🆕 Add GrandQC Tissue Segmentation Model #965

Jiaqi-Lv · 2025-10-25T19:20:34Z

🚀Summary

This PR introduces a new GrandQC Tissue Detection Model for digital pathology quality control and integrates EfficientNet-based encoder architecture into the TIAToolbox framework.

✨Key Changes

New Model Architecture
- Added grandqc.py implementing a UNet++ decoder with EfficientNet encoder for tissue segmentation.
- Includes preprocessing (JPEG compression + ImageNet normalization), postprocessing (argmin-based mask generation), and batch inference utilities.
EfficientNet Encoder
- Added timm_efficientnet.py providing configurable EfficientNet encoders with dilation support and custom input channels.
Pretrained Model Config
- Updated pretrained_model.yaml to register grandqc_tissue_detection_mpp10 with associated IO configuration.
- Corrected IOSegmentorConfig references and adjusted resolutions for SCCNN models.
Testing
- Added comprehensive unit tests for:
  - GrandQCModel functionality, preprocessing/postprocessing, and decoder blocks.
  - EfficientNet encoder utilities and scaling logic.

Impact

Enables high-resolution tissue detection for WSI quality control using state-of-the-art architectures.
Improves flexibility for segmentation tasks with EfficientNet encoders.
Enhances code quality and consistency through updated linting and formatting tools.

Tasks

codecov · 2025-10-25T20:05:57Z

Codecov Report

❌ Patch coverage is 96.31148% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 94.76%. Comparing base (c535eab) to head (9c62b72).

Files with missing lines	Patch %	Lines
...iatoolbox/models/architecture/timm_efficientnet.py	92.74%	3 Missing and 6 partials ⚠️

Additional details and impacted files

@@                    Coverage Diff                     @@
##           dev-define-engines-abc     #965      +/-   ##
==========================================================
+ Coverage                   94.72%   94.76%   +0.04%     
==========================================================
  Files                          73       75       +2     
  Lines                        9234     9478     +244     
  Branches                     1208     1238      +30     
==========================================================
+ Hits                         8747     8982     +235     
- Misses                        452      455       +3     
- Partials                       35       41       +6

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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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tiatoolbox/models/architecture/grandqc.py

tiatoolbox/wsicore/wsireader.py

Copilot

Pull Request Overview

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

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tiatoolbox/models/architecture/grandqc.py

Copilot

Pull Request Overview

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

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tiatoolbox/models/architecture/grandqc.py

shaneahmed · 2025-11-17T11:03:58Z

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

…tics/tiatoolbox into dev-add-grandQC

for more information, see https://pre-commit.ci

Copilot

Pull request overview

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

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tests/models/test_arch_timm_efficientnet.py

tiatoolbox/models/architecture/timm_efficientnet.py

tiatoolbox/models/architecture/grandqc.py

tiatoolbox/models/architecture/timm_efficientnet.py

tiatoolbox/models/architecture/grandqc.py

tiatoolbox/models/architecture/timm_efficientnet.py

tests/models/test_arch_grandqc.py

tiatoolbox/data/pretrained_model.yaml

shaneahmed

Thanks @Jiaqi-Lv
I have updated docstrings in this commit.
1895e38

Can you check these?

tiatoolbox/models/architecture/grandqc.py

tiatoolbox/models/architecture/timm_efficientnet.py

shaneahmed · 2025-11-26T10:25:10Z

tiatoolbox/models/architecture/grandqc.py

+        super().__init__(conv1, conv2)
+
+
+class UnetPlusPlusDecoder(nn.Module):


I am not sure why this is part of grandqc.

add grandqc tissue model

b18b98f

Jiaqi-Lv self-assigned this Oct 25, 2025

Jiaqi-Lv added the enhancement New feature or request label Oct 25, 2025

Jiaqi-Lv added 2 commits October 25, 2025 20:30

add example

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fix tests

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Jiaqi-Lv requested a review from Copilot October 25, 2025 20:22

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fix error

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Jiaqi-Lv added 2 commits October 28, 2025 15:07

update docstring

fd692da

improve test coverage

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Jiaqi-Lv requested a review from Copilot October 31, 2025 10:05

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Jiaqi-Lv marked this pull request as draft October 31, 2025 12:26

Jiaqi-Lv and others added 2 commits November 6, 2025 16:54

add unet++ model

93a24a1

Merge branch 'dev-define-engines-abc' into dev-add-grandQC

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shaneahmed reviewed Nov 17, 2025

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shaneahmed changed the title ~~🆕 Add GrandQC tissue detection model~~ 🆕 Add GrandQC Tissue Segmentation Model Nov 17, 2025

Jiaqi-Lv and others added 5 commits November 18, 2025 16:52

Merge branch 'dev-add-grandQC' of https://github.com/TissueImageAnaly…

283b888

…tics/tiatoolbox into dev-add-grandQC

[pre-commit.ci] auto fixes from pre-commit.com hooks

94c43ee

for more information, see https://pre-commit.ci

remove smp dependency

98cef83

refactor code

d47fa0a

add tests

d2a66ca

Jiaqi-Lv requested a review from Copilot November 21, 2025 18:08

Jiaqi-Lv marked this pull request as ready for review November 21, 2025 18:09

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Copilot finished reviewing on behalf of Jiaqi-Lv November 21, 2025 18:11

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address comments

19cca90

shaneahmed reviewed Nov 25, 2025

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📝 Update docstring for grandqc.py and timm_efficientnet.py

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shaneahmed added 2 commits November 25, 2025 10:30

🐛 Fix docstring

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📝 Remove duplicate docstring for classses.

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Jiaqi-Lv and others added 3 commits November 25, 2025 15:07

address comments

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update test

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✅ Add test to improve coverage

9c62b72

shaneahmed reviewed Nov 26, 2025

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		super().__init__(conv1, conv2)


		class UnetPlusPlusDecoder(nn.Module):

🆕 Add GrandQC Tissue Segmentation Model #965

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🆕 Add GrandQC Tissue Segmentation Model #965

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Jiaqi-Lv commented Oct 25, 2025 • edited by shaneahmed Loading Uh oh! There was an error while loading. Please reload this page.

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🚀Summary

✨Key Changes

Impact

Tasks

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Jiaqi-Lv commented Oct 25, 2025 •

edited by shaneahmed

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