Dear all,
I am now working with the published BBP cells and especially with pyramidal cells for single cell simulations using NEURON.
However taking a look at the biophysic hoc script, I noticed that all channel mechanisms were not present in all compartments. Particularly, in basal dendrite only Ih mechanism is attached and Im, NaTs2_t, SKv3_1 and Ih in apical dendrites. Is there any reason for that ? Indeed, in the 2015 article, it is claimed in supplementary material (p. 12 in the Conductance distribution sub-section) that :
For pyramidal cell models, all ion channel mechanisms were uniformly distributed in the soma, AIS, basal and apical dendrites, except Ih, which was exponentially distributed in apical dendrites
It is also surprising to not have any Ca mechanism in dendrites.
Finally, I have an additionnal question because I’m not sure to understand properly this part, the biophysic of each numerical cell model was optimized using the two compartment AIS or the full axonal arbor ?
Many thanks for your consideration and time.
Gaugain Gabriel
PhD candidate - CNRS IETR UMR 6164