Touching labels

Transforms the segmented cells to connected labels (touching)

Select Misc:Touching labels in the action choice list to do this step

In general after segmentation, the labels (the cells) are separated by one (or more) black pixels corresponding to the junctions. This option expands the labels so that they all touch, so that it can be loaded into other plugins like Griottes to generate the graph of the cells neighboring relationship.

Napari-Griottes interoperability

This option allows to use the napari-Griottes plugin to generate spatial graph of cell relationships.

To install this plugin, do:

    pip install napari-griottes

in your virtual environment.

To use the plugin, start it in Plugins>Griottes>Make graph. Choose the layer TouchingCells in the label layer parameter, and run it with the normal Griottes paramters.

When the computation is finished, Griottes displays the results in the pixel scale. As the images in FishFeats are scaled from their metadata, they might not be the same size in the display. To adjust the output of Griottes to the same scale as your data, click the Scale Griottes image in the Touching labels panel of FishFeats.