ImpShape

[mshamada]

It is possible to assign different colours to neuronal sections of the neuromorphic rendering (lower panel) in the ImpShape[] window?

The PlotShape[0].color_list(section, x) command doesn't work in the ImpShape window.

Thanks.

[ted]

PlotShape.color_list works perfectly well. I just tried it on the amputated pyramidal cell that is part of neurondemo. How I did this:

1. Get a model cell to work with.
At the command line execute
neurondemo
Select Pyramidal (click on the radio button).
Click on RunControl's "Init & Run" (ensure that all channels have been initialized to steady state values at resting membrane potential.

2. Bring up the "Impedance Shape" tool
NEURON Main Menu / Tools / Impedance / Shape

3. Build a SectionList whose elements are the sections whose colors that I want to specify.
First, discover some names by
forall print secname()
I arbitrarily decided to work with the 9 sections called dendrite_7[0]..[8].

Code: Select all

oc>objref redsecs
oc>redsecs = new SectionList()
oc>for i=0,8 dendrite_7[i] redsecs.append()

Verify that redsecs contains the sections of interest
oc>forsec redsecs print secname()
which printed their names.

4. Discover the names of the Shapes whose sections I wanted to color.
neurondemo's Pyramidal cell model includes a PointProcessManager that contains a Shape plot.
Discover its name by clicking on the menu box in the left upper corner of that Shape plot, dragging the mouse cursor into the Shape plot's secondary menu, and dragging down to select "Object Name"
In the interpreter window appears
Shape[0]
Do the same for the two shapes that are part of the Impedance Shape tool; their names are Shape[1] and Shape[2].

5. Color the dendrites of interest.
oc>Shape[0].color_list(redsecs, 2)
(2 is the color index for red)
Sure enough, a small cluster (probably a subtree) of sections in Shape[0] turn red.
Do the same for Shape[1] and [2]--and the expected results occur.