Re: pyramidal spine-neck EPSPs
Posted: Wed Dec 28, 2022 1:37 pm
I should mention that I was unable to save my changes with various attempts at new folder names and ses names.
Some problems here.I drastically increased the neck resistance from 100 ohm to 100 Mohm (1e-9) based on the published range of about 25-800 Mohm)
The link doesn't work for me.I’ve linked the plot here:
Probably because you probably set Ra to 1e-9, which is an extremely low resistivity for any conductive medium. That would make the resistance between the spine head and dendritic shaft too small to have any effect on the spread of electrical signals between the spine head and adjacent dendrite.The spine_head (kopf) and spine_neck had identical EPSP waveforms peaking at - 57 mV. I was not expecting that given that the resistance in the neck is much greater.
Also surprising to me, the soma had a small response of about 2 mV.
The problem is in the way I built init.hoc. I built it in several steps.I should mention that I was unable to save my changes with various attempts at new folder names and ses names.
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load_file("cell.ses")
load_file("basicrig.ses") // RunControl, v vs. t, and v along paths
load_file("syndrive.ses") // PPMs as NetStim and ExpSyn
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/*
load_file("cell.ses")
load_file("basicrig.ses") // RunControl, v vs. t, and v along paths
load_file("syndrive.ses") // PPMs as NetStim and ExpSyn
*/
load_file("necklength.ses")
Yep. The fancy term for this is "low code" software development. The quickest and most powerful way to work with NEURON is to combine use of the GUI and programming in a way that takes advantage of both while minimizing user effort.What a fast solution for saving stuff.
You mean "Ra".I changed Rm to 200, since it is a measure of resistivity not resistance.
Yep, no need to run a long simulation if your primary interest is in the effect of a single synaptic activation.I shortened the RunControl to Tstop to 20 ms.
There's a problem here. Experimentalists like to see a flat baseline before they apply a stimulus--otherwise how can one know that observed activity was actually provoked by the stimulus and not just "spontaneous" or "background" activity? Modelers need to do the same, because there is no guarantee that a particular model is actually starting from a "resting" point.I changed Net Stim to interval 10ms and number of stim to 1, and start time to 0.
It doesn't matter where the NetStim is "located." It's an artificial spiking cell, which in NEURON means it doesn't have any sections at all. It just happens that the PointProcessManager GUI tool provides a convenient GUI interface for managing an artificial spiking cell's parameters. But the PointProcessManager (AKA PPM) was originally developed to manage the parameters and spatial location of objecs whose spatial location really DOES matter. Instead of implementing a new tool specifically intended to manage the properties of artificial spiking cells, it was quicker and simpler to just use the PPM.NetStim location at soma
Nope. The small damped oscillation that you're seeing is caused by the fact that the hh mechanism's resting potential isn't actually -65 mV--it's closer to -64.98 mV, but even if you changed v_init to that value there would still be a damped oscillation, albeit a smaller one.I wondered if I had left an ol' Alpha Synapse lying around
Because the scale of the image on your computer screen is such that the spine is too small to be seen. You'll have to zoom in on the shape plot to see it. But, as discussed above the "position" of an artificial spiking cell such as a NetStim has nothing to do with anything. In particular it has nothing to do with the synaptic mechanisms that it drives with events. That is controlled by the "target" parameter of the hoc or Python statement that creates the NetCon that conveys events from a presynaptic source (in this case, a NetCon) to the synaptic target. See the statementI tried to use Shape to move the Net Stim location to kopf where the spine_head is . . . I found only the soma and dendrites on the stick shape
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https://nrn.readthedocs.io/en/latest/hoc/modelspec/programmatic/network/netcon.html#netcon