https://github.com/bayer-group/pado

PAthological Data Obsession - cloud native digital pathology datasets

Science Score: 13.0%

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Low similarity (15.1%) to scientific vocabulary

Keywords

digital-pathology python

Last synced: 6 months ago · JSON representation

Repository

PAthological Data Obsession - cloud native digital pathology datasets

Basic Info

Host: GitHub
Owner: Bayer-Group
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage:
Size: 888 KB

Statistics

Stars: 18
Watchers: 4
Forks: 2
Open Issues: 19
Releases: 0

Topics

digital-pathology python

Created over 3 years ago · Last pushed about 3 years ago

Metadata Files

Readme Changelog Contributing License Codeowners

README.md

PADO: PAthological Data Obsession

Welcome to pado :wave:, a dataset library for accessing histopathological datasets in a standardized way from Python.

pado's goal is to provide a unified way to access data from diverse datasets. Its scope is very small and the design tries to keep everything simple.

As always: If pado is not pythonic, unintuitive, slow or if its documentation is confusing, it's a bug in pado. Feel free to report any issues or feature requests in the issue tracker!

Development happens on github :octocat:

Quickstart

To quickly get a pado dataset, for testing and familiarizing with the interface you can create a fake dataset, that's also used in the internal tests.

```pycon

from pado.mock import mockdataset ds = mockdataset(None) ds PadoDataset('memory://pado-f5869e41-5246-4378-9057-96fda1c40edf', mode='r+') ```

This creates a test dataset in memory with 3 images and some fake metadata

```pycon

len(ds) 3 ds.index (ImageId('mockimage0.svs', site='mock'), ImageId('mockimage1.svs', site='mock'), ImageId('mockimage2.svs', site='mock')) ds[0].image Image(...) ds[0].metadata A B C D ImageId('mockimage0.svs', site='mock') a 2 c 4 ```

Documentation

The documentation is currently provided in this repository and has to be build via sphinx. It'll be available online soon.

To build it, in the repository root, run bash python -m pip install -e ".[docs]" cd docs make html Access the documentation then at docs/build/html/index.html

Development Installation

pado can be installed directly via pip: bash pip install "git+https://github.com/Bayer-Group/pado@main#egg=pado[cli,create]"

or for development you can clone and install via: bash git clone https://github.com/Bayer-Group/pado.git cd pathdrive-pado pip install -e ".[cli,create,dev]"

if you prefer conda environments: bash git clone https://github.com/Bayer-Group/pado.git cd pathdrive-pado conda install conda-devenv conda devenv conda activate pado

Note that in this environment pado is already installed in development mode, so go ahead and hack.

Contributing Guidelines

Please use numpy docstrings.
When contributing code, please try to use Pull Requests.
tests go hand in hand with modules on tests packages at the same level. We use pytest.
Please install pre-commit and install the hooks by running pre-commit install in the project root folder.

You can setup your IDE to help you adhering to these guidelines.
(Santi is happy to help you setting up pycharm in 5 minutes)

Acknowledgements

Build with love by Santi Villalba and Andreas Poehlmann from the Machine Learning Research group at Bayer.

Owner

Name: Bayer Open Source
Login: Bayer-Group
Kind: organization

Website: https://bayer.com/
Repositories: 98
Profile: https://github.com/Bayer-Group

Science for a better life

GitHub Events

Total

Watch event: 1

Last Year

Watch event: 1

Committers

Last synced: about 1 year ago

All Time

Total Commits: 874
Total Committers: 5
Avg Commits per committer: 174.8
Development Distribution Score (DDS): 0.109

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Andreas Poehlmann	a**s@p**o	779
alessiamarcolini	a**i@b**m	36
marcomulinex	m**x@g**m	28
Jake Pencharz	j**z@b**m	18
Santi Villalba	s**l@g**m	13

Committer Domains (Top 20 + Academic)

bayer.com: 2 poehlmann.io: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 23
Total pull requests: 5
Average time to close issues: 1 day
Average time to close pull requests: about 1 hour
Total issue authors: 3
Total pull request authors: 1
Average comments per issue: 0.61
Average comments per pull request: 0.0
Merged pull requests: 5
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ap-- (18)
wolny (3)
marcomulinex (2)

Pull Request Authors

ap-- (5)

Top Labels

Issue Labels

⭐ enhancement (11) 🚧 refactor (2) 🦁 good first issue (2) 🐛 bug (1) 🦸 help wanted (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- pypi 51 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 6
Total maintainers: 1

pypi.org: pado

cloud-native dataset library for accessing histopathological datasets

Homepage: https://github.com/Bayer-Group/pado
Documentation: https://pado.readthedocs.io/
License: BSD
Latest release: 0.12.0
published about 3 years ago

Versions: 4
Dependent Packages: 1
Dependent Repositories: 0
Downloads: 51 Last month

Rankings

Dependent packages count: 6.6%

Downloads: 13.2%

Average: 18.4%

Stargazers count: 18.6%

Forks count: 23.2%

Dependent repos count: 30.6%

Maintainers (1)

poehlmann

Last synced: 6 months ago

conda-forge.org: pado

Homepage: https://github.com/bayer-group/pado
License: BSD-3-Clause
Latest release: 0.11.0
published over 3 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Average: 49.0%

Dependent packages count: 51.2%

Stargazers count: 53.5%

Forks count: 57.4%

Last synced: 7 months ago

Dependencies

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