how to print a model neuron with diameter information

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xyang

how to print a model neuron with diameter information

Post by xyang » Mon Aug 29, 2005 5:39 pm

how to print a model cell including detailed diameter and length? The model show in pointprocess manager could not tell the diamter difference.

Thanks!

Raj
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How to print a model neuron with diameter information

Post by Raj » Tue Aug 30, 2005 5:31 am

I'm not fully sure what you want, but there are at least two ways to get access to this information.

1.
You can print a (potentially long) list containing section names, diam length and other information you like to extract:

Code: Select all

forall {fprint("%s, %g, %g \n", secname(), diam, L)}
Before using these, especially if you want to export this information to a file, you might want to read up on the following commands: forall, forsec , printf and fprint. Pay special attention to the format strings needed for determining the output format.

2.
When using the graphical user interface. You make sure that you have access to a cell by entering on the command line something like:

Code: Select all

access Mycell.soma
from the main menu you select the graph menu in which you select shape plot. Right clicking your mouse (at least under windows) gives you a menu including shape style, if you select show diam from this menu you get to see the diam of the sections.

If you have a network the first method might be the better one, if you study an individual (3D reconstructed) cell the second method is probably the best way to quickly see whether you imported it correctly.

ted
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Re: how to print a model neuron with diameter information

Post by ted » Tue Aug 30, 2005 6:01 pm

Another interpretation of your question is "how do I print a picture of the
cell that shows how diameter changes along each section."

Many of NEURON's GUI tools include a Shape plot that displays a
projection of the cell onto the xy plane. By default, Shape plots show
just the centroid of each section. This saves time, but no matter how
much you zoom in, or how large you expand the Shape plot, it's just
a bunch of skinny lines.

To see diameter variation, click on the Shape plot's menu box (in the
upper left corner) and select Shape style / show diam. Branches that
are rendered smaller than a pixel wide may completely disappear from
your computer monitor, but if you zoom in or print to a PostScript
printer, you'll see that they still exist.

If you want to save the Shape plot to a graphics file, the best format
is either Postscript or encapsulated Postscript. You can do this with
the Print & File Window Manager, but that's a different story (go to
NEURON's FAQ list
http://www.neuron.yale.edu/neuron/faq/general-questions
and find the link
How do I print a hard copy of a NEURON window?
).

Many vector graphics ("draw") programs, such as CorelDraw, can
import the Postscript and idraw (encapsulated Postscript) files that
NEURON generates. You can also print graphs of voltage, current, etc.
to Postscript or idraw files, for subsequent revision and annotation with
a vector graphics program.

xyang

Thanks for the help

Post by xyang » Thu Sep 01, 2005 10:13 am

Thanks for the help. Both helps me. I got the print copy with detailed diameter information finally.

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