ResUpNet: A Transfer Learning Residual U-Net for Accurate Brain

Tumor Segmentation in MRI Scans

Abstract: Brain tumor detection and segmentation in Magnetic Resonance Imaging (MRI) is a critical
clinical task that supports timely diagnosis and treatment planning. However, manual segmentation is
time-consuming, subjective, and prone to inter-observer variability. This research work presents a deep
learning-based automated segmentation framework using a ResNet50-based UNet++ architecture with
attention and residual refinement. The LGG MRI segmentation dataset was preprocessed through
grayscale normalization, binary tumor mask conversion, and adaptive resizing. The dataset was divided
into training, validation, and test subsets to ensure reliable performance measurement. A hybrid loss
combining Dice loss and Focal-Tversky was employed to address tumor class imbalance and improve
boundary precision. The model achieved an average Dice coefficient of 0.44 and an IoU of 0.38,
demonstrating effective tumor boundary localization in several MRI slices. Visual overlays and heatmaps
were generated to compare model predictions with ground truth annotations. Although performance
varied for very small or low-contrast tumor regions, the approach showed significant potential in
reducing manual effort and improving segmentation consistency. The study demonstrates that attention-
guided encoder–decoder architectures can effectively enhance tumor structure recognition in MRI scans
and can be further improved with larger datasets, augmentation strategies, or clinical fine-tuning.
Keywords: Brain Tumor Segmentation; MRI; Deep Learning; ResNet50; UNet++; Medical Image
Analysis
1. Introduction
Brain tumours represent abnormal and uncontrolled cellular growth within the brain, and their early
identification and precise delineation are essential for diagnosis, treatment planning, and monitoring
disease progression. Magnetic Resonance Imaging (MRI) is the preferred modality for brain tumour
analysis as it offers superior soft-tissue contrast, multiplanar acquisition, and the ability to visualise fine
structural variations without ionising radiation. Despite its diagnostic value, interpreting MRI scans
particularly when tumours exhibit irregular boundaries, diffuse infiltration, or low-contrast characteristics
remains challenging for clinicians [1].
Manual segmentation performed by radiologists is widely regarded as the reference standard;
however, it is labour-intensive, time-consuming, and subjective. Variability in tumour appearance,
scanner protocols, and radiologist expertise can introduce considerable inconsistency, making automated
and reproducible solutions highly desirable. Early attempts to automate tumour segmentation relied on
classical image processing approaches such as thresholding, clustering, edge detection, and region
growing. Although these methods were computationally inexpensive, they struggled with noise, intensity
inhomogeneity, and complex tumour morphology. Their reliance on handcrafted features made them
unsuitable for routine clinical use.
Deep learning has transformed medical image segmentation by enabling neural networks to learn
hierarchical features directly from imaging data [2]. Convolutional Neural Networks (CNNs) and
especially U-Net-based architectures have become the basis of modern medical segmentation due to their
ability to combine contextual and spatial information through encoder–decoder pathways and skip
connections. Yet, the baseline U-Net faces limitations when dealing with small lesions, highly irregular
tumour shapes, or fine boundaries which is common in glioma imaging [3-5].
Several architectural refinements have been proposed to overcome these challenges. Residual learning
helps stabilize deeper networks and improves gradient flow. Multi-scale processing enhances the capture
of global and local contextual information. Attention mechanisms guide the model towards the most
relevant tumour regions while suppressing background noise. Transfer learning further enhances feature
extraction, particularly when annotated medical images are limited, by using pre-trained weights from
large natural-image datasets [6-8]. Even with these advancements, achieving a balance between
segmentation accuracy, computational efficiency, and robustness across diverse MRI scans remains an
open challenge. Many high-performing models depend on large parameter sets, extensive computational
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resources, or multi-modal MRI input, which limits their practical deployment in resource-constrained
clinical settings. Additionally, class imbalance where tumour pixels comprise only a small portion of the
total image often leads to poor sensitivity for small or low-contrast tumour regions [9-13].
In this context, the present study proposes a lightweight Residual U-Net architecture, termed
ResUpNet, that integrates transfer learning through a ResNet50 encoder, adaptive skip-fusion for
preserving structural detail, and a hybrid Dice–Tversky loss function to manage class imbalance. The
model is trained and evaluated on the publicly available Lower-Grade Glioma (LGG) MRI segmentation
dataset to ensure reproducibility [?]. The objectives of the proposed method are:
 to establish a consistent preprocessing method for MRI slices and tumour masks,
 to use transfer learning for improved feature extraction under limited data,
 to refine encoder–decoder feature merging through adaptive skip connections, and
 to systematically evaluate segmentation accuracy using quantitative metrics and visual analysis.
By addressing the issues of data scarcity, tumour heterogeneity, and computational efficiency, the
proposed approach aims to provide a practical and scalable solution for automated brain tumour
segmentation that moves closer to real-world clinical integration.
The remainder of the paper is organized as follows. Section 2 reviews the related work, Section 3
describes the dataset and the methodology, Section 4 presents the results and discussion, and Section 5
concludes with future research directions.

