QuPath - Open-source bioimage analysis for research

StarDist - Object Detection with Star-convex Shapes

Segment Anything for Microscopy

Vision-Language Pathology Foundation Model - Nature Medicine

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

AI-based pathology predicts origins for cancers of unknown primary - Nature

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

A tool for cell instance aware segmentation in densely packed 3D volumetric images

Solid Tumor Associative Modeling in Pathology

Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering

computer vision models for single-cell phenotyping

Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.

A deep-learning pipeline for segmentation of ambiguous microscopic images.

C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.

ImageJ macros and scripts written at the imaging facility MRI

Fiji plugin for object(s) detection using template(s) matching

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

Python libraries for loading, running and packaging bioimage.io models

Tool for segmentation in bioimaging