Griottes 🍒 in napari!
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
Starting with labels:¶
- Open the plugin in Plugins/napari-griottes
- Make sure the layer with labels is selected
- Click Run once to get centers
- Click Run second time to get graph
- Select the right kind of graph in the drop-down menu
- Adjust the distance
- Adjust thickness
Starting with Segmented cells¶
- Open sample data: File / Open Sample / napari-griottes / Zebrafish 2D with labels
- Select the top layer and covert it to labels (right click - Convert to labels)
- Run the plugin once to get the centers of labels
- Run the plugin twice to get the connections
- Proceed with graph creation
Saving and recovering the graph¶
Any graph you see in napari can be saved in .griottes format which is networkx.gpickle inside.
- Select he layers with connections
- Click File/Save Selected Layer
- Choose Griottes in drop-down menu
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.
Otherwise, you can open the graph with neworkx.read_gpickle function
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.
Distributed under the terms of the BSD-3 license, "napari-griottes" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
- 10 March 2023
- 09 March 2023
- Information not submitted
- Stars: 3
- Forks: 0
- Issues + PRs: 2