🆕 Add KongNet Model and Example Notebook#987
🆕 Add KongNet Model and Example Notebook#987shaneahmed merged 120 commits intodev-define-engines-abcfrom
Conversation
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
# Conflicts: # tiatoolbox/models/engine/engine_abc.py # tiatoolbox/models/engine/semantic_segmentor.py
There was a problem hiding this comment.
Pull request overview
Copilot reviewed 12 out of 13 changed files in this pull request and generated 7 comments.
💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.
|
Can you add a link to your notebook in examples/README.md? So that it appears on this page https://tia-toolbox--987.org.readthedocs.build/en/987/usage_examples.html |
|
View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2026-02-19T11:26:03Z Links to NucleusDetection, KongNet should be to Jiaqi-Lv commented on 2026-02-19T20:14:44Z Changed to blob/develop |
|
View / edit / reply to this conversation on ReviewNB shaneahmed commented on 2026-02-19T11:26:04Z Provide some background on AnnotationStore which is the format you need to visualize in TIAViz. Jiaqi-Lv commented on 2026-02-19T20:35:51Z Done |
|
Changed to blob/develop View entire conversation on ReviewNB |
|
Done View entire conversation on ReviewNB |
…ev-define-KongNet-model
|
Jupyter notebook runs successfully with changes in #1001 |
Summary
This PR integrates KongNet, a state‑of‑the‑art multi‑headed deep learning architecture for nucleus detection and classification. It adds complete documentation, examples, and notebook support covering both patch‑based and whole‑slide image (WSI) processing. Multiple pretrained models are now available for major pathology datasets, each demonstrated through updated example notebooks. The PR also introduces a new visualization image and practical usage patterns for the NucleusDetector class, enabling streamlined workflows for researchers using TIAToolbox.
What’s New
🧠 KongNet Model Integration
Added pretrained KongNet models:
📘 New Example Notebook: Nucleus Detection
A comprehensive example notebook demonstrates:
Patch‑level and WSI‑level detection
Mitosis and immune‑cell detection
Use of NucleusDetector with KongNet pretrained models
Interactive visualization via TIAViz
Add KongNet Model
Add tests
Add example notebook (Nucleus Detector)