GitHub - saketkc/pyvirchow: Tools for whole slide image processing and classification

pyvirchow


target ./logo/virchow_480x480.jpg
* Free software: BSD license
Documentation: https://www.saket-choudhary.me/pyvirchow/
Features

See the Demo or browser all notebooks.
Training InceptionV4 on Tumor/Normal patches

We currently rely on InceptionV4 model for training. It is one of the
deepest and most sophesticated models available. Another model we would ideally
like to explore is Inception-Resnet, but later.
Step 1. Create tissue masks


pyvirchow create-tissue-masks --indir /CAMELYON16/testing/images/
--level 5 --savedir /CAMELYON16/testing/tissue_masks
Step 2. Create annotation masks


pyvirchow create-annotation-masks --indir /CAMELYON16/testing/images/
--level 5 --savedir /CAMELYON16/testing/annotation_masks
--jsondir /CAMELYON16/testing/lesion_annotations_json
Step 3A. Extract tumor patches


pyvirchow extract-tumor-patches --indir /CAMELYON16/testing/images/
--annmaskdir /CAMELYON16/testing/annotation_masks
--tismaskdir /CAMELYON16/testing/tissue_masks
--level 5 --savedir /CAMELYON16/testing/extracted_tumor_patches
Step 3B. Extract normal patches


pyvirchow extract-normal-patches --indir /CAMELYON16/training/normal
--tismaskdir /CAMELYON16/training/tissue_masks --level 5
--savedir /CAMELYON16/training/extracted_normal_patches
Dataset download

Ftp

Name		Name	Last commit message	Last commit date
Latest commit History 173 Commits
.github		.github
data		data
docs		docs
logo		logo
notebooks		notebooks
notes		notes
pyvirchow		pyvirchow
retrain		retrain
scripts		scripts
snakemake		snakemake
tests		tests
.editorconfig		.editorconfig
.gitattributes		.gitattributes
.gitignore		.gitignore
.travis.yml		.travis.yml
AUTHORS.rst		AUTHORS.rst
CONTRIBUTING.rst		CONTRIBUTING.rst
HISTORY.rst		HISTORY.rst
LICENSE		LICENSE
MANIFEST.in		MANIFEST.in
Makefile		Makefile
README.rst		README.rst
requirements.txt		requirements.txt
requirements_dev.txt		requirements_dev.txt
setup.cfg		setup.cfg
setup.py		setup.py

saketkc/pyvirchow