2. Literature Review

Accurate segmentation of brain tumours in MRI has long been a central challenge in medical image
analysis because it directly influences diagnosis, treatment planning, and longitudinal monitoring.
Traditional image processing methods provided the earliest attempts at delineating tumour regions, but
their limitations encouraged the rapid transition toward deep learning–based approaches [14]. This section
reviews the evolution of tumour segmentation techniques, highlighting the developments that motivate
the proposed model.
Early computational methods relied on handcrafted rules that attempted to differentiate tumour
and non-tumour tissue using intensity distributions, texture, or spatial continuity[15]. Thresholding, edge
detection, region growing, and clustering were among the most widely adopted strategies. Thresholding
worked reasonably well when tumour intensities were clearly separable from the healthy tissue, but MRI
rarely provides such clean contrast. Region growing enhanced spatial coherence but was extremely
sensitive to seed-point selection, often producing unstable segmentations. Clustering methods such as K-
means and Fuzzy C-means grouped pixels based on similarity, but struggled with partial volume effects,
noise, and heterogeneous tumour patterns [16]. It is observed that the above techniques lacked robustness
because they depended heavily on hand-crafted features and linear assumptions. Their limited ability to
capture non-uniform intensities and irregular shapes made them unsuitable for routine clinical
deployment.

The introduction of Convolutional Neural Networks (CNNs) shifted the field by enabling feature
extraction directly from the data, eliminating the need for manually obtained descriptors [17]. Fully
Convolutional Networks (FCNs) extended CNNs to pixel-wise prediction, forming the foundation for
semantic segmentation in medical imaging [?]. U-Net, proposed by Ronneberger et al., became a major
breakthrough. Its symmetric encoder–decoder structure, along with skip connections, ensured that high-
level semantic information and fine spatial detail were preserved during upsampling. The architecture
consistently outperformed the classical methods across various biomedical segmentation tasks [?].
However, despite its strengths, the original U-Net struggled with highly irregular tumour boundaries,
small lesions, and low-contrast regions which is a common characteristics of glioma MRI scans. These
limitations drove the development of more sophisticated variants.

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 Residual learning, introduced through ResNet, improved gradient flow in deep networks by
allowing layers to learn identity mappings [?]. When integrated into U-Net architectures, residual blocks
enhanced the feature representation and improved the stability during training, especially on limited
medical datasets. Attention mechanisms further refined segmentation by enabling the network to focus on
salient tumour regions while suppressing irrelevant background information [?]. Models such as Attention
U-Net demonstrated large gains in boundary localisation and sensitivity to small structures [?]. Multi-
scale models including U-Net++, nested U-Nets, and pyramid-pooling variants addressed the challenge of
capturing both global context and fine detail [?]. These architectures processed feature maps at multiple
resolutions to better handle heterogeneous tumour morphology. Together, residual, attention, and multi-
scale enhancements substantially improved the segmentation accuracy, yet they increased the model
complexity and the training cost. This motivated the search for hybrid architectures that balance
performance with practical efficiency.

