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OpenSourceBrain / MiglioreEtAl14_OlfactoryBulb3D

3D model of the olfactory bulb (Migliore et al. 2014)
http://www.opensourcebrain.org/projects/miglioreetal14_olfactorybulb3d
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cell with multiple specificCapacitances OR directly connect segments of different cells together #17

Closed JustasB closed 8 years ago

JustasB commented 8 years ago

In this model, there is one hoc definition for granule cells and one for GranuleSpine. Instances of each are later connected together directly at a specific location along a segment of the GC. The GC has cm of 4 and Spine has cm of 1.

In NeuroML, I cannot find a way to have a cell have more than one specCap value, nor can I find a way to connect segments of different cells directly either. @pgleeson What's the best route here?

Both definitions are in this file: https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/blob/master/NEURON/granule.hoc

The direct connection is made here: https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/blob/c15d316aa73be725a80ed67c7fe20f63d80294d0/NEURON/mgrs.py#L110

pgleeson commented 8 years ago

There's no way to connect electrically segments in different cells (well there is now, with gap junctions/analogue synapses but that's probably not the best approach).

It would be best to get these extra segs into the cells (e.g. with python), make a segmentGroup for them and then you should be able to set specCap on different regison with:

<specificCapacitance value="1.0 uF_per_cm2" segmentGroup="soma"/>
<specificCapacitance value="2.0 uF_per_cm2" segmentGroup="dend"/>
<specificCapacitance value="3.0 uF_per_cm2" segmentGroup="spines"/>
JustasB commented 8 years ago

Ok, I'll give the specCap per segmentGroup a try.