SWC skeleton viewers on Colab

[JohnTigue]

Goal is to view SWCs on Colab.

[Viewing on desktop apps is nice but this project has an explicit goal of realizing all UI in Jupyter. But the ShuTu desktop app runs on windows, macOS, Linux – if one wishes to go desktop app old-school.]

Various potential types of tools, simplest first:

• Static is easiest
  • [x] plot SWC a la AllenSDK examples (2 subplot mugshot) (#51)
  • [x] swc_renderer.ipynb
  • [x] SWC overlaid on inverted MinIP image, a la Allen Cell Types
• Interactive 3D on Colab
  • [ ] 3D interactive
  • [ ] #132 Plotly 3D camera
  • [ ] Neuroglancer as a Jupyter widget
    • Demo neuroglancer reading a .swc file
    • Each SWC a layer
    • Nyroglancer is where to pick up the baton
• [ ] ShuTu desktop

Note: The gold standard SWCs distinguish between axon and dendrites. What of somas?

Styling

See #62.

Initially, following the style of the paper handout from the first Challenge meeting, the viewer should do render

• Dendrites: blue
• Axon: red

Various existing skeleton viewer codebases:

• Cloud-volume's wiki: Skeletons

[JohnTigue]

Lowest hanging fruit (with minimum requirements of Colab supported features) would be static image generation.

[JohnTigue]

One really crude solution is to download the SWC and then upload it to, say, https://neuroinformatics.nl/HBP/morphology-viewer/

[JohnTigue]

AllenSDK Cell Types example code: The Alleneurs plotting SWCs as 2 part mugshot (front and side) via matplotlib

Cell Morphology Reconstructions The Cell Types Database also contains 3D reconstructions of neuronal morphologies. The data are presented in the SWC format. We'll download a particular cell's reconstrution here. The AllenSDK contains a module that makes it easier to work with the SWC files. We can use this data to draw lines between each node and all its children to get a drawing of the cell. We'll do it looking at it from the front and from the side.

[JohnTigue]

If interactivity happens, to sync both mugshot subviews: Linking two similar widgets.