Indices and tables¶

PyPI PyPI - Python Version GitHub

Convert Helper for Histopathological / Cytopathological Machine Learning Tasks

Main Flow¶

Scan some WSIs.
Make some annotations with WSI annotation tools
Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.

WSIPatcher will give you GUI. Command Helper will recommend commands to run.

Installation¶

Install libvips
- Linux - apt install libvips
- MacOS - brew install vips
- Windows - Install tarball from here
Install wsiprocess
```
pip install wsiprocess
```

Example¶

As a python module¶

Basic Usage¶

import wsiprocess as wp
slide = wp.slide("xxx.tiff")
annotation = wp.annotation("xxx.xml")
rule = wp.rule("xxx.json")

annotation.make_masks(slide, rule, foreground=True)

patcher = wp.patcher(slide, "classification", annotation)
patcher.get_patch_parallel("benign")

Export annotaton xml of one class as mask image¶

import wsiprocess as wp
slide = wp.slide("xxx.tiff")
annotation = wp.annotation("xxx.xml")
annotation.make_masks(slide)
annotation.export_mask("xxx/masks", "benign")

Export annotation xml with inclusion definition as mask images, and save their thumbs¶

import wsiprocess as wp
slide = wp.slide("xxx.tiff")
annotation = wp.annotation("xxx.xml")
rule = wp.rule("xxx.json")
annotation.make_masks(slide, rule)
annotation.export_thumb_masks("xxx/masks")

As a command line tool¶

wsiprocess xxx.tiff method --annotation xxx.xml

Need recommendation for choice of arguments? -> Command Helper

As a docker command line tool¶

# build the image
docker build . -t wsiprocess_image

# run the container
docker run --name wsiprocess_container -v [your files directory]:/data -it -d wsiprocess_image [commands] etc.

see Command Helper for commands

Available WSIs¶

Test ongoing

From below we tested wsi data.
- 😄 => worked well.
- ☔ => did not work well.
- otherwise => did not check
Aperio
- CMU-1-JP2K-33005.svs
- 😄 CMU-1-Small-Region.svs
- 😄 CMU-1.svs
- CMU-2.svs
- CMU-3.svs
- JP2K-33003-1.svs
- JP2K-33003-2.svs
Generic-TIFF
- ☔ CMU-1.tiff
  - Can not set magnification.
Hamamatsu-vms
- 😄 CMU-1.zip
- CMU-2.zip
- CMU-3.zip
  - Could not DOWNLOAD from http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/
Hamamatsu
- 😄 CMU-1.ndpi
- CMU-2.ndpi
- CMU-3.ndpi
- OS-1.ndpi
- OS-2.ndpi
- OS-3.ndpi
Leica
- 😄 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
- ☔ 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
- ☔ CMU-1.zip
  - ASAP can not show the image properly, and it’s hard to annotate.
- CMU-2.zip
- CMU-3.zip
Ventana
- OS-1.bif
- OS-2.bif
☔ Zeiss : Can not load slide - ☔ Zeiss-1-Merged.zvi - ☔ Zeiss-1-Stacked.zvi - ☔ Zeiss-2-Merged.zvi - ☔ Zeiss-2-Stacked.zvi - ☔ Zeiss-3-Mosaic.zvi - ☔ Zeiss-4-Mosaic.zvi

Test¶

Download sample WSI¶

curl -O -C - http://openslide.cs.cmu.edu/download/openslide-testdata/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¶

@article{wsiprocess,
    Author = {Takumi Ando},
    Title = {WSIPROCESS - Whole Slide Image Processing Library for Histopathological / Cytopathological Machine Learning Tasks},
    Url = {https://github.com/tand826/wsiprocess},
    Year = {2019}
}

TODO¶

pathology_viewer to be public
add link to WSIPatcher
add to conda
slow free server on heroku
paste results on the thumbnails

Welcome to wsiprocess’s documentation!¶