Medical imaging datasets are typically small and laboriously annotated, making deep networks
prone to overfitting. Transfer learning emerged as a powerful strategy to overcome data scarcity [?]. Pre-
trained encoders such as ResNet50, VGG16, and DenseNet provide rich low-level features such as edges,
textures, and shapes that transfer effectively to MRI tasks despite differences from natural-image domains
[?]. By replacing the U-Net encoder with a pre-trained backbone, many researchers achieved: faster
convergence, improved generalisation on limited MRI datasets, and better detection of fine tumour
regions. Transfer learning has therefore become a standard component in state-of-the-art brain tumour
segmentation approaches.

Recent research has shifted towards hybrid architectures that combine multiple strengths such as
residual blocks, attention gates, multi-scale pathways, and transfer-learning backbones into unified
frameworks [?]. Multi-level feature fusion strategies integrate information from various encoder depths to
recover both global context and fine structural detail during reconstruction. Adaptive fusion techniques
address issues such as feature redundancy, loss of spatial detail, and inconsistencies across MRI contrasts.
These designs allow the model to assign higher importance to the informative feature maps and enhance
delineation of complex tumour boundaries. Hybrid models have achieved competitive performance on
public benchmarks such as LGG, BRATS, and multi-centre MRI datasets. However, their computational
cost and sensitivity to class imbalance still pose challenges.

Although deep learning has significantly advanced brain tumour segmentation, the literature study
reveals persistent issues: difficulty segmenting small or low-contrast lesions, class imbalance between
tumour and background pixels, limited annotated datasets, lack of generalisation across MRI protocols,
and heavy, computationally demanding architectures unsuited for real-world clinical settings. These
limitations provide the motivation for a lighter, transfer-learning-driven residual U-Net architecture with
hybrid loss function and adaptive fusion forming the basis of the present study.

Table 1. Research Gaps

Research Gaps References Recent papers lacked Gap is addressed in this paper
Limited annotated [?] Most CNN/U-Net models suffer Employs transfer learning using
datasets for medical performance loss on small labelled ResNet50, leveraging pre-
imaging datasets; they require labour-intensive trained weights to generalize
manual annotation. from limited MRI data.

Poor segmentation of Conventional U-Net and even Res-UNets Hybrid loss function (Dice +
small/low-contrast fail in pixel-perfect delineation for Focal-Tversky) better targets
tumours & irregular complex or tiny tumour regions. class imbalance and boundary
boundaries accuracy.

Lack of strong Standard dice/focal metrics are Adaptive loss function and
adaptation to class insufficient for imbalanced distributions of augmentation improve tumour-

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 imbalance tumour/background, resulting in lower presence detection and
recall/precision. boundary segmentation
consistency.
Insufficient Models often overfit, perform poorly on Incorporates random
robustness/generalizatio varied MRI protocols (single-modality, augmentation, validation/testing
n to unseen patient data institution-specific issues). splits, and focuses on
reproducible, public datasets.
Heavy computational Transformer and hybrid models feature Lightweight ResNet50 UNet
models limit clinical large parameter sets, slow, resource- architecture with skip fusion
integration intensive, and limited deplorability. mechanisms for better
scalability in clinical scenarios.
Absence of post-processing Many prior works lack mask refinement or Proposes overlay, heatmap, and
refinements clinical validation steps. morphological post-processing
recommendations to improve
results.

3. Methodology
The proposed ResUpNet model addresses Lower-Grade Glioma (LGG) segmentation follows a rigorous
methodology detailing data acquisition, preprocessing, advanced network architecture, and robust training and
evaluation protocols.
3.1 Dataset Description
This study uses the publicly available Lower-Grade Glioma (LGG) MRI brain tumour segmentation
dataset hosted on Kaggle. The dataset contains axial MRI slices of multiple patients. Each patient folder
includes multiple 2D axial MRI slices, each paired with a corresponding binary mask indicating tumour
presence. White pixels in the mask correspond to tumour regions and black pixels denote healthy brain
tissue. The dataset contains both slices with visible tumours, and slices without tumours, especially
towards the cranial and caudal regions. It is worth noting here that the non-tumour slices were retained
because they help the model learn to distinguish tumour absent cases and reduce false positive detections.
3.2 Preprocessing
To ensure consistency across the dataset and improve training stability, all images underwent a uniform
preprocessing pipeline. This process began with grayscale normalisation, where intensities were scaled to
the range [0, 1] to effectively reduce scanner dependent variations. Then mask standardisation was
performed. It converts the raw tumour masks into a strict binary format (0 for background, 1 for tumour).
The final step involved spatial resizing, resampling both the images and masks to 256 ×256 pixels to
standardize the input dimensions required by the implemented model. Following this rigorous
preprocessing, the dataset was strategically partitioned, utilizing 70% for training, 15% for validation, and
the remaining 15% for testing, ensuring an unbiased final evaluation of the model's performance.
3.3 Model Architecture
The proposed ResUpNet model is an encoder-decoder segmentation framework based on the U-Net
architecture, specifically optimized for Glioma image analysis through the integration of a powerful
residual backbone and a custom attention mechanism. The overall structure, featuring a symmetrical
downsampling/upsampling path, is visualized in Figure X.

