OpenSourceBrain / MiglioreEtAl14_OlfactoryBulb3D

3D model of the olfactory bulb (Migliore et al. 2014)
http://www.opensourcebrain.org/projects/miglioreetal14_olfactorybulb3d
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Export or create NML2 cell file(s) for granule cell #15

Closed pgleeson closed 6 years ago

pgleeson commented 8 years ago

While Mitral cells are all different, it seems that the GCs are all the same (but probably positioned at different locations, see #12)

If they are all the same, a single GC.cell.nml should suffice, otherwise the export script should be updated to handle these too.

Re the question here: https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/issues/6#issuecomment-168417334, the numberInternalDivisions is equal to nseg, which can be set to any integer value >=1 independent of the number of points in the NEURON segment (which translate to segments in the segmentgroup in the exported NML). Usually for, e.g. a neurolucida reconstruction there will be many 3d points (~20) in a section, but only ~3 points required to evaluate v along it, so nseg =3.

In the generated Mitral cells the number of 3D internal segments in the generated sections == nseg, probably just for convenience/a good approximation. This doesn't necessarily hold for the GC... Note this in the definition of GC: https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/blob/master/NEURON/granule.hoc#L61

JustasB commented 8 years ago

The script for exporting GCs is now under Python/Export/export_granule.py

JustasB commented 6 years ago

This has been implemented here: https://github.com/OpenSourceBrain/MiglioreEtAl14_OlfactoryBulb3D/pull/25