Ability to set additional cell parameters such synapse, biophysics, and geometry.

This is done by: <div class="highlight highlight-source-python notranslate positio

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GUI cell parameters about hnn-core HOT 3 CLOSED

gtdang commented on September 26, 2024

GUI cell parameters

from hnn-core.

Comments (3)

jasmainak commented on September 26, 2024

This is done by:

net_jones = jones_2009_model()

jones_rise = net_jones.cell_types['L5_pyramidal'].synapses['gabab']['tau1']
law_rise = net.cell_types['L5_pyramidal'].synapses['gabab']['tau1']
print(f'GABAb Rise (ms): {jones_rise} -> {law_rise}')

jones_fall = net_jones.cell_types['L5_pyramidal'].synapses['gabab']['tau2']
law_fall = net.cell_types['L5_pyramidal'].synapses['gabab']['tau2']
print(f'GABAb Fall (ms): {jones_fall} -> {law_fall}\n')

as documented in this example:

https://jonescompneurolab.github.io/hnn-core/stable/auto_examples/workflows/plot_simulate_beta.html#sphx-glr-auto-examples-workflows-plot-simulate-beta-py

from hnn-core.

kmilo9999 commented on September 26, 2024

@ntolley @gtdang
I'm having difficulties finding the Dendrite capacitive density and Dendrite resistivity parameters inside the cell types L2 and L5 pyramidal structures.
I do see:

Apical Dendrite Trunk length
Apical Dendrite 1 length
Apical Dendrite 1 diameter
Apical Dendrite Tuft length
Apical Dendrite Tuft diameter
Oblique Apical Dendrite length
Oblique Apical Dendrite diameter
Basal Dendrite 1 length
Basal Dendrite 1 diameter
Basal Dendrite 2 length
Basal Dendrite 2 diameter
Basal Dendrite 3 length
Basal Dendrite 3 diameter

But not the ones I mentioned.
Can you point me to them in the hnn_core/cells_default.py code?

from hnn-core.

ntolley commented on September 26, 2024

Hey @kmilo9999 you can access them from the code like this:

from hnn_core import jones_2009_model
net = jones_2009_model()
section = net.cell_types['L5_pyramidal'].sections['soma']
print(section.Ra) # resistance
print(section.cm) # capacitance