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

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.
- :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.
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

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}
}

Metadata

Release files for wsiprocess 1.1.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for wsiprocess 1.1.1
File	Size	Uploaded
wsiprocess-1.1.1.tar.gz	38.4 kB	Sep 8, 2023	Details

Built distribution (wheel)

Table of built distributions (wheels) for wsiprocess 1.1.1
File	Interpreter	ABI	Platform	Reset
wsiprocess-1.1.1-py3-none-any.whl 48.4 kB Sep 8, 2023	Python 3	none	any	Details

Total release size: 86.7 kB

Release files / wsiprocess-1.1.1.tar.gz

Download URL	wsiprocess-1.1.1.tar.gz
Size	38.4 kB
Tags	Source
SHA-256 checksum How to use checksums	`d8e450092e552e623589caeacf196da8f925796b8f7cde9ad2d6fcc6ce2d91c3`
BLAKE2b-256 checksum How to use checksums	`e9d0795cf60e2a486ef7905702fb4ece5cea795d7343017cd1116f7287eade6e`
Upload date	Sep 8, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.10.8`

Release files / wsiprocess-1.1.1-py3-none-any.whl

Download URL	wsiprocess-1.1.1-py3-none-any.whl
Size	48.4 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`99cba6dc3ac52aadff43fd6f940c8bb363781a1027efedb60cc6789123c2d053`
BLAKE2b-256 checksum How to use checksums	`328be3d1b4513b9d16fbf451c41ac06b27c64f486b2e7ef1ab40065dcfb36a9d`
Upload date	Sep 8, 2023
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/4.0.2 CPython/3.10.8`