Skip to main content

A plugin to automatically count lung organoids

Project description


DOI License PyPI Python Version tests codecov napari hub

A napari plugin to automatically count lung organoids from microscopy imaging data. The original implementation can be found in the Organoid-Counting repository, which has been adapted here to work as a napari plugin.

Alt Text

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.


You can install napari-organoid-counter via pip:

pip install napari-organoid-counter

To install latest development version :

pip install git+


Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.


Distributed under the terms of the MIT license, "napari-organoid-counter" is free and open source software


napari-organoid-counter uses the napari-aicsimageio[1] plugin for reading and processing CZI images.

[1] AICSImageIO Contributors (2021). AICSImageIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub.


If you encounter any problems, please file an issue along with a detailed description.


If you use this plugin for your work, please cite it using the following:

  author       = {Christina Bukas},
  title        = {{HelmholtzAI-Consultants-Munich/napari-organoid- 
                   counter: first release of napari plugin for lung
                   organoid counting}},
  month        = apr,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v0.1.0-beta},
  doi          = {10.5281/zenodo.6457904},
  url          = {}

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

napari-organoid-counter-0.1.1.tar.gz (4.0 MB view hashes)

Uploaded source

Built Distribution

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page