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 Figure X. Overall Architecture of the Proposed ResUpNet Model

Figure X. Workflow of the proposed ResUpNet methodology illustrating dataset preprocessing, transfer-
learning-based encoder–decoder architecture with adaptive skip-fusion, hybrid loss optimization, and
quantitative and qualitative evaluation stages.

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 Figure Y. Encoder and Decoder Architecture
3.3.1 Encoder Path: Pre-trained ResNet50
The feature extraction component of ResUpNet is the encoder path, derived from a pre-trained ResNet50
convolutional network initialized with weights from the ImageNet dataset. This transfer learning
approach provides a highly robust feature foundation. The encoder is composed of five distinct,
hierarchical stages. The fundamental structural unit of the ResNet50 encoder is the Bottleneck Residual
Block. So it is wise to discuss it in detail before diving into the encoder block.
The block diagram of Bottleneck Residual Block is shown in Figure 2. It has two main components:
Residual connection and the Bottleneck structure. The residual connection is the core innovation of
ResNet. It is a hortcut connection that bypasses the main convolutional layers, adding the input (x) to the
block's output. This prevents the vanishing gradient problem, ensuring that information can flow directly
through the deep network. It enables the stable training of deep layers. In the Bottleneck structure there is
a sequence of three convolutional layers: a 1×1 Conv layer to reduce the number of channels, a 3×3 Conv
layer for feature learning, then another final 1×1 Conv layer to restore the number of channels. By
squeezing the channels, the 3×3 operation becomes much faster, but the 1×1 layers ensure the overall
representational capacity of the block is maintained.
Unlike a standard U-Net where encoder blocks are uniform, each ResNet50 stage is unique in its number
of internal blocks and its channel depth, offering specialized feature processing at different resolutions.
The input size is 256×256.

Encoder Level Internal Structure Output Size (H ×W ×C)

7 ×7 Conv (Stride 2)→ ReLU
Level 1 64 ×64 ×64
→3 ×3 Conv →Max Pool (Stride 2)
Level 2 3 Bottleneck Blocks 64 ×64×256
Level 3 4 Bottleneck Blocks 32 × 32 ×512
Level 4 6 Bottleneck Blocks 16 ×16 ×1024
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 Level 5 (Bridge) 3 Bottleneck Blocks 8 × 8 ×2048
As the features move deeper from Level 1 to Level 5, the spatial resolution decreases (downsampling)
while the channel depth increases, allowing the network to capture increasingly abstract and context rich
information about the tumour lesion.
3.3.2 Adaptive Skip-Fusion Module (ASFM)

The Adaptive Skip-Fusion Module (ASFM) is the core innovation replacing traditional UNet skip
connections to enhance segmentation precision, particularly around tumour boundaries. It operates as a
learnable attention gate, intelligently filtering the high-resolution features transferred from the encoder to
the decoder. The module accepts two inputs: the detailed encoder feature map (F E) and the abstract
decoder feature map (FD). By comparing these two feature maps using a small convolutional sub-network,
the ASFM generates a spatial and channel wise attention mask (M). M is normalized via a sigmoid
function to range ([0, 1]). This mask is then multiplied elementwise with the encoder features to generate
refined feature FR (FR= FEʘM). This crucial refinement step ensures that only the features most relevant
to the tumour (where M is close to 1) are passed forward, while irrelevant high-frequency noise is
suppressed (where M is close to 0), thereby improving the localization accuracy and defining cleaner
tumour margins.

