napari organoid counter

A napari plugin to automatically count lung organoids from microscopy imaging data. Note: this plugin only supports single-channel grayscale images.

Hold it for the demo!

This demo showcases the features of Version 0.2.13.

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

Installation

This plugin has been tested with python 3.11 - you may consider using conda or mamba to create your dedicated environment before running the napari-organoid-counter.

1. You can install napari-organoid-counter via pip:

   pip install napari-organoid-counter

   To install for a developer:

   git clone https://github.com/HelmholtzAI-Consultants-Munich/napari-organoid-counter pip install -e .

For installing on a Windows machine directly from within napari, follow the instuctions here.

Latest version features

Checkout Features of the latest version here.

How to use?

1. To launch the plugin directly from your terminal:

napari -w napari-organoid-counter

2. For convenience you can add a shell alias by adding this to your ~/.zshrc (macOS) or ~/.bashrc (Linux):

alias organoid='napari -w napari-organoid-counter'

Then reload your shell config:

source ~/.zshrc   # macOS
source ~/.bashrc  # Linux

You can now launch the plugin simply by running:

organoid

3. Alternatively, you can also start napari manually and select the plugin from the drop down menu.

For more information on this plugin, its intended audience, and a Quickstart guide go to our Quickstart guide.

Contributing

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

License

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

Dependencies

napari-organoid-counter uses the BioIO^[1] for reading and processing images.

[1] Eva Maxfield Brown, Dan Toloudis, Jamie Sherman, Madison Swain-Bowden, Talley Lambert, Sean Meharry, Brian Whitney, AICSImageIO Contributors (2023). BioIO: Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Pure Python [Computer software]. GitHub. https://github.com/bioio-devs/bioio

Issues

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

Citing

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

Christina Bukas, Francesco Campi, Abdulkader Ghandoura, & Piraud, M. (2026). HelmholtzAI-Consultants-Munich/napari-organoid-counter: v0.2.6 (v0.2.6). Zenodo. https://doi.org/10.5281/zenodo.19824587

bibtex:

@software{christina_bukas_2026_19824587,
  author       = {Christina Bukas and
                  Francesco Campi and
                  Abdulkader Ghandoura and
                  Piraud, Marie},
  title        = {HelmholtzAI-Consultants-Munich/napari-organoid-
                   counter: v0.2.6
                  },
  month        = apr,
  year         = 2026,
  publisher    = {Zenodo},
  version      = {v0.2.6},
  doi          = {10.5281/zenodo.19824587},
  url          = {https://doi.org/10.5281/zenodo.19824587},
}