napari OrganoidCounter


A plugin to automatically count lung organoids


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. The CannyEdgeDetection algorithm is used for detecting the organoids and pre-processing steps ahve been added, specific to this type of data to obtain optimal resutls.

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Intended Audience & Supported Data

This plugin has been developed and tested with 2D CZI microscopy images of lunch organoids. The images had been previously converted from a 3D stack to 2D using an extended focus algorithm. This plugin may be used as a baseline for developers who wish to extend the plugin to work with other types of input images and/or improve the detection algorithm.


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.


The use of the napari-organoid-counter plugin is straightforward. After loading the image or images you wish to process into the napari viewer, you must first pre-process them by clicking the Preprocess button and the image layer will automatically be updated with the result. Next, you can adjust any of the parameters used in the algorithm (downsamppling, minimum organoid diamtere and sigma, i.e. kernel sixe for the Cannny Edge Detection algorithm) by using the corresponding sliders. By clicking the Run Organoid Counter button the detection algorithm will run and a new shapes layer will be added to the viewer, with bounding boxes are placed around the detected organoid. You can add, edit or remove boxes using the layer controls window and update the Number of detected organoids displayed by clicking the Update Number button.

The Take Screenshot button has the same functionality as File -> Save screenshot. The Reset Configs button will reset the image and all parameters to the original settings. To save your results, first select the shapes layer you wish to save form the dropdown menu. To save features of the detected organoids (diameters when approximating organoid as an ellipse and organoid area) in a csv file click Save features. To save the bounding boxes as a json file click Save boxes.

Getting Help

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

How to Cite

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          = {}


  • 0.1.1

Last updated:

  • 09 September 2022

First released:

  • 13 April 2022


  • MIT

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 3
  • Forks: 2
  • Issues + PRs: 1

Python versions supported:

Operating system:


  • napari[all] (>=0.4.15)
  • napari-aicsimageio (>=0.6.1)

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