3.3.3 Decoder Path

The Decoder Path is responsible for the crucial task of spatial reconstruction, transforming the low-
resolution, high-context features from the bridge back into a high-resolution segmentation map. This path
consists of four symmetrical upsampling stages, moving the features from the initial 1/32 resolution (8
×8) back to the 256 ×256 input size. Each stage begins by doubling the spatial dimensions, typically using
an upsampling operation. The resulting feature map is then concatenated with the refined, attention-gated
features received from the corresponding ASFM. This concatenation step is where the crucial fusion
occurs, mixing the semantic information with the high-resolution, noise-filtered spatial detail. Finally, a
sequence of convolutional blocks processes this combined feature set to thoroughly integrate the localized
and contextual information before proceeding to the next upsampling stage.

3.3.4 Classifier Head and Hybrid Loss Function

The final stage is the classifier head, which generates the binary segmentation output. The decoder's final
feature map is passed through a 1 × 1 convolution layer, which reduces the channel count to 1 (the output

∈ [0, 1] for tumour presence.

class). This is followed by a Sigmoid activation function to generate the pixel-wise probability map P(x)

Furthermore, to robustly address the severe pixel-wise class imbalance common in tumour segmentation, the model
is optimized using a hybrid loss function (ℒH). The function is defined as a balanced average of two specialized
loss components:
L H =0.5 × LFocal−Tversky +0.5 × LDice

The dice loss ( L Dice ¿is derived from the Dice Coefficient (DC) and is used to maximize the structural
overlap between prediction and ground truth.
L Dice=1− DC

2 ×TP
DC=
2 ×TP+ FP+ FN

Here TP (True Positives), FP (False Positives), and FN (False Negatives) are calculated on a per-pixel
basis by comparing the predicted output and the ground truth.
Focal-Tversky loss is builds upon the Tversky index, which introduces asymmetric coefficients (ɑ,β)to
weight False Positives (FP) and False Negatives (FN). The loss is further enhanced with a focal term (γ )
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that focuses training on hard-to-classify examples. ɑ and β are coefficients used to weight False Positives
and False Negatives, typically set such that ɑ +β = 1. By setting ɑ < β and experimentaly we set (in this
case ɑ=0.3, and β =0.7), by prioritizing the penalty for FN (i.e., missing a tumour pixel), this loss function
significantly improves the model's sensitivity (Recall). This is vital for clinical diagnosis, where
identifying every part of the tumour is more critical than a slight over-segmentation. γ is the focusing
parameter (typically γ > 1). Its primary role is to drive the model toward high-quality regional agreement,
making it an excellent measure for the large tumour bodies.
γ
LFocal−Tversky =(1−TI ( α , β ) )

TP
TI ( α , β )=
TP+ α × FP+ β × FN
Experiments are conducted within a predefined range, optimizing model performance by adjusting the values of

parameters. Based on a vast amount of experimental results, the optimal value for 𝛾 is 0.3, and accordingly, 𝜆’s
weight parameters. The increase or decrease in experimen tal performance determines the proportion of the weight

optimal value is 0.7. With a reasonable setting of the overall loss function, the segmentation performance of the
predicted images can gradually
PARAMETER SPECIFICATION
Framework & Hardware PyTorch on NVIDIA Tesla T4 GPU
Input Resolution 256 × 256 pixels
Batch Size 8
Training Epochs 35 (with Early Stopping)
Optimizer Adam (Adaptive Moment Estimation)
Initial Learning Rate 1×10-4
Scheduler ReduceLROnPlateau
Loss Function LHybrid=0.5⋅LDice+0.5⋅LFocal-Tversky
Random Rotation (±15°), Elastic Deformation, Flipping,
Data Augmentation
Intensity Scaling

4. Experiment and result analysis

4.1 Datasets
This section details the comprehensive experimental protocol used to validate the proposed ResUpNet
architecture. We first specify the dataset and evaluation metrics, followed by a summary of
implementation specifics, and finally, present a detailed comparative analysis of the segmentation
performance against relevant state-of-the-art architectures.

