Question about CellBuilder tutorial

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nianwosuh
Posts: 39
Joined: Tue Jul 27, 2010 11:00 pm

Question about CellBuilder tutorial

Post by nianwosuh »

I have another problem with the tutorial under the Neuron page in cell builder tutorial:
using cell builder; Managing a model cell with complex anatomy.

I have repeated this several time and have the same problem. When I bring up the point manger to insert IClamp at the soma,
The show parameter/shape window simply reads "IClamp[0]" at (0.5). It does not indicate it is at the soma. The blue point seems to be where the soma should be. When I plot the graph, all I have is a short linear segement that fllatens below -45mV.

When I move the blue point around it indicates the names of other sectiion of the tree where it is located, but never shows the soma.

When I pull up the "variables to plot from the graph menu" "plot what?" I see neither soma nor axon.

In the Cell builder window under geometry, when I click on each section, soma, axon, apical in the special strategy window, each of this section on the tree is hilighted each time, only when I click on itsname under the special strategy window. indicated that it is on the tree.

I don't understand why neither soma, nor axon, whill not appear under the variables to plot and why my graph is quite different from what is in the tutorial.

Thank you
ted
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Re: Question about CellBuilder tutorial

Post by ted »

nianwosuh wrote:When I bring up the point manger to insert IClamp at the soma,
The show parameter/shape window simply reads "IClamp[0]" at (0.5). It does not indicate it is at the soma. The blue point seems to be where the soma should be.
The default section for this particular model is the soma. The PointProcessManager does not necessarily show the name of the section when the point process is located in the default section. If you are not familiar with the concepts "currently accessed section" and "default section" then please read
http://www.neuron.yale.edu/neuron/stati ... sedSection
and also read this article
The NEURON Simulation Environment
http://www.neuron.yale.edu/neuron/stati ... /nctoc.htm
especially
4.2.2 Second step: assign anatomical and biophysical properties
When I plot the graph, all I have is a short linear segement that fllatens below -45mV.
The graph of what? Membrane potential? Membrane potential where? Do you mean a plot of membrane potential vs. time, or is it a "space plot" (plot of membrane potential vs. anatomical distance)?
When I pull up the "variables to plot from the graph menu" "plot what?" I see neither soma nor axon.
Are you absolutely sure? Are there no section names at all in the left column of the "Plot what?" tool?
nianwosuh
Posts: 39
Joined: Tue Jul 27, 2010 11:00 pm

Re: Question about CellBuilder tutorial

Post by nianwosuh »

Thank you for the references, I'll read them. and also for letting me know the PointProcessManger doesn't have to indicate the name of the section on which the point process is located.

The graphs I mean are: graphs of membrane potential Vs time and the space plot.

In the first graph I plotted, supposed ly the membrame potential of the default section(soma); the plot of membrane potential Vs time starts off as a ramp (linear graph (positive direction)) and flattens out below -45mv. While the space plot simply shows a horizontal line.

I plotted membrane potential Vs time for other sections, the graph is as I described above

In the graph menu(plot what?) Every other section name (dendrites) appears expect soma and axon and apicals (subsection I created ). I scrolled down to the end of the list but did not see soma, axon, nor apical sections.

Thank you
ted
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Re: Question about CellBuilder tutorial

Post by ted »

Are you quite sure that you followed the steps described in the CellBuilder tutorial exactly, and left nothing out?

When you start NEURON (just double click on nrngui in the NEURON program group), what is the exact message that NEURON prints to the terminal? (please copy and paste it into your reply)
nianwosuh
Posts: 39
Joined: Tue Jul 27, 2010 11:00 pm

Re: Question about CellBuilder tutorial

Post by nianwosuh »

This is the message that is printed out when I start nrngui : NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

I'm very sure I followed the instructions to the "letter". I repeated it several times and got the same result so I decieded to ask for help.

Irepeated the same tutorial following all the steps expect that I used a different morphological neuron I imported into the cell builder from http://www.compneuro.org/CDROM/nmorph/cellArchive.html . The plot of membrane potential Vs time and the space plot are similar to what is shown in the tutorial. My guess is that there may be some problem with the cell in the NEURON demo.

I also observed that when I used the passive conductance (g_pas) value of 3.333S/cm2, the plot on the two mentioned graphs are flat, but using g_pass of 0.00033 gives plots on both graphs. So I guess the g_pas should be 0.00033S/cm2 (1/R, 1/30,000)and not what is specified

Thank you
ted
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Re: Question about CellBuilder tutorial

Post by ted »

nianwosuh wrote:Irepeated the same tutorial following all the steps expect that I used a different morphological neuron
So you were doing the second CellBuilder tutorial--the one called "Managing a model cell with complex anatomy"?

To discover what went wrong, I will have to be able to reproduce the symptom. Can you save a session file
NEURON Main Menu / File / save session
then zip up the session file and email it to me
ted dot carnevale at yale dot edu
?

This will allow me to see the phenomena you observed--
When I plot the graph, all I have is a short linear segement that fllatens below -45mV.

When I pull up the "variables to plot from the graph menu" "plot what?" I see neither soma nor axon.

the plot of membrane potential Vs time starts off as a ramp (linear graph (positive direction)) and flattens out below -45mv. While the space plot simply shows a horizontal line.
I imported into the cell builder from http://www.compneuro.org/CDROM/nmorph/cellArchive.html
I wouldn't use those morhpologies for any computational modeling--they are riddled with z axis artifacts that make branch lengths completely unreliable. Read
Scorcioni, R., Lazarewicz, M.T., and Ascoli, G.A.
Quantitative morphometry of hippocampal pyramidal cells:
differences between anatomical classes and reconstructing laboratories.
J. Comp. Neurol. 473:177-193, 2004.
I also observed that when I used the passive conductance (g_pas) value of 3.333S/cm2, the plot on the two mentioned graphs are flat, but using g_pass of 0.00033 gives plots on both graphs. So I guess the g_pas should be 0.00033S/cm2 (1/R, 1/30,000)and not what is specified
That "3.333 S / cm2" is one ugly typographical error, isn't it. Thank's for catching that. The number should be "3.333e-5 S / cm2". I have updated the tutorial and the zip file that contains all of the CellBuilder tutorials.
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