11
window 13-8
description 1-6
instrument states 3-4, 6-6, 9-1, 12-1
label guidelines 8-2
IP address, changing 13-4
guidelines
chemiluminescent sample preparation 11-1
fluorescent sample preparation 8-1 to 8-5

Index-4 ● Typhoon User’s Guide

 Index

L microarray slide holder

labels cleaning and protecting 14-6
high-voltage hazard 2-10 guidelines 8-4
laser warning 2-11 placing on glass platen 8-13 to 8-16
location on blue laser module 2-5 microarray slides
location on Image Eraser 2-6 guidelines 8-4
location on instrument 2-4 minimize scan time 8-8
replacing 2-2 placing on glass platen 8-13 to 8-16
lasers position on holder 8-7
safety precautions 2-12 microplate
selecting for fluorescence scanning 9-11 placing on glass platen 8-7, 11-3
setting shutoff time 13-3 using 8-5
troubleshooting A-3 microplate strip
types 2-11 placing on glass platen 8-7
warning label 2-11 using 8-5
LE screen models of Typhoon instrument 1-3
cleaning 5-4 mounted storage phosphor screen 4-3, 5-8, 6-4,
description 4-4 6-21
using plastic wrap 5-2 moving instrument 13-19 to 13-22
using with wel gels 5-2 multichannel
light, excessive exposure 8-2 description 7-6
limit of detection, setting 9-12, 12-9 label guidelines 8-2
linear dynamic range, phosphor screen 4-2 multilabel
link warning, disable in Fluorescence Setup description 7-6
window 9-16 guidelines 8-2
Link With area in Fluorescence Setup window 9-13 multilabel-excited fluorescence
linking fluorescent scans 9-12 to 9-16 description 1-6
long-pass emission filter 7-3 multiple gels
low-fluorescence sample support 8-3 orientation 8-7
placing on glass platen 8-17 to 8-21
M Multiple Sample Naming window
membrane description 6-17, 9-20, 12-13
guidelines 8-4 quick reference B-8
handling 8-10, 11-6
placing on glass platen 8-9 N
menus network, remote scanning 6-16, 6-17, 9-19, 9-20,
File B-1 9-21, 12-12, 12-14, 12-15
Help B-2 nonfatal scan errors 6-20, 9-25, 12-19
Tray B-2 note statement, defined xiv

Typhoon User’s Guide ● Index-5

Index

O R
opaque samples, placing 8-7 radiation and storage phosphor screen 4-1
operating voltage 2-7 radioactive standards 5-3
optical filter red-excited fluorescence
see also emission filter choosing laser 9-11
bar code for 13-6 description 1-6
changing 13-9 label guidelines 8-2
changing filter definition 13-16 Remove Optical Filter from Filter Changer
cleaning 13-10 window 13-14
filter and holder 13-11 replacing files 6-16, 9-19, 12-12
inserting in instrument 13-10
installation procedure 13-6 to 13-13 S
registering in Scanner Control 13-12 safety
removing 13-13 electrical 2-6
optical system overview 1-5 fuse 2-7
organic solvents 5-2 general precautions 2-1
orientation of sample 5-8, 6-10, 8-7, 9-4, 11-3, 12-4 hazardous materials 2-14
overwriting files 6-16, 9-19, 12-12 high-voltage 2-8
interlocks 2-11
P laser 2-11
Park Scanner for Shipping window 13-21 radiation exposure 2-12
photobleaching 8-2 standards xiv
pinching hazard warning 2-13 sample
pixel size 6-13, 9-6, 12-6 accurate quantitation 9-10, 12-10
PMT enhancers 2-14, 5-2
overview 1-5 exposing thick 5-6
Voltage box 9-10, 12-10 exposure cassette placement guidelines 5-7
polyacrylamide 8-3 handling 8-10, 11-6
powder 8-1 intense 9-11, 12-10
power indicator light matrix 8-3
description 3-1 orientation 5-8, 6-10, 8-7, 9-4, 11-3, 12-4
troubleshooting A-1 placement guidelines 5-7 to 5-8
power switch placing in exposure cassette 5-8
Image Eraser 14-2 placing on glass platen 8-8 to 8-9, 11-3
Typhoon instrument 3-2 precautions 2-14
Press Sample parameter 9-6, 12-6 preparation guidelines 5-1
publications, related xiii removing from instrument 9-27
scanning several at once 8-8, 11-4
Q scintillants 2-14, 5-2
quick reference for menus and windows B-1 solvents 2-14

