Access current across a receptor?

[wagdy88]

Hi everyone,

I was wondering if there's a way to access the current across pyramidal cell compartments? We are making changes to GABAb receptor that doesn't show up in the model and we wanted to access individual cells to check:

• The current across different compartments of the cell
• The current across the GABAb receptor of the cell

Appreciate your help!
Thanks
Mohamed

[jasmainak]

In the development version, I believe you can do that using record_isec: https://jonescompneurolab.github.io/hnn-core/dev/generated/hnn_core.simulate_dipole.html#hnn_core.simulate_dipole and then access it using cell_response.isec

[ntolley]

Very timely as this was merged just last month in #502!

To clarify with the development version installed you specify simulate_dipole(..., record_vsec='all', record_isec='all') to turn on recordings of voltages and synaptic currents for all compartments in the model.

You'll have to run pip install -e hnn-core after cloning the github repository to a local folder to test the development version. Hope that helps!

[wagdy88]

Thank you both! I'll try it out and come back for any questions :)

[wagdy88]

Hi @ntolley

I tried the code below with @jasmainak and it didn't work

import hnn_core
from hnn_core import  jones_2009_model, simulate_dipole
net = jones_2009_model(add_drives_from_params= True)
simulate_dipole(net, tstop = 100, record_vsec= 'all')
vsec = net.cell_response.vsec
print(vsec[0][0].keys())

There's no recording from outside the soma

[ntolley]

@wagdy88 can you try looking at a different gid (the second index of vsec)? gid=0 corresponds to an L2_basket cell which only has one compartment in the model (the soma).

You can see the default gid ranges with print(net.gid_ranges)

{'L2_basket': range(0, 35),
 'L2_pyramidal': range(35, 135),
 'L5_basket': range(135, 170),
 'L5_pyramidal': range(170, 270)}

[wagdy88]

I just tried it again, and I can see the different keys for each cell. Thanks

[wagdy88]

@ntolley and @jasmainak
I tried to use isec function to record around gabab receptors in soma, but I keep getting this error message:

import hnn_core
from hnn_core import  jones_2009_model, simulate_dipole
net = jones_2009_model(add_drives_from_params= True)
simulate_dipole(net, tstop = 100, record_vsec= 'all')
isec = net.cell_response.isec[0][36]['soma_gabab']
print(isec[0][36].keys())

KeyError: 'soma_gabab'

The tutorial mentioned that's how to get it:
https://jonescompneurolab.github.io/hnn-core/dev/generated/hnn_core.Cell.html

Thoughts?

[ntolley]

Since this is a nested dictionary you can print the keys if you get a key error. Can you try

print(net.cell_response.isec[0][36].keys())

and paste the output?

[wagdy88]

Sure, here's the output I got:
dict_keys([])

[ntolley]

Oh! I think you forgot to turn on current recordings. You need to enable it with:

dpl = simulate_dipole(..., record_isec='all')

[ntolley]

To clarify your code above only has record_vsec='all' specified so I think you're only recording the voltages right now

[wagdy88]

Perfect! Thanks a lot, I just tried it and it works flawlessly :)

[jasmainak]

@ntolley Could the tutorial be updated to use net.gid_ranges instead of hardcoding a gid ?