<div align="center">
<img src="https://raw.githubusercontent.com/tand826/wsiprocess/main/images/wsiprocess.svg" style="width: 50%">
</div>
Convert Helper for Histopathological / Cytopathological Machine Learning Tasks
# Main Flow
<div align="center">
<img src="https://raw.githubusercontent.com/tand826/wsiprocess/main/images/description.gif" style="max-width: 80%">
</div>
1. Scan some WSIs.
2. Make some annotations with WSI annotation tools. ([ASAP](https://github.com/computationalpathologygroup/ASAP/releases) and [SlideRunner v.1.31.0](https://github.com/DeepPathology/SlideRunner), [QuPath v0.2.3](https://github.com/qupath/qupath) are now available. See [wiki](https://github.com/tand826/wsiprocess/wiki) for details.)
3. Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.
[WSIPatcher](https://github.com/tand826/WSIPatcher) will give you GUI.
See [Wiki](https://github.com/tand826/wsiprocess/wiki) for
1. [available applications for annotation](https://github.com/tand826/wsiprocess/wiki/annotation_applications),
2. [speed comparison](https://github.com/tand826/wsiprocess/wiki/speed_comparison) between patched images and loading from raw WSIs,
3. [how to use the other annotatiion files](https://github.com/tand826/wsiprocess/wiki/How-to-use-custom-annotation-parser).
# Installation
### pip User
1. Install [openslide](https://openslide.org/) or [libvips](https://libvips.github.io/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](https://tand826.github.io/wsiprocess/)
# Example
### As a python module
- see [examples](https://github.com/tand826/wsiprocess/tree/main/examples)
- see [wsiprocess/cli.py](https://github.com/tand826/wsiprocess/blob/main/wsiprocess/cli.py) to check the detailed flow.
### As a command line tool
- see [examples](https://github.com/tand826/wsiprocess/tree/main/examples).
# Available annotation tools
- [ASAP](https://github.com/computationalpathologygroup/ASAP/)
- [SlideRunner version 1.31.0](https://github.com/DeepPathology/SlideRunner)
- [QuPath v0.2.3](https://github.com/qupath/qupath)
- [NDP.View2](https://www.hamamatsu.com/jp/ja/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html)
- and your favorite tools with [custom parser](https://github.com/tand826/wsiprocess/wiki/How-to-use-custom-annotation-parser)
details: [wiki](https://github.com/tand826/wsiprocess/wiki)
# Available WSIs
<details>
<summary>Test ongoing</summary>
<div>
- 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
</div>
</details>
# 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}
}
```
Raw data
{
"_id": null,
"home_page": "https://github.com/tand826/wsiprocess",
"name": "wsiprocess",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": "",
"keywords": "histopathology,cytopathology,medical-imaging,whole-slide-imaging,machine-learning",
"author": "Takumi Ando",
"author_email": "takumi.ando826@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/e9/d0/795cf60e2a486ef7905702fb4ece5cea795d7343017cd1116f7287eade6e/wsiprocess-1.1.1.tar.gz",
"platform": "any",
"description": "<div align=\"center\">\n<img src=\"https://raw.githubusercontent.com/tand826/wsiprocess/main/images/wsiprocess.svg\" style=\"width: 50%\">\n\n\n\n\n\n\n</div>\n\nConvert Helper for Histopathological / Cytopathological Machine Learning Tasks\n\n# Main Flow\n\n<div align=\"center\">\n<img src=\"https://raw.githubusercontent.com/tand826/wsiprocess/main/images/description.gif\" style=\"max-width: 80%\">\n</div>\n\n1. Scan some WSIs.\n2. Make some annotations with WSI annotation tools. ([ASAP](https://github.com/computationalpathologygroup/ASAP/releases) and [SlideRunner v.1.31.0](https://github.com/DeepPathology/SlideRunner), [QuPath v0.2.3](https://github.com/qupath/qupath) are now available. See [wiki](https://github.com/tand826/wsiprocess/wiki) for details.)\n3. Then wsiprocess helps converting WSI + Annotation data into patches and easy-to-use annotation data.\n\n\n[WSIPatcher](https://github.com/tand826/WSIPatcher) will give you GUI.\n\nSee [Wiki](https://github.com/tand826/wsiprocess/wiki) for \n1. [available applications for annotation](https://github.com/tand826/wsiprocess/wiki/annotation_applications), \n2. [speed comparison](https://github.com/tand826/wsiprocess/wiki/speed_comparison) between patched images and loading from raw WSIs,\n3. [how to use the other annotatiion files](https://github.com/tand826/wsiprocess/wiki/How-to-use-custom-annotation-parser).\n\n# Installation\n\n### pip User\n\n1. Install [openslide](https://openslide.org/) or [libvips](https://libvips.github.io/libvips/). See [wiki] for installation hints.\n\n2. Install wsiprocess\n\n ```\n pip install wsiprocess\n ```\n\n### Anaconda User\n\n```\n# Only for python 3.6 or higher\nconda install -c tand826 wsiprocess\n```\n\n# Documentation\n\n- [Documentation](https://tand826.github.io/wsiprocess/)\n\n# Example\n\n### As a python module\n\n- see [examples](https://github.com/tand826/wsiprocess/tree/main/examples)\n- see [wsiprocess/cli.py](https://github.com/tand826/wsiprocess/blob/main/wsiprocess/cli.py) to check the detailed flow.