Implement support for neuroglancer visualisation

[SridharJagannathan]

It would be useful to implement visualisation of objects of class neurons (and by default extensions of that) in the neuroglancer format. The following are the task check list that need to be completed (this is ongoing and hence will be frequently updated):

• Implement conversion to precomputed format:
  1. Format spec for segments(skeletons) here:
  https://github.com/google/neuroglancer/blob/master/src/neuroglancer/datasource/precomputed/skeletons.md
  2. See python implementation here for conversion from swc: https://github.com/seung-lab/cloud-volume/blob/c3d1f8005397f72d04720f864e9c95d63725b0c0/cloudvolume/skeleton.py#L908
  3. See misc here:
  How to view a SWC file on Neuroglancer? google/neuroglancer#207
  How to display a SWC file from a nodejs server google/neuroglancer#169
• Implement starting a Node.js session to communicate to http port:
  1. See example in python here: https://github.com/google/neuroglancer/tree/master/python
  2. An example r package that does that is here: https://github.com/ColinFay/bubble
• Further add segments, layers to the port for display

The ideal output in the http port would be like below:

[SridharJagannathan]

This task would be taken up once the urgent tasks in https://github.com/natverse/fafbseg/issues/ are completed

[jefferis]

Dear Sri, I think this is a very interesting idea. Ideally one might be able to post to the same neuroglancer instance via python or R (not sure how easy that would be). Integrating local data in neuroglancer views with external data would certainly bring lots of possibilities. @perlman has a fair bit of experience with this.

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On 16 Jul 2020, at 12:52, Sridhar Jagannathan ***@***.***> wrote:  This task would be taken up once the urgent tasks in https://github.com/natverse/fafbseg/issues/ are completed — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[SridharJagannathan]

Some issues wrt to ongoing implementation here: google/neuroglancer#261