This repository provides Bio-Totem algorithm try out scripts for Tumor InfiltratinG lymphocytes in breast cancER challenge.
We got 1st at Segmentation and Detection (Final) Leaderboard:
This subdirectory provides scripts for building TIGER challenge algorithm-docker image base on https://tiger.grand-challenge.org/Requirements/
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./submit_docker_script/pkgs is the storage of binary package(deb format for system software installtion and whl format for python package installtion) which would be installed in docker image by Dockerfile. You should download from other ways and put them to ./submit_docker_script/pkgs
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./submit_docker_script/tigeralgorithmexample is the main process code in algorithm-docker image for prediction, based on pathology-tiger-algorithm-example · GitHub
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Notice that there is no real model weight file in this repository, you can train the model you need by yourself and edit your model weight file path at ./submit_docker_script/tigeralgorithmexample/processing.py and ./submit_docker_script/tigeralgorithmexample/nuclei_det/det_processing_loader_merge.py
There are two subdirectories,./train_script/Segmentation to segment several tissue compartments and ./train_script/Detection to detect lymphocytes and plasma cells.
Model weights used in our submission are provided at https://drive.google.com/drive/folders/1aDyOLXyyfEW9Fz1OJCiiuLV2mG0CH0hZ?usp=sharing