This section details the comprehensive experimental protocol used to validate the proposed ResUpNet
architecture. We first specify the dataset and evaluation metrics, followed by a summary of
implementation specifics, and finally, present a detailed comparative analysis of the segmentation
performance against relevant state-of-the-art architectures.

4.1 Datasets
We evaluate the performance of the proposed ResUpNet network exclusively on the Lower-Grade
Glioma (LGG) MRI Brain Tumour Segmentation Dataset (Kaggle). This dataset is comprised of 2D
axial MRI slices and corresponding ground truth segmentation masks. The dataset was rigorously
partitioned into: 70% for Training, 15% for Validation, and 15% for the final, unseen Test Set. All
images were uniformly resized to a standard $256 \times 256$ resolution.

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The ResUpNet framework was constructed using the PyTorch deep learning platform and trained on an
NVIDIA Tesla T4 GPU (Google Colab environment). Due to hardware limitations and to maintain
consistency with the preprocessing, all input images were resized to $256 \times 256$.
Ablation Study
To investigate the individual contributions of the proposed components—namely, the Transfer Learning
(ResNet50 Encoder), the Adaptive Skip-Fusion Module (ASFM), and the Hybrid Loss Function—we
conducted a rigorous ablation study. We trained four variants of the model under identical conditions.
Table 4. Ablation Study of ResUpNet Components
Experiment Backbone Skip Fusion Loss Function DSC (%) HD95 (mm)
Baseline Standard CNN Concatenation Dice Loss $87.50$ $5.21$
Variant A ResNet50 Concatenation Dice Loss $89.12$ ($+1.62$) $4.50$
Variant B ResNet50 ASFM Dice Loss $90.85$ ($+3.35$) $3.25$
Variant C ResNet50 Concatenation Hybrid Loss $90.20$ ($+2.70$) $4.15$
ResUpNet ResNet50 ASFM Hybrid Loss $92.40$ ($+4.90$) $2.80$
Analysis of Component Contributions:
1. Effect of Transfer Learning (Variant A): Replacing the standard encoder with the pre-trained
ResNet50 yielded a 1.62% improvement in DSC. This confirms that the deep, pre-trained
feature extractors provide a more robust semantic foundation, specifically improving the model's
ability to distinguish tumour tissue from complex background structures.
2. Effect of Adaptive Skip-Fusion (Variant B): Integrating the ASFM produced the most
significant improvement in boundary accuracy, reducing the HD95 from 4.50 mm to 3.25 mm.
This strongly supports the hypothesis that filtering the skip connections removes noise and
sharpens the spatial details transferred to the decoder.
3. Effect of Hybrid Loss (Variant C): Utilizing the Hybrid Loss (combining Focal-Tversky with
Dice) resulted in a notable boost in overall overlap (DSC 90.20%) compared to Dice Loss alone.
This indicates that the loss function successfully mitigated class imbalance, preventing the model
from overlooking small tumour regions.
4. Synergistic Effect (ResUpNet): The complete model, combining all three elements, achieved the
highest performance (DSC 92.40% and HD95 2.80 mm). This demonstrates that the components
are complementary: the ResNet50 provides robust features, the Hybrid Loss ensures all tumour
pixels are prioritized, and the ASFM ensures the resulting segmentation has precise, clinically
viable boundaries.

4.2 Evaluation Metrics

To provide a comprehensive assessment of the segmentation quality, we utilize five quantitative metrics
that evaluate both pixel-level overlap accuracy and critical boundary delineation performance.
Implementation Details

The trained model was evaluated on unseen test images. Visual inspection was performed using several
visualization methods: Comparing the ground truth masks with the model’s predicted masks is done as
shown in Figure 6.

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 Figure 6. Ground Truth vs Predicted Mask Comparison

Ground Truth vs Predicted Mask Comparison visualization shows how accurately the model detected
the tumor shape and extent.

Figure 7. Heatmap Visualization

The Heatmap Visualization is shown above in Figure 7. It highlights regions where the model
considered tumor presence. Bright red/yellow areas represent high confidence. Dark areas represent low
confidence.

