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[HackathonMar21] Test and improve Arbor<->NeuroML interactions #144

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pgleeson opened this issue Mar 19, 2021 · 5 comments
Open

[HackathonMar21] Test and improve Arbor<->NeuroML interactions #144

pgleeson opened this issue Mar 19, 2021 · 5 comments

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@pgleeson
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pgleeson commented Mar 19, 2021

@pgleeson
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@thorstenhater I've installed arbor-gui and managed to load a few nml files, including a newly generated example here: https://github.com/OpenSourceBrain/ArborShowcase/blob/main/NeuroML2/BallAndStick.cell.nml.

The points/morphology is getting imported fine, but the segment groups are not correct, e.g. the soma is going in the dendrite_group too, etc.

Screenshot 2021-03-23 at 18 11 59

Screenshot 2021-03-23 at 18 15 25

@thorstenhater
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Good to hear you got it working, if you have any comments I can add to the Readme to ease the process for the next person,
please tell me.

Thanks for catching that, although I assume that our NML import is at fault here, rather than the display. I will open an issue against arbor.

@thorstenhater
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OK, I got down to the bottom of this with the help of @halfflat: Turning a morphology into line segments sometimes returns partial segments. Currently the renderer does not deal with that and shows the full segment, even if the to be shown fraction is zero.

@pgleeson
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Good progress after chatting with @noraabiakar about cell compartmentalisation.
Aell in NML originally was simulated in Neuron (left) and Arbor (right) and produced the same output:

Screenshot 2021-03-24 at 19 16 20

@thorstenhater
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Hi, the rendering bug has been partially addressed. It remains to be seen whether the more complex case needs to be addressed.

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