place dot on neuron

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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pfortier
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Joined: Thu Apr 20, 2006 8:02 am
Location: University of Ottawa

place dot on neuron

Post by pfortier » Wed Apr 24, 2013 12:02 pm

I can view my anatomically detailed neuron using "Tools/Point Processes/Managers/Point Manager" and then by clicking on a section I see its section name and range.

How could I code the addition of a dot at a specific section and range so that I can visibly see where it is in the dendritic tree? How can I add several dots to see different selected sites in the dendritic tree?

Thanks,
Pierre

ted
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Location: Yale University School of Medicine
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Re: place dot on neuron

Post by ted » Wed Apr 24, 2013 1:56 pm

Easiest is to create a new IClamp at each point of interest.
objref foo
secname foo = new IClamp(x)
where secname and x are the section name and location along that section.

pfortier
Posts: 47
Joined: Thu Apr 20, 2006 8:02 am
Location: University of Ottawa

Re: place dot on neuron

Post by pfortier » Wed Apr 24, 2013 3:15 pm

I played around a bit with the GUI and determined the following which doesn't seem right.

I added an IClamp (let's say #5) at the tip of a dendrite section from the hoc console, as you indicated.
I accessed "Tools/Point Processes/Managers/Point Manager" but could not see the dot. So I selected "SelectPointProcess/IClamp" which seem to have created a new IClamp (let's say #6) without parameters. Menu "Show/Shape" was selected but the shape was not visible so I then selected "Show/Paramaters" and then "Show/Shape" to view the shape. The selected section had a dot for the IClamp[6]. Each section I clicked had a dot for IClamp[6]. Nothing for IClamp[5].

How can I show all the blue dots representing IClamps that were previously set through hoc? Can multiple colors be generated?

Thanks,
Pierre

ted
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Joined: Wed May 18, 2005 4:50 pm
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Re: place dot on neuron

Post by ted » Wed Apr 24, 2013 5:57 pm

I should have mentioned using the Shape class's point_mark() method to reveal the locations of the point processes. Sorry.

If plist is a List that contains all point process instances that you want to see,

Code: Select all

objref sh
sh = new Shape()
for ii=0,plist.count()-1 sh.point_mark(plist.o(ii), 2)
will put a red circle where each point process is attached.

Be sure to read the Programmer's Reference about the List and Shape classes, and the Shape class's point_mark() method.

pfortier
Posts: 47
Joined: Thu Apr 20, 2006 8:02 am
Location: University of Ottawa

Re: place dot on neuron

Post by pfortier » Thu Apr 25, 2013 4:06 pm

That worked perfectly.
Thanks

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