Visualize and edit graph like data in napari

🚀 Feature

graph-layer to visualize and edit graph data in napari.

Motivation

I have graph-like data such as neurons paths or vertex model of epithelium. I would like to visualize it with my favorite image viewer in Python. More generally I suppose that graph-like data such as twitter-network, molecules, … could also use this layer type?

Pitch

• create new graph-layer
• load existing graph from a graph library (such as networkx? or other)
• visualize in the viewer the graph and change the layout of edge/node
• edit the graph by deleting only one node or a sub-branch

Alternatives

It is already possible to visualize graph data in napari using point, label or shape layer but is not optimal to edit.

• vector and label layer example: skan

track-layer also have utils/visualization that can be reused?

Additional context

This issue follows a discussion with @alisterburt and @JoOkuma.

[JoOkuma]

Hi, everyone.

I implemented an initial version of the napari-graph. With this implementation, we’ll speed up the graph initialization and it’ll allow us to manipulate the graph.

Beyond that, I think it might be doable to have a single layer for graphs and tracks, where tracks are a directed graph with a sliding window (thick slices) over the time dimension.

I’m going to start working soon on the graph layer and do the final changes to the initial graph data structures of napari-graph.

Anyone interested in napari’s graph layer is welcome to review napari-graph#1.

[jni]

I want to add an additional option for the graph data structure, which is the trackmate graph, implemented in java here (I think that’s the right implementation link). @DragaDoncila thinks that it wouldn’t be too hard to implement in Python + numba. To me it feels like a lot of effort but not an insurmountable amount, and of all the solutions so far it is the only one that has been battle tested in this exact use case. Does anyone have the bandwidth to work on this directly? We can make a napari/graph repo and start work there.

I also want to reiterate that both @sofroniewn and I think automatic generation of graph layouts is out of scope for napari. The Graph layer input must include node coordinates. Edge paths are optional but should also be supported.