gui interface

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apoorva bedekar
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Joined: Wed Jan 26, 2011 11:57 pm

gui interface

Post by apoorva bedekar » Thu Jan 27, 2011 12:55 am

[quote] i created two neuron model using gui, the 2 neurons are identical , with one dendrite , one soma and one axon . We placed 2 synapses one on axon and other on dendrite in both cells , hence we knew the exact location in target cell i.e either synapse on axon or dendrite, But how do we know which part of the source cell (axon,soma,.dendrite) is getting attached ? [quote]

ted
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Re: gui interface

Post by ted » Thu Jan 27, 2011 8:52 pm

Referring to the documentation of the NetCon class
http://www.neuron.yale.edu/neuron/stati ... etcon.html
the first usage example is
section netcon = new NetCon(&v(x), target)
which means that netcon will monitor v at the x location of section for a positive-going threshold crossing. If v crosses threshold, an event will be generated that will be delivered to target. The delay between detection of threshold crossing and the arrival of the event at target, and the weight associated with that event, have default values of 1 ms and 0, respecitively, and can be changed by hoc statements.

apoorva bedekar
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Joined: Wed Jan 26, 2011 11:57 pm

Re: gui interface

Post by apoorva bedekar » Sat Feb 19, 2011 8:40 am

My sincere apologies for the late feedback .Thank you for the suggestion.So far we have successfully connected two bidirectionally coupled neurons.

ted
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Re: gui interface

Post by ted » Sat Feb 19, 2011 9:58 am

On re-reading your original question, I see that I may have misinterpreted what you were asking about.

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how do we know which part of the source cell (axon,soma,.dendrite) is getting attached ?
If you used the Network Builder to set up the connections between the cells, then you would have used the NetReadyCellGUI tool (brought up by NEURON Main Menu / Build / Network Cell / From Cell Builder) to specify the properties of the model cells used by your net. With the NetReadyCellGUI tool, the locations of synapses are known because you actually have to use the GUI to place them on your model cell. However, the spike source location (the location that is watched by any NetCon that uses this cell for a source) is not so obvious because the NetReadyCellGUI tool automatically sets that to be the 1 end of the root section (the section that is the parent of all other sections in the model cell). So here's how to discover the spike source location:
1. Bring up the NetReadyCellGUI tool's CellBuilder (click on Info / CellBuilder).
2. Click on that CellBuilder's Management button.
3. In the right hand panel of that CellBuilder, click on the Cell Type radio button.
4. Below the Cell Type radio button, look for a radio button labeled "Select Output" (you may have to drag down the bottom edge of the CellBuilder to expose this button).
Just beneath the Select Output button you'll probably see soma.v(1). If you want to change this to the 1 end of some other section, click on the Select Output button, then click on any section in the model, and the label below the Select Output button will change to reflect your choice.

Also below the Select Output button you'll see a "threshold (mV)" button with a numeric field that can be used to specify the threshold that NetCons will use to determine whether a spike has occurred. The default value of 10 mV is OK for most applications.

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