Doubts about ion channel distribution

[HengyeZhu]

Regarding cakcium ion channels Resolved
In what situations should we use channelDensityNernst or channelDensity?

Regarding Ih channel
The IT2_reduced lacks hoc files. I don't know the non-uniform conductance distribution of the ih channel, for example:
distribute($o1.apical,"gIhbar_Ih","(-0.869600 + 2.087000*exp((%g-0.000000)*0.003000))*0.000049") in S1 Model

[HengyeZhu]

The first doubt has been resolved. I found that it is written in the mod file(e.g. IT.mod)

[sanjayankur31]

Here, ascale/bscale from IT2_reduced_cellParams.json seems to apply to this mod file:

https://github.com/OpenSourceBrain/Macaque_auditory_thalamocortical_model_data/blob/feat-neuroml-gsoc/model/mod/h_kole.mod#L65

It's just being used to calculate alpha/beta, which are both exponentials, but alpha also has a shift term---so one will have to define a new component type for that.

The IT2_reduced lacks hoc files. I don't know the non-uniform conductance distribution of the ih channel, for example:
distribute($o1.apical,"gIhbar_Ih","(-0.869600 + 2.087000*exp((%g-0.000000)*0.003000))*0.000049") in S1 Model

What is %g in the equation you've noted above? Is it distance from soma? That's to be implemented like this (also Ih):

https://github.com/sanjayankur31/Human-L2-3-Cortical-Microcircuit/blob/feat/neuroml/NeuroML2/postprocess_cells.py#L276

[HengyeZhu]

Yes! My question is, when inserting the Ih channel into the cell, should its conductance be fixed, or should it vary depending on the distance from the soma, as in the link
https://github.com/sanjayankur31/Human-L2-3-Cortical-Microcircuit/blob/feat/neuroml/NeuroML2/postprocess_cells.py#L276？

Because this aspect cannot be reflected in the MOD files, and the A1 Model only has JSON file, I'm unsure how to handle Ih. Since I noticed in the models you converted, the Ih conductance is related to the distance from the soma, instead of being a fixed value.

[sanjayankur31]

In this case, it does not seem to be dependent on distance from the soma. I can't find anything in the json files either. So, it's a constant conductance. We can check the paper to see if it says otherwise (we can also contact Salavdor for clarification if required)

[HengyeZhu]

Regarding the Ih channel: I observed that in the S1 Model, although the Ih conductance is defined in the hoc file as varying with soma distance, it appears as a constant value in the exported JSON file (though potentially different between compartments/nseg). However, since NetPyNE still imports this JSON data into netParams, should we simply treat it as a constant value?

[sanjayankur31]

Yes, if the JSON treats it as constant, that's what the model will use too. We can double check with Salvador, though. Let's keep this issue open for the moment.