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kidney-wsi-seg

https://github.com/hula-ai/kidney-wsi-seg

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: hula-ai
  • License: apache-2.0
  • Language: Python
  • Default Branch: main
  • Size: 14.9 MB
Statistics
  • Stars: 2
  • Watchers: 0
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created over 2 years ago · Last pushed over 2 years ago
Metadata Files
Readme License Citation

README.md

Kidney WSI segmentation of diagnostic tissue compartments

3-stage model

  • Tissue segmentation: tree structure
  • Instance segmentation: mmdet
  • Post-processing step: only in inference stage

Commands for running

Generate data

  • QuPath script: how to use groovy file
  • Python script: generate json files

Installation and some problems

If you want to generate glom,artery, arteriole on a new collection of WSIs.

Evaluation

The Python generation file also contains evaluation code

Discriminate Qupath scripts and Python scripts for generating labels

Crop vs multi, Pad vs no pad

Trained checkpoints and norm files

Acknowledgement

mmdet library

Owner

  • Name: HULA-AI
  • Login: hula-ai
  • Kind: organization
  • Location: Houston, TX

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - name: "MMDetection Contributors"
title: "OpenMMLab Detection Toolbox and Benchmark"
date-released: 2018-08-22
url: "https://github.com/open-mmlab/mmdetection"
license: Apache-2.0

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
Last Year
  • Issues event: 1
  • Watch event: 1

Dependencies

docker/Dockerfile docker
  • pytorch/pytorch ${PYTORCH}-cuda${CUDA}-cudnn${CUDNN}-devel build
docker/serve/Dockerfile docker
  • pytorch/pytorch ${PYTORCH}-cuda${CUDA}-cudnn${CUDNN}-devel build
requirements/albu.txt pypi
  • albumentations >=0.3.2
requirements/build.txt pypi
  • cython *
  • numpy *
requirements/docs.txt pypi
  • docutils ==0.16.0
  • recommonmark *
  • sphinx ==4.0.2
  • sphinx-copybutton *
  • sphinx_markdown_tables *
  • sphinx_rtd_theme ==0.5.2
requirements/mminstall.txt pypi
  • mmcv-full >=1.3.17
requirements/optional.txt pypi
  • cityscapesscripts *
  • imagecorruptions *
  • scipy *
  • sklearn *
  • timm *
requirements/readthedocs.txt pypi
  • mmcv *
  • torch *
  • torchvision *
requirements/runtime.txt pypi
  • matplotlib *
  • numpy *
  • pycocotools *
  • six *
  • terminaltables *
requirements/tests.txt pypi
  • asynctest * test
  • codecov * test
  • flake8 * test
  • interrogate * test
  • isort ==4.3.21 test
  • kwarray * test
  • onnx ==1.7.0 test
  • onnxruntime >=1.8.0 test
  • pytest * test
  • ubelt * test
  • xdoctest >=0.10.0 test
  • yapf * test
requirements_my.txt pypi
  • aicsimageio ==4.9.4
  • chardet ==5.1.0
  • h5py ==3.7.0
  • kneed ==0.8.1
  • openslide-python ==1.2.0
  • paquo ==0.6.0
  • scikit-image ==0.19.3
  • scikit-learn ==1.2.0
  • seaborn ==0.12.2
  • slideio ==2.0.0
  • tifffile ==2022.10.10
  • torch ==1.12.1
  • torchaudio ==0.12.1
  • torchvision ==0.13.1
  • tqdm ==4.64.1
  • wandb ==0.13.7
setup.py pypi