🆕 Add GrandQC Tissue Segmentation Model

[Jiaqi-Lv]

This PR adds GrandQC tissue detection (Unet++) model to TIAToolBox models. GrandQC Official Github.

Tasks

• Re-host GrandQC model weights on TIA Hugging Face
• Update pretrained_model.yaml
• Update requirements.txt
• Define GrandQC model architecture
• Add example usage
• Remove segmentation-models-pytorch dependency
• Wait for response from GrandQC authors
• Add tests
• Tidy up

[codecov]

Codecov Report

❌ Patch coverage is 95.06173% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.73%. Comparing base (c535eab) to head (19cca90).

Files with missing lines	Patch %	Lines
...iatoolbox/models/architecture/timm_efficientnet.py	92.74%	3 Missing and 6 partials ⚠️
tiatoolbox/models/architecture/grandqc.py	97.47%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@                   Coverage Diff                    @@
##           dev-define-engines-abc     #965    +/-   ##
========================================================
  Coverage                   94.72%   94.73%            
========================================================
  Files                          73       75     +2     
  Lines                        9234     9477   +243     
  Branches                     1208     1238    +30     
========================================================
+ Hits                         8747     8978   +231     
- Misses                        452      457     +5     
- Partials                       35       42     +7     

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[Copilot]

Pull Request Overview

This PR integrates the GrandQC tissue detection model into TIAToolBox, adding a UNet++ based tissue segmentation capability trained at 10 microns per pixel resolution. The implementation leverages the segmentation-models-pytorch library to avoid reimplementing the UNet++ architecture.

• Adds GrandQC tissue detection model architecture and pretrained weights
• Integrates model with existing tissue masking functionality
• Adds comprehensive test coverage and example usage

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tiatoolbox/models/architecture/grandqc.py	Defines the TissueDetectionModel class with UNet++ architecture and custom preprocessing/postprocessing
tiatoolbox/data/pretrained_model.yaml	Adds GrandQC model configuration and fixes IOConfig class references across multiple models
tests/models/test_arch_grandqc.py	Implements unit tests for model creation, weight loading, and inference
requirements/requirements.txt	Adds segmentation-models-pytorch dependency
tiatoolbox/wsicore/wsireader.py	Integrates GrandQC masker into tissue_mask method with 10mpp resolution handling

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[Copilot]

Pull Request Overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.

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[Copilot]

Pull Request Overview

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

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[shaneahmed]

GrandQC authors have confirmed that we are allowed to integrate the model in TIAToolbox. Please add appropriate licensing and citation information.

[Copilot]

Pull request overview

Copilot reviewed 5 out of 5 changed files in this pull request and generated 10 comments.

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