napari-cellfinder

This tool is no longer under development, please use brainglobe-napari-io instead

Visualise cellfinder results with napari

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Installation

You can install napari-cellfinder via pip:

pip install napari-cellfinder

Usage

• Open napari (however you normally do it, but typically just type napari into your terminal)
• Load your raw data (drag and drop the data directories into napari, one at a time)
• Drag and drop your cellfinder output directory into napari.

The plugin will then load your detected cells (in yellow) and the rejected cell candidates (in blue). If you carried out registration, then these results will be overlaid (similarly to the napari-brainreg plugin, but transformed to the coordinate space of your raw data).

Loading raw data

Loading cellfinder results

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 MIT license, "napari-cellfinder" is free and open source software

Issues

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