napari-griottes 0.3.8

Create graphs

napari-griottes

Use 🍒 Griottes 🍒 in napari!

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

Installation

Install from napari

You can install napari-griottes via pip:

pip install napari-griottes

To install latest development version :

pip install git+https://github.com/BaroudLab/napari-griottes.git

https://user-images.githubusercontent.com/11408456/167825541-29f48bd3-ed71-4553-8079-e70733d5ae48.mp4

Usage

Starting with labels:

1. Open the plugin in Plugins/napari-griottes
2. Make sure the layer with labels is selected
3. Click Run once to get centers
4. Click Run second time to get graph
5. Select the right kind of graph in the drop-down menu
6. Adjust the distance
7. Adjust thickness

https://user-images.githubusercontent.com/11408456/167825581-47c39884-34cf-4b5c-ad84-a4572217559d.mp4

Starting with Segmented cells

1. Open sample data: File / Open Sample / napari-griottes / Zebrafish 2D with labels
2. Select the top layer and covert it to labels (right click - Convert to labels)
3. Run the plugin once to get the centers of labels
4. Run the plugin twice to get the connections
5. Proceed with graph creation

https://user-images.githubusercontent.com/11408456/168237170-b43afd5a-26a4-4cdc-bc42-d3f46f138536.mp4

Saving and recovering the graph

Any graph you see in napari can be saved in .griottes format which is networkx.gpickle inside.

1. Select he layers with connections
2. Click File/Save Selected Layer
3. Choose Griottes in drop-down menu
4. Save

In order to recover a previously saved graph in napari, you can simply drag-n-drop your file into napari, or use file open fialog.

https://user-images.githubusercontent.com/11408456/167845853-e7071199-3f58-4d11-8d7b-c1358a150e6b.mp4

Otherwise, you can open the graph with neworkx.read_gpickle function

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, "napari-griottes" is free and open source software

Issues

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