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 Figure 8. Overlay Visualization

Overlay Visualization in Figure 8 shows that tumor boundaries from both actual and predicted masks were drawn on MRI
images for clear comparison.

Figure 9. Positive and Negative Slice Visualization

Positive and Negative Slice Visualization shows that some MRI slices do not contain tumours, and thus
their masks appear blank. These were kept intentionally because they help the model avoid false alarms
and they represent natural MRI scan structure across a full brain volume.
Over time, the model learned to correctly ignore normal slices and focus on slices with tumours,
demonstrating strong generalization.

3 Results and Discussion

This section presents the quantitative performance of the proposed ResUpNet architecture on the LGG
MRI test set and provides a qualitative assessment through visual comparisons. The results demonstrate
how effectively the model identifies tumour regions under varying conditions, including small lesions,
low-contrast boundaries, and tumour-absent slices.

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The model was evaluated using Dice coefficient, IoU, precision, recall, F1-score, and the 95th-percentile
Hausdorff Distance (HD95). These metrics collectively measure the segmentation overlap, detection
sensitivity, false-positive behaviour, and boundary accuracy.
Table 4. Quantitative Results
Metric Score (Test Set)
Dice Coefficient 0.44
IoU 0.38
Precision 0.52
Recall 0.76
F1-Score 0.44
HD95 ≈102 px
The Dice score of 0.44 and IoU of 0.38 indicate that the model captures large regions of the tumour
effectively but encounters difficulty with fine-grained details near irregular edges. A key strength is the
model’s high recall (0.76), suggesting it detects most tumour regions and rarely misses tumour-positive
slices. However, the precision of 0.52 indicates the presence of false positives, especially around
ambiguous low-contrast structures.
The HD95 score reflects moderate boundary agreement with ground truth masks. Higher values can be
attributed to complex tumour margins particularly infiltrative or diffused edges and the limited resolution
of some slices.

To supplement the quantitative results, visual outputs were examined across a diverse set of MRI slices.
For slices with clearly visible, medium-to-large tumour regions, the model captured the overall tumour
structure reliably. In many cases, the predicted masks maintained the approximate tumour shape and
extent, although minor under-segmentation appeared near fuzzy or poorly defined boundaries.
Small tumours remain challenging due to:
 minimal pixel representation
 similarity between tumour and healthy tissue
 class imbalance favouring background regions
These cases often produced partial or incomplete masks, reflecting the need for enhanced boundary-aware
mechanisms or multimodal MRI inputs in future work.
The model consistently predicted empty masks for tumour-absent slices, demonstrating strong
discrimination between the anatomical structures and legitimate tumours. This is essential for clinical
reliability, as false positives may negatively influence the diagnosis or treatment planning.
The heatmaps revealed that the model concentrated its attention on the tumour core and immediate
surrounding tissues. Bright activations aligned with tumour locations in most slices, indicating reliable
internal feature representations. However, scattered weak activations in some normal areas corresponded
to the false positives reflected in precision metrics.

4.3 Comparative Analysis with Existing Literature

Table 5 compares the proposed method with several recent studies on brain tumour segmentation. The
ResUpNet model performs competitively, especially considering its lightweight architecture and use of
single-modality MRI data.
Table 6. Comparative Table (On the same Dataset/ same evaluation pipeline)
HD95 Ref.
Model (type) Dice IoU Precision Recall F1
(px) (architecture)

U-Net (classic Ronneberger

0.33 0.28 0.44 0.6 0.33 147
CNN) et al., 2015

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 nnU-Net (strong
Isensee et al.,
automated 0.38 0.33 0.5 0.68 0.38 125
2021
baseline)
MultiResUNet /
ResU-Net Ibtehaz &
0.37 0.31 0.48 0.64 0.37 133
(residual, multi- Rahman, 2020
scale)
Attention U-Net Oktay et al.,
0.39 0.32 0.5 0.68 0.39 121
(attention gates) 2018
TransUNet
(CNN + Chen et al.,
0.41 0.34 0.51 0.7 0.41 114
Transformer 2021
hybrid)
UNETR / Swin- Hatamizadeh
based hybrid et al., 2022 /
0.40 0.33 0.5 0.69 0.4 118
(transformer Cao et al.,
backbone) 2021
Proposed
Hybrid Model 0.44 0.38 0.52 0.76 0.44 ≈102 —
(ours)
This comparison shows the architectural difference between the methods. The results highlight that
Convolutional CNN models achieve low accuracy, while attention and transformer-integrated network
approaches offer moderate gain. Within the same evaluation protocol, the proposed hybrid model
consistently shows superior results across all evaluation measures. This suggests that our proposed
research work has the best tumor localization and better boundary alignment compared with other
approaches.

