Implementing a CHIRP stim and recording the soma

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nemomortus
Posts: 11
Joined: Fri Jan 08, 2016 11:05 pm

Implementing a CHIRP stim and recording the soma

Post by nemomortus »

Hello all,

My ultimate first goal is to implement a CHIRP stimulus into this model (https://senselab.med.yale.edu/modeldb/s ... del=139653) at various points and record the neuron at different points. This information will be then used to find the resonance of this model. I have been working for a few days and I am still at a loss. Is there a straight forward way to implement a CHIRP stimulus to a specific point in the model and record its output?

In particular I've read these two posts: (viewtopic.php?f=8&t=2404&p=9483#p9483) and (viewtopic.php?f=15&t=2946&p=12031&hilit=CHIRP#p12031) for help. I am unsure how to "use" the izap.mod file Ted has created. More specifically I do not understand this part of the code:

Code: Select all

//Begin PointProcessManager
{
load_file("pointman.hoc")
}
{
soma ocbox_ = new PointProcessManager(0)
}
{object_push(ocbox_)}

{
mt.select("Izap") i = mt.selected()
ms[i] = new MechanismStandard("Izap")
ms[i].set("del", 10, 0)
ms[i].set("dur", 1000, 0)
ms[i].set("f0", 0, 0)
ms[i].set("f1", 100, 0)
ms[i].set("amp", 0.0005, 0)
mt.select("Izap") i = mt.selected() maction(i)
hoc_ac_ = 0.5
sec.sec move() d1.flip_to(0)
}

{object_pop() doNotify()}
{
ocbox_ = ocbox_.v1
ocbox_.map("PointProcessManager", 135, 481, 208.32, 316.8)
}
objref ocbox_
//End PointProcessManager
Thanks for your help in advance!
ted
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Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Implementing a CHIRP stim and recording the soma

Post by ted »

I do not understand this part of the code
That's part of a ses file, generated by NEURON, which recreates a PointProcessManager. Like most computer-generated code, it's not meant to be read by humans.

The PointProcessManager is one of the GUI tools that makes it easier to create, instrument, and debug NEURON models, and the most flexible way to use NEURON involves combining the GUI and programming in order to take advantage of their respective strengths. That said, it's not all that difficult to create point process instances with code.
objref foo
soma foo = new AlphaSynapse(0.5)
creates a new instance of the AlphaSynapse class that is attached to the section called soma.
hoc syntax is detailed in chapter 12 of The NEURON Book, and the online Programmer's Reference contains extensive documentation.

You may find something useful for your particular needs in these threads:
viewtopic.php?f=8&t=2832
viewtopic.php?f=13&t=2380
nemomortus
Posts: 11
Joined: Fri Jan 08, 2016 11:05 pm

Re: Implementing a CHIRP stim and recording the soma

Post by nemomortus »

Thanks so much Ted! I've read both links as well as messed with more NUERON coding, testing my understanding of how the language works. In regards to the second link you provided, I had a question about the outline of a program you were discussing.

Corinne tried to write "a program that determines peak PSP amplitude throughout a cell produced by a synapse attached to any point on the cell..." and you gave him a rough outline on what a program would have to do. My question is about the second bullet "2. attach a synapse to a particular location on the cell, and make that location the reference point for distance measurements..."

Why is it important to know the distance measurements after you've inserted a signal stimulus into the cell? My guess is that the distance allows you to know where you are in the neuron relative to where you start. This may be necessary because you might need to somehow update all the sections in the model cell accordingly.
ted
Site Admin
Posts: 5810
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Implementing a CHIRP stim and recording the soma

Post by ted »

nemomortus wrote:Why is it important to know the distance measurements
See the first sentence of that thread.
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