Convert Helper for Histopathological / Cytopathological Machine Learning Tasks

Main Flow

1. Scan some WSIs.
2. 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.)
3. Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.

WSIPatcher will give you GUI.

See Wiki for

1. available applications for annotation,
2. speed comparison between patched images and loading from raw WSIs,
3. how to use the other annotatiion files.

Installation

pip User

1. Install openslide or libvips. See [wiki] for installation hints.

2. Install wsiprocess

   pip install wsiprocess
   

Anaconda User

# Only for python 3.6 or higher
conda install -c tand826 wsiprocess

Documentation

• 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

• ASAP
• SlideRunner version 1.31.0
• QuPath v0.2.3
• NDP.View2
• and your favorite tools with custom parser

details: wiki

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 - 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_2022_5938308,
  author       = {Takumi Ando},
  title        = {tand826/wsiprocess: version 0.9},
  month        = feb,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v0.9},
  doi          = {10.5281/zenodo.5938308},
  url          = {https://doi.org/10.5281/zenodo.5938308}
}