Index-6 ● Typhoon User’s Guide

 Index

weak 9-11 Press Sample parameter 9-6, 12-6

wet 5-8 registering new optical filter 13-12
wet gel guidelines 5-2 sample orientation buttons 6-10, 9-4, 12-4
sample lid selecting default template 3-19
cleaning 6-3, 8-7, 11-3 selecting focal plane 9-8, 12-7
closing 6-6, 8-10, 8-11, 8-16, 11-6 selecting scan area 6-8, 9-3, 12-3
opening 6-5, 8-9, 11-5 selecting template 3-18
sample orientation buttons starting scan 6-15, 9-17, 12-11
illustrated 6-12, 9-5, 12-5 User Comment area 6-15, 9-8, 12-8
Scanner Control window 6-10, 9-4, 12-4 using DIGE file naming format 9-21, 12-15
sample orientation, in exposure cassette 5-8 using templates 3-15
sample support, low-fluorescence 8-3 using tray definition (DIGE) 9-21, 12-15
sandwich gel using tray definition (non-DIGE) 6-16, 9-19,
assembling 8-10 12-13
placing 8-7 scanning
placing on glass platen 8-10 to 8-12 aborting scan 6-20, 9-25, 12-19
saturated data 6-20, 9-26, 12-19 accurate quantitation 9-10, 12-10
Save As Template window 3-18 canceling 6-18, 9-24, 12-17
Save as window 6-16, 9-18, 12-12 chemiluminescence workflow 3-8
scan acquisition mode cleaning after 6-21, 9-27, 12-20
chemiluminescence 1-6, 12-3 DIGE gels 9-21, 12-15
fluorescence 1-6, 9-3 end of scan 6-20, 9-26, 12-20
storage phosphor 1-6, 6-8 fatal errors 6-20, 9-25, 12-19
scan area fluorescence workflow 3-7
defining for multiple samples 3-10 to 3-15 ImageQuant Preview window 6-19, 9-24, 12-18
glass platen 8-9, 11-5 initialization process 6-18, 9-24, 12-17
selecting 6-8, 9-3, 12-3 intense sample 9-11, 12-10
scan coordinates 8-10, 8-11, 11-6 minimizing image file size 8-8, 11-4
scan errors 6-20, 9-25, 12-19 minimizing time required 8-8, 11-4
scan head, securing for move 13-20 modes 1-6
Scanner Control window multiple samples 6-16, 9-19, 12-13
closing 3-20 multiple scan areas 6-16, 9-19, 12-13
commands B-2 naming 6-15, 9-17, 12-11
creating template 3-15 nonfatal errors 6-20, 9-25, 12-19
deleting template 3-19 overview 1-5
grid 6-8, 9-3, 12-3 sample orientation 6-10, 8-7, 9-4, 11-3, 12-4
Image Analysis Software box 6-14, 9-8, 12-8 saturated data 6-20, 9-26, 12-19
modifying template 3-18 single sample 6-15
opening 3-3 single scan area 6-15
Pixel Size box 6-13, 9-6, 12-6 starting 6-15, 9-17, 12-11

Typhoon User’s Guide ● Index-7

Index

storage phosphor workflow 3-5 exposing 5-9

troubleshooting A-3 exposure guidelines 5-6
weak sample 9-11 exposure temperature 5-9
scintillants 2-14, 5-2 exposure time 4-2, 5-12
screen cleaner 5-4 function 4-1
SE600 gel alignment guides 8-19 GP description 4-4
Select A Laser Shut Off Time window 13-3 LE description 4-4
Select Filter ID to Eject window 13-15 light leak A-5
sensitivity of storage phosphor screen 4-2 linear dynamic range 4-2
sensitivity, setting 9-12, 12-9 loading in instrument 6-5
serial number mounted 4-3
blue laser module 2-2 placing in cassette 5-9, 5-12
Image Eraser 2-2 protecting 5-3
Typhoon instrument 2-2 removing from exposure cassette 6-4
service, calling for xvi saturated data 6-20
short-pass emission filter 7-3 scintillants 2-14, 5-2
shutoff time, laser 13-3 sensitivity 4-2
site requirements xv solvents 5-8
slide holder see microarray slide holder storing 6-21
software requirements 1-5 TR description 4-4
solutions, filtering 8-1 units 5-3
solvent unmounted 4-3
organic 2-14, 5-2 using plastic wrap 5-2
spectroscopic grade 8-5 subnet mask, changing 13-4
special safety text definitions xiv substrate 10-2, 11-1
standards, radioactive 5-3 surge protector 2-6
Stokes shift 7-1
storage phosphor T
description 4-1 TCP/IP address, changing 13-4
scan acquisition mode 1-6, 6-8 Technical Support xvi
selecting a template 6-8 template
workflow 3-5 creating 3-15
storage phosphor screen Delete Template(s) window 3-20
advantages 4-2 deleting 3-19
background 5-5, 5-9 modifying 3-18
checking for contamination 5-4 Save As Template window 3-18
cleaning 5-4 selecting 3-18
condensation 5-9 selecting default 3-19
enhancers 2-14, 5-2 selecting for chemiluminescence 12-2
erasing 5-4 selecting for fluorescence 9-2

