[MRG] Record calcium concentration

[katduecker]

Recording calcium concentration in all sections of the L5 pyramidal neurons

[jasmainak]

@ntolley monthly issue metrics fails !

[ntolley]

@ntolley monthly issue metrics fails !

Fixed!

[ntolley]

Here's the plot with the spikes/Ca overlaid. At first I thought something was wrong but realized I hadn't set the times correctly.

Very nice work @katduecker! This definitely looks good

from hnn_core import simulate_dipole, jones_2009_model
import numpy as np
import matplotlib.pyplot as plt

net = jones_2009_model()
net.add_evoked_drive('evprox', mu=20.0, sigma=2.0, numspikes=1,
                     location='proximal', weights_ampa={'L5_pyramidal': 0.1})

plt.figure()
fig, ax = plt.subplots(2, 1, figsize=(5, 4), sharex=True, tight_layout=True)
plot_data = np.array([net.cell_response.ca[0][gid]['soma'] for gid in net.gid_ranges['L5_pyramidal']]).T
ax[0].plot(dpl[0].times, plot_data)
ax[0].set_title('Somatic Ca$^{2+}$')
ax[1].set_title('Spike Raster')
net.cell_response.plot_spikes_raster(ax=ax[1])

[katduecker]

Thanks both! I haven't managed to look at the rest of this yet, as I have been busy with the NEURON workshop. One thing I learned today at the workshop is that calcium concentration should be at the order a few hundred nM, but our calcium concentration is at the order of 0.1 mM (mod file of ca shows that cai is in mM). This is 1000 times too high... Am I missing something obvious with a conversion of the units?

[jasmainak]

We use reduced neurons acc to Bush and Sejnowski 93, so do we actually expect physical units?

Sent from my iPhone

On Tue 18 Jun 2024 at 21:24, Katharina Duecker @.***> wrote:

Thanks both! I haven't managed to look at the rest of this yet, as I have been busy with the NEURON workshop. One thing I learned today at the workshop is that calcium concentration should be at the order a few hundred nM, but our calcium concentration is at the order of 0.1 mM (mod file of ca shows that cai is in mM). This is 1000 times too high... Am I missing something obvious with a conversion of the units?

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[katduecker]

I asked Stephanie about this and she said that it may be possible that the conductance had to be scaled up to get the desired dynamics. To confirm this, I will read out the concentration for sodium and potassium as well, to see if they are in a similar regime. I remember @ntolley saying that an option to read out concentrations for all ions may not be a useful functionality in general, but if it allows sanity checks of the scale of the conductance, couldn't it be helpful for users to have access to this? I'd be happy to write a tutorial on this if we decide to integrate.