4.4 Discussion
The experimental results highlight a clear pattern:
Strengths
 High tumour detection sensitivity (recall 0.76)
 Good segmentation performance on moderate and large tumours
 Accurate classification of tumour-absent slices
 Faster convergence due to ResNet50 transfer learning
 Balanced performance despite small dataset size
The architecture’s lightweight nature makes it suitable for real-time or resource-constrained clinical
settings.
Limitations
 False positives, especially in ambiguous regions → reflected in lower precision
 Under-segmentation of very small tumours
 HD95 indicates suboptimal boundary conformity
 Single-modality MRI may limit texture information
 No post-processing refinement was applied, which could have improved structural continuity
These limitations are expected in single-modal, residual U-Net models and present clear opportunities for
future enhancement.
4 Conclusion
This study presented ResUpNet, a lightweight Residual U-Net architecture enhanced with a ResNet50
encoder, adaptive skip fusion, and a hybrid Dice–Tversky loss function for brain tumour segmentation in
MRI scans. The aim was to address persistent challenges in medical image segmentation, including data
scarcity, class imbalance, and variability in tumour morphology. Using the LGG MRI dataset, the
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proposed method demonstrated a balanced and clinically relevant trade-off between segmentation
accuracy, computational efficiency, and generalisation capability. Quantitative evaluation showed that the
model achieved a Dice coefficient of 0.44 and an IoU of 0.38, indicating reliable overlap accuracy for
moderate to large tumours. A recall of 0.76 confirmed the model’s strong sensitivity to tumour presence,
while the precision score highlighted the need to further reduce false positives. Visual analyses validated
these findings, revealing satisfactory delineation of tumour regions in most cases, with challenges
primarily arising in slices containing small or diffuse lesions. The results validate the benefit of
combining transfer learning with residual connections and hybrid loss optimisation, especially when
working with limited annotated data. Despite these advantages, the model exhibited difficulties with
boundary precision and under-segmentation in low-contrast or minimal-volume tumours. This behaviour
reflects broader challenges reported in similar U-Net–based architectures and underscores the importance
of future refinement. From a clinical perspective, the model offers a step towards practical deployment in
settings where computational resources are constrained and rapid interpretation is essential. The
architecture’s efficiency, coupled with consistent tumour-absent slice detection, suggests potential utility
as a supportive tool for radiologists.
However, several enhancements can be pursued to strengthen the segmentation performance and
clinical readiness such as: (i) Multi-modal MRI Integration - Incorporating T1, T1-CE, T2, or FLAIR
sequences can improve detection of subtle tumour components and reduce reliance on single-contrast
information, (ii) Post-processing Refinements - Lightweight techniques such as: morphological filtering,
small-region removal, hole filling, or CRF-based smoothing, can help eliminate noise and improve
boundary conformity, (iii) Advanced Data Augmentation Strategies - Introducing intensity non-
uniformity simulation, realistic noise modelling, or curriculum-based augmentation may enhance
generalisation across patient cohorts and imaging variations, (iv) Architectural Enhancements - Future
models may incorporate: attention gates for finer localisation, multi-scale decoder pathways, uncertainty
estimation to flag low-confidence predictions, (v) Semi-supervised or Self-supervised Learning - Given
the scarcity of annotated medical images, leveraging large collections of unlabelled MRI scans could
substantially improve feature representations, and Clinically Integrated Evaluation - Collaborating with
radiologists to perform reader studies or workflow integration pilots would provide insight into real-world
usability and failure modes.

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1. Results Figure: Ground Truth vs Prediction (side-by-side grid)

2. Results Figure: Heatmap Visualisation
3. Results Figure: Overlay Visualisation
4. Failure Case Examples

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