Plotting synapses on morphology through RTNeuron

[anirban6908]

Hi @hernando,
Since you directed me here regarding the visualization of networks through RTNeuron, I am creating the issue here. I have been able to visualize the circuits here through RTNeuron, example 300 cell network:

but I could not plot synapses on individual neurons. As example for the same network if I wanted to plot synapses on cell id 0 using:
display_synapses(0, attributes=rtneuron.AttributeMap({'color': [1, 1, 0, 1], 'radius': 3}))
I am getting this error:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
/tmp/.mount_rtneurgetTjE/usr/lib/python3.7/site-packages/rtneuron/__init__.py in <module>
----> 1 display_synapses(1, attributes=rtneuron.AttributeMap({'color': [1, 1, 0, 1], 'radius': 3}))

/tmp/.mount_rtneurgetTjE/usr/lib/python3.7/site-packages/rtneuron/__init__.py in display_synapses(targets, afferent, attributes)
    411         attributes = AttributeMap()
    412     if afferent:
--> 413         synapses = scene.circuit.afferent_synapses(gids)
    414         scene.addAfferentSynapses(synapses, attributes)
    415     else:

RuntimeError: Unimplemented

Adding @kaeldai to this if he has any inputs on how to resolve this.

Thanks again.

[hernando]

Hi @anirban6908, as the error message states, that feature is not implemented for SONATA circuits. It has not been planned yet to add this support to the data access library, but as more people are requesting this, we may consider implementing it sooner.

[anirban6908]

Hi @hernando
I need to prepare a visualization to show synapses along the dendritic morphology for the showcase for the institute (mid November). Just wanted to check if implementing this for sonata format is within scope?
Thanks

[hernando]

Hi @anirban6908 I'm afraid I can't be very helpful in this regard. I changed job last April and I'm not involved in SONATA or RTNeuron any more, so you will have to ask somebody else. Maybe @jdcourcol or @jplanasc can answer your question.

[straaljager]

Hi @anirban6908, I'm leading the visualization team at the Blue Brain. As Juan mentioned, RTNeuron is no longer supported, but it is now replaced by Brayns (https://github.com/BlueBrain/Brayns), a powerful ray tracing framework for large scale circuit visualization. Juan helped implement Sonata support in Brayns. We also have a plugin for visualizing synapses.

Can you try to install Brayns and load your circuit? If you encounter any snags, please let me know. You can also email me directly at [email protected]
Thanks

[hernando]

Hi @straaljager, testing Brayns would be just the first step. The main issue is that Brion doesn't support SONATA synapses at the moment. That part was not implemented.

[straaljager]

Noted. I will add this to the roadmap.

[anirban6908]

Thanks @straaljager @hernando I pulled the docker container and ran the web ui. But when I add a model (.json file) and use mesh type (or any type for that matter) I get unsupported type error. This is the same config file that produced the visualization for RTNeuron with display_circuit at the top of this thread. Could you probably point me to some examples? Thanks again for your help.

[straaljager]

Hi @anirban6908 Can you please open an issue on the Brayns github page instead? We will be able to offer better support there. Thanks!

[anirban6908]

Done. thanks