\n\n### As a command line tool\n\n- see [examples](https://github.com/tand826/wsiprocess/tree/main/examples).\n\n# Available annotation tools\n\n- [ASAP](https://github.com/computationalpathologygroup/ASAP/)\n- [SlideRunner version 1.31.0](https://github.com/DeepPathology/SlideRunner)\n- [QuPath v0.2.3](https://github.com/qupath/qupath)\n- [NDP.View2](https://www.hamamatsu.com/jp/ja/product/life-science-and-medical-systems/digital-slide-scanner/U12388-01.html)\n- and your favorite tools with [custom parser](https://github.com/tand826/wsiprocess/wiki/How-to-use-custom-annotation-parser)\n\ndetails: [wiki](https://github.com/tand826/wsiprocess/wiki)\n\n# Available WSIs\n\n<details>\n <summary>Test ongoing</summary>\n <div>\n\n- From below we tested wsi data.\n\n - :smile: => worked well.\n - :umbrella: => did not work well.\n - otherwise => did not check\n\n- Aperio\n\n - CMU-1-JP2K-33005.svs\n - :smile: CMU-1-Small-Region.svs\n - :smile: CMU-1.svs\n - CMU-2.svs\n - CMU-3.svs\n - JP2K-33003-1.svs\n - JP2K-33003-2.svs\n\n- Generic-TIFF\n\n - :umbrella:CMU-1.tiff\n - Can not set magnification.\n\n- Hamamatsu-vms\n\n - :smile:CMU-1.zip\n - CMU-2.zip\n - CMU-3.zip\n - Could not DOWNLOAD from http://openslide.cs.cmu.edu/download/openslide-testdata/Hamamatsu-vms/\n\n- Hamamatsu\n\n - :smile:CMU-1.ndpi\n - CMU-2.ndpi\n - CMU-3.ndpi\n - OS-1.ndpi\n - OS-2.ndpi\n - OS-3.ndpi\n\n- Leica\n\n - :smile:Leica-1.scn\n - Leica-2.scn\n - Leica-3.scn\n - Leica-Fluorescence-1.scn\n\n- Mirax\n\n - CMU-1-Exported.zip\n - CMU-1-Saved-1_16.zip\n - CMU-1-Saved-1_2.zip\n - :umbrella:CMU-1.zip\n - Can not make the foreground mask.\n - CMU-2.zip\n - CMU-3.zip\n - Mirax2-Fluorescence-1.zip\n - Mirax2-Fluorescence-2.zip\n - Mirax2.2-1.zip\n - Mirax2.2-2.zip\n - Mirax2.2-3.zip\n - Mirax2.2-4-BMP.zip\n - Mirax2.2-4-PNG.zip\n\n- Olympus\n\n - OS-1.zip\n - OS-2.zip\n - OS-3.zip\n\n- Trestle\n\n - :umbrella:CMU-1.zip\n - ASAP can not show the image properly, and it's hard to annotate.\n - CMU-2.zip\n - CMU-3.zip\n\n- Ventana\n\n - OS-1.bif\n - OS-2.bif\n\n- :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\n</div>\n</details>\n\n# Test\n\n### Download sample WSI\n\n```\ncurl -O -C - https://data.cytomine.coop/open/openslide/hamamatsu-ndpi/CMU-1.ndpi\n```\n\n### Make random annotation\n\n- Install ASAP ( Linux / Windows ) - https://github.com/computationalpathologygroup/ASAP/releases\n- Open CMU-1.ndpi and make some random annotation. - Save the annotation xml as \"CMU-1.xml\".\n\n### Run test.py\n\n```\ncd tests\npytest tests.py\n```\n\n# Citation\n\n```\n@software{takumi_ando_2022_5938308,\n author = {Takumi Ando},\n title = {tand826/wsiprocess: version 0.9},\n month = feb,\n year = 2022,\n publisher = {Zenodo},\n version = {v0.9},\n doi = {10.5281/zenodo.5938308},\n url = {https://doi.org/10.5281/zenodo.5938308}\n}\n```\n",
"bugtrack_url": null,
"license": "Apache License 2.0",
"summary": "Whole Slide Image (WSI) Processing Library",
"version": "1.1.1",
"project_urls": {
"Homepage": "https://github.com/tand826/wsiprocess"
},
"split_keywords": [
"histopathology",
"cytopathology",
"medical-imaging",
"whole-slide-imaging",
"machine-learning"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "328be3d1b4513b9d16fbf451c41ac06b27c64f486b2e7ef1ab40065dcfb36a9d",
"md5": "8bab6444e397b29da9a55bdf80caaa3b",
"sha256": "99cba6dc3ac52aadff43fd6f940c8bb363781a1027efedb60cc6789123c2d053"
},
"downloads": -1,
"filename": "wsiprocess-1.1.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "8bab6444e397b29da9a55bdf80caaa3b",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 48357,
"upload_time": "2023-09-08T04:58:19",
"upload_time_iso_8601": "2023-09-08T04:58:19.446069Z",
"url": "https://files.pythonhosted.org/packages/32/8b/e3d1b4513b9d16fbf451c41ac06b27c64f486b2e7ef1ab40065dcfb36a9d/wsiprocess-1.1.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "e9d0795cf60e2a486ef7905702fb4ece5cea795d7343017cd1116f7287eade6e",
"md5": "0fa896c7ac33fccd641885bfb057a8f8",
"sha256": "d8e450092e552e623589caeacf196da8f925796b8f7cde9ad2d6fcc6ce2d91c3"
},
"downloads": -1,
"filename": "wsiprocess-1.1.1.tar.gz",
"has_sig": false,
"md5_digest": "0fa896c7ac33fccd641885bfb057a8f8",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 38355,
"upload_time": "2023-09-08T04:58:21",
"upload_time_iso_8601": "2023-09-08T04:58:21.481394Z",
"url": "https://files.pythonhosted.org/packages/e9/d0/795cf60e2a486ef7905702fb4ece5cea795d7343017cd1116f7287eade6e/wsiprocess-1.1.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-09-08 04:58:21",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "tand826",
"github_project": "wsiprocess",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "wsiprocess"
}
JSON
