Notes on interacting with skeletons in napari

[jni]

Some functionality ideas requested by @kevinyamauchi:

• pick a pixel -> orient skeleton
• pick a pixel -> prune skeleton
• pruning: do we mark as pruned or delete and return new Skeleton?

Some potentially useful functions:

• mapping from coordinates to path id. This would allow e.g. picking from a shapes layer.
• need to build a cKDTree of only valid coordinates from Skeleton.coordinates. Note that skeleton.coordinates contains some dummy coordinates because some pixel ids become invalid during skeleton construction.

With upcoming PR from @kevinyamauchi, we should be able to do:

skeleton = Skeleton(...)
summary = summarize(skeleton)
summary['index'] = np.arange(summary.shape[0]) + 1  # not sure about this one

label_layer = napari.view_labels(np.asarray(skeleton), properties=summary)
label_layer.color = 'main'

Other ideas:

• displaying skeleton branches as Shapes layer. BUT, Shapes is still slow for many shapes. Need to improve performance there before this is practical.