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A napari plugin to detect and visualize collective signaling events


Automated Recognition of Collective Signalling (ARCOS) is an algorithm to identify collective spatial events in time series data, that was written by Maciej Dobrzynski (https://github.com/dmattek). It is available as an R (ARCOS) and python (arcos4py) package. ARCOS can identify and visualize collective protein activation in 2- and 3D cell cultures over time.

This plugin integrates ARCOS into napari. Users can import tracked time-series data in CSV format. The plugin provides GUI elements to process this data with ARCOS. Layers containing the detected collective events are subsequently added to the viewer.

Following analysis, the user can export the output as a CSV file with the detected collective events or as a sequence of images to generate a movie.

export_data

Installation

You can install arcos-gui via pip:

pip install arcos-gui

System Requirements

Since version "0.0.2" this plugin is python native with the arcos4py package available.

Demo Video

arcos_demo

Contributing

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.

License

Distributed under the terms of the BSD-3 license, "arcos-gui" is free and open-source software

Issues

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

Credits

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