napari ARCOS

A napari plugin to detect and visualize collective signaling events

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• Package specific Documentation: https://bgraedel.github.io/arcos-gui
• ARCOS documentation: https://arcos.gitbook.io

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.

Watch full demo on youtube

You can install arcos-gui via pip:

pip install arcos-gui

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.

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