Index-8 ● Typhoon User’s Guide

 Index

selecting for storage phosphor 6-8 moving

selecting parameters, illustrated 3-16 completing 13-21
selecting setup parameters, illustrated 3-17 determining new location 13-19
timer on eraser 5-5 preparing for 13-20
TLC plate securing scan head 13-20
exposing 5-6 optical filter
guidelines for using 5-1 access door 13-7, 13-9
accessing filter changer 13-8
orientation on glass platen 8-7
changing definition 13-16
precaution 2-14
changing, illustrated 13-9
TR screen closing access door 13-12
caution 5-8 closing filter door 13-12
cleaning 5-4 filter changer 13-7
description 4-4 inserting 13-10
erasing 5-5 installation procedure 13-6 to 13-13
using with wet gel 5-2 registering in Scanner Control 13-12
trained operator definition xiv removing 13-13
transparency support 8-5 replacing front cover 13-12
tray definition overview 1-5
copying 3-13 power indicator light 3-1, A-1
creating 3-11 power switch 3-2
deleting 3-15 serial number 2-2
predefined 3-11 serial number label 2-3
Tray Editor window setting laser shutoff time 13-3
description 3-10 turning off 3-20
quick reference B-7 turning on 3-1
Tray menu B-2 Typhoon system
troubleshooting A-1 counts 5-3
Typhoon Direct Instrument Access software 13-1 hardware components 1-1 to 1-2
Typhoon Direct Instrument Access window 13-2 optional accessories 1-3
Typhoon instrument
changing fuse 13-17 U
contamination 6-1 uneven samples, placing 8-7
electrical safety 2-6 unit of measure 5-3
fuse location 13-17 Unlink All button in Fluorescence Setup window
fuse type 2-7 9-13
high-voltage hazard 2-8 unlinking fluorescent scans 9-16
label locations 2-4 unmounted storage phosphor screen 4-3, 5-3, 5-8,
laser safety 2-11 5-11, 6-4, 6-5
laser safety precautions 2-12 Use check box in Fluorescence Setup window 9-9
models 1-3 User Comment area 6-15, 9-8, 12-8

Typhoon User’s Guide ● Index-9

Index

V Park Scanner for Shipping 13-21

voltage Remove Optical Filter from Filter Changer 13-14
safety 2-6 Save as 6-16, 9-18, 12-12
selecting for Image Eraser 14-5 Save As Template 3-18
Scanner Control
W chemiluminescence 12-2
fluorescence 9-2
warning
quick reference B-2
fuse 2-7
storage phosphor 6-7
general safety 2-1 Select A Laser Shut Off Time 13-3
label replacement 2-2 Select Filter ID to Eject 13-15
laser light 2-11 Tray Editor
pinching hazard 2-13 description 3-10
radiation exposure 2-12 quick reference B-7
statement, defined xiv Typhoon Direct Instrument Access 13-2
wet gel workflow
caution 5-8 chemiluminescence 3-8
exposing 5-2 fluorescence 3-7
guidelines for using 5-2 storage phosphor 3-5
window cleaners, using 8-6, 11-3
windows
Change Instrument IP Address 13-5
Chemiluminescence Setup
description 12-8
quick reference B-6
Define the Filter 13-13, 13-17
Delete Template(s) 3-20
DIGE File Naming Format
description 9-22, 12-16
quick reference B-9
Edit Sample Tray 3-12
Enter New IP Address 13-5
Enter New IP Subnet Mask 13-5
Filter Changer Maintenance Page 13-7
Fluorescence Setup
description 9-9
quick reference B-4
ImageQuant Preview 6-19, 9-24, 12-18
Insert New Optical Filter into Filter Changer 13-8
Multiple Sample Naming
description 6-17, 9-20, 12-13
quick reference B-8

Index-10 ● Typhoon User’s Guide