wsiprocess 0.0.1

Whole Slide Image (WSI) Processing Library

Convert Helper for Histopathological / Cytopathological Machine Learning Tasks

Main Flow

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

Command Helper will recommend commands to run.

Installation

1. Install libvips

   • Linux
     • apt install libvips
   • MacOS
     • brew install vips
   • Windows
     • Install tarball from here

2. Install wsiprocess

   pip install -r requirements.txt
   pip install wsiprocess
   

Example

As a python module

Basic Usage

import wsiprocess as wp
slide = wp.slide("xxx.tiff")
annotation = wp.annotation("xxx.xml")
inclusion = wp.inclusion("xxx.txt")

annotation.make_masks(slide, inclusion, 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")
inclusion = wp.inclusion("xxx.txt")
annotation.make_masks(slide, inclusion)
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. - :smile: : worked well. - :umbrella: : did not work well. - otherwise : did not check

Classification

• 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.

• 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

• 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

1. Download sample WSI

curl -O -C - http://openslide.cs.cmu.edu/download/openslide-testdata/CMU-1.ndpi

2. 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".

3. Run test.py

python test.py

Citation

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

TODO

• other annotation tools
  • Cytomine : hard to install
  • ImageJ with SlideJ -> only to view one patch???
  • JVSView
  • OMERO
  • Orbit
  • PMA.start : still cannot properly view the image
  • QuPath : run script to save polygon or rectangles
  • caMicroscope OUTPUT SIZE alart
• add to conda
• slow free server on heroku
• paste results on the thumbnails
• if method == detection, like segmentation flow, use mask to check on_annotation.