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

PAthological Visualization Obsession - visualization playground for pado datasets

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

Science Score: 13.0%

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    Low similarity (15.3%) to scientific vocabulary

Keywords

digital-pathology python visualization

Keywords from Contributors

interactive archival projection generic sequences genomics packaging versions tracing charts
Last synced: 6 months ago · JSON representation

Repository

PAthological Visualization Obsession - visualization playground for pado datasets

Basic Info
  • Host: GitHub
  • Owner: Bayer-Group
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 1.2 MB
Statistics
  • Stars: 5
  • Watchers: 3
  • Forks: 2
  • Open Issues: 20
  • Releases: 0
Topics
digital-pathology python visualization
Created over 4 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog Contributing License Codeowners

README.md

PAVO: PAthological Visualization Obsession

Welcome to pavo :wave:, a visualization tool for pado datasets.

pavo's goal is to provide a testbed for easy prototyping of data visualizations of whole slide images and metadata of digital pathology datasets.

We strive to make your lives as easy as possible: If setting up pavo is hard or unintuitive, if its interface is slow or if its documentation is confusing, it's a bug in pavo. Always feel free to report any issues or feature requests in the issue tracker!

Development happens on github :octocat:

Installation

To install pavo clone the repo and run pip install . Note that you need a "nodejs==16.*" installation to be able to build from source.

Usage

pavo is used to visualize pado datasets. If you have a pado dataset just run:

shell pavo production run /path/to/your/dataset

and access the web ui under the printed address.

Development Environment Setup

  1. Install git and conda and conda-devenv
  2. Clone pavo git clone https://github.com/bayer-group/pavo.git
  3. Change directory cd pavo
  4. Run conda devenv --env PAVO_DEVEL=TRUE -f environment.devenv.yml --print > environment.yml
  5. Run conda env create -f environment.yml
  6. Activate the environment conda activate pavo
  7. Setup the javascript dependencies npm install . (optional, handled in setup.py)

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

  • Run tests via pytest
  • Run the static type analysis via mypy pavo
  • Launch a development instance via pavo development run

Contributing Guidelines

  • Check the contribution 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.

Acknowledgements

Build with love by the Machine Learning Research group at Bayer.

pavo: copyright 2020 Bayer AG

Owner

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

Science for a better life

GitHub Events

Total
Last Year

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 146
  • Total Committers: 5
  • Avg Commits per committer: 29.2
  • Development Distribution Score (DDS): 0.096
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 132
dependabot[bot] 4****] 10
Jake Pencharz j****z@b****m 2
Santi Villalba s****l@g****m 1
marcomulinex m****x@g****m 1
Committer Domains (Top 20 + Academic)
bayer.com: 1 poehlmann.io: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 49
  • Total pull requests: 38
  • Average time to close issues: 4 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 0.73
  • Average comments per pull request: 0.32
  • Merged pull requests: 29
  • Bot issues: 0
  • Bot pull requests: 18
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-- (32)
  • Jake-Jay (12)
  • marcomulinex (5)
Pull Request Authors
  • dependabot[bot] (18)
  • Jake-Jay (13)
  • ap-- (6)
Top Labels
Issue Labels
Priority: Low (9) Priority: Medium (8) Priority: High (8) enhancement (5) good first issue (4) bug (4) Priority: Critical (3) waiting for upstream (2) documentation (1)
Pull Request Labels
dependencies (18)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 15 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
pypi.org: pavo

PAthological Visualisation Obsession

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 15 Last month
Rankings
Dependent packages count: 6.6%
Average: 18.6%
Dependent repos count: 30.6%
Maintainers (1)
poehlmann
Last synced: 7 months ago