Getting the name of a section from the Shape plot?

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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Sherif
Posts: 27
Joined: Thu Oct 13, 2005 4:32 pm

Getting the name of a section from the Shape plot?

Post by Sherif »

Hi,

I work with 3D morphological data in which the dendritic tree of a cell is described by around 1000 sections. I want to know if there is a way to get the name of any required section from the Shape plot? Actually, when I right click the mouse on the Shape plot I find an option called 'section'. When I click over the required section it then becomes red, but I don't know how to access this section?

Thanks
ted
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discovering the name of a section, and vice versa

Post by ted »

Discovering the mapping between section names and branches in a shape plot really
involves two tasks:
A. Given a branch in a shape plot, can you figure out the name of the corresponding
section?
B. Given the name of a section, can you figure out the corresponding branch in a shape
plot?

At present NEURON has three GUI tools for discovering this mapping. One works for
task A, another works for task B, and the third solves both problems.

1. If you're working with a model that is managed by a CellBuilder, and you know the
name of a section, the CellBuilder can help you find out which branch corresponds to
it. Go to the Geometry or Biophysics page, scroll through the list of section names
(middle panel of the CellBuilder), and click on the one you're interested in. The
corresponding section will turn red in the left panel. However, for the sake of speed,
the CellBuilder's left panel displays only a very simplified "stick figure" approximation
to the shape of the cell, and it can be hard to relate some of these sticks to what you
see in a "real" shape plot.

2. If you know which branch you are interested in, and need to discover the name of
the corresponding section, a quick and dirty trick is to bring up a Shape plot
NEURON Main Menu / Graph / Shape plot
Click on the Shape plot's menu box (upper left corner), and choose
Time Plot
Now click on any branch in the Shape plot. It will turn red, and a voltage axis graph
will pop up that has two variables in its plot list: v(.5) (i.e. at the middle of the default
section), and sectionname.v(x) where sectionname will be the name of the
section that you clicked on. These names will be displayed as labels along the right
edge of the voltage axis graph. If the section name extends beyond the right border
of the window frame, click on the voltage axis graph's menu square, and choose
Move Text
Then click on the section's name and drag it to the left so you can see it. To see
the names of more sections, just click on them and their names will be added
to the voltage axis graph's plot list.

3. The third GUI tool lets you discover the secton name for a branch, or the branch
that corresponds to a section name, but it may tempt you into doing things that impair
"conceptual control." First let's talk about the helpful things it does, and then we'll
discuss the "primrose path" aspect of this tool.

Click on
NEURON Main Menu / Tools / Distributed Mechanisms / Viewers / Shape Name
This brings up a window with a shape plot in the left panel, and a scrollable list of
section names in the right panel. At this point you can click on one of the section
names, and you'll see the section turn red. Or you can click on one of the branches
in the shape plot, which turns it red and highlights the corresponding item in the list
of section names (you may have to scroll the list up & down to find the selected name).

OK, now for the risky part. If you double click on one of the section names, you'll bring
up one or more panels that show the names and values of model parameters and
variables. You may be tempted to use the parameter panel to specify model
parameters. That is a risky thing do do if your model is managed by a CellBuilder,
because
--none of the changes you make with the parameter panel will be reflected back into
the CellBuilder
and
--anything you do in the CellBuilder will overwrite any changes you have made with
the parameter panel.
In either case, you can see how easy it would be to lose track of what the actual model
specification is. So if you accidentally bring up one of those parameter panels, just
dismiss it by clicking on its Close button.

--Ted
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