Whole Slide Image (WSI) Processing Library
Project description
Convert Helper for Histopathological / Cytopathological Machine Learning Tasks
Main Flow
- Scan some WSIs.
- Make some annotations with WSI annotation tools. (ASAP and SlideRunner v.1.31.0, QuPath v0.2.3 are now available. See wiki for details.)
- Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.
WSIPatcher will give you GUI.
See Wiki for
- available applications for annotation,
- speed comparison between patched images and loading from raw WSIs,
- how to use the other annotatiion files.
Installation
pip User
-
Install openslide or libvips. See [wiki] for installation hints.
-
Install wsiprocess
pip install wsiprocess
Anaconda User
# Only for python 3.6 or higher
conda install -c tand826 wsiprocess
Documentation
Example
As a python module
- see examples
- see wsiprocess/cli.py to check the detailed flow.
As a command line tool
- see examples.
Available annotation tools
details: wiki
Available WSIs
Test ongoing
-
From below we tested wsi data.
- :smile: => worked well.
- :umbrella: => did not work well.
- otherwise => did not check
-
Aperio
- CMU-1-JP2K-33005.svs
- :smile: CMU-1-Small-Region.svs
- :smile: CMU-1.svs
- CMU-2.svs
- CMU-3.svs
- JP2K-33003-1.svs
- JP2K-33003-2.svs
-
Generic-TIFF
- :umbrella:CMU-1.tiff
- Can not set magnification.
- :umbrella:CMU-1.tiff
-
Hamamatsu-vms
- :smile:CMU-1.zip
- CMU-2.zip
- CMU-3.zip
- Could not DOWNLOAD from http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/
-
Hamamatsu
- :smile:CMU-1.ndpi
- CMU-2.ndpi
- CMU-3.ndpi
- OS-1.ndpi
- OS-2.ndpi
- OS-3.ndpi
-
Leica
- :smile:Leica-1.scn
- Leica-2.scn
- Leica-3.scn
- Leica-Fluorescence-1.scn
-
Mirax
- CMU-1-Exported.zip
- CMU-1-Saved-1_16.zip
- CMU-1-Saved-1_2.zip
- :umbrella:CMU-1.zip
- Can not make the foreground mask.
- CMU-2.zip
- CMU-3.zip
- Mirax2-Fluorescence-1.zip
- Mirax2-Fluorescence-2.zip
- Mirax2.2-1.zip
- Mirax2.2-2.zip
- Mirax2.2-3.zip
- Mirax2.2-4-BMP.zip
- Mirax2.2-4-PNG.zip
-
Olympus
- OS-1.zip
- OS-2.zip
- OS-3.zip
-
Trestle
- :umbrella:CMU-1.zip
- ASAP can not show the image properly, and it's hard to annotate.
- CMU-2.zip
- CMU-3.zip
- :umbrella:CMU-1.zip
-
Ventana
- OS-1.bif
- OS-2.bif
-
:umbrella:Zeiss : Can not load slide - :umbrella:Zeiss-1-Merged.zvi - :umbrella:Zeiss-1-Stacked.zvi - :umbrella:Zeiss-2-Merged.zvi - :umbrella:Zeiss-2-Stacked.zvi - :umbrella:Zeiss-3-Mosaic.zvi - :umbrella:Zeiss-4-Mosaic.zvi
Test
Download sample WSI
curl -O -C - https://data.cytomine.coop/open/openslide/hamamatsu-ndpi/CMU-1.ndpi
Make random annotation
- Install ASAP ( Linux / Windows ) - https://github.com/computationalpathologygroup/ASAP/releases
- Open CMU-1.ndpi and make some random annotation. - Save the annotation xml as "CMU-1.xml".
Run test.py
cd tests
pytest tests.py
Citation
@software{takumi_ando_2021_4629396,
author = {Takumi Ando},
title = {tand826/wsiprocess: version 0.8},
month = mar,
year = 2021,
publisher = {Zenodo},
version = {v0.8},
doi = {10.5281/zenodo.4629396},
url = {https://doi.org/10.5281/zenodo.4629396}
}
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