Inserting channels (some distribution) after loading SWC fil

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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dilawar
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Location: NCBS Bangalore

Inserting channels (some distribution) after loading SWC fil

Post by dilawar » Fri Apr 10, 2015 9:13 am

I was searching if one can specify channel distribution once a cell is created by loading SWC file into NEURON. I am thinking of specifying a region of cell and distribution of channel by an expression valid in that region. I am using Neuron-7.4 with python support enabled. Is there a snippet/example or document for doing this?

best,
Dilawar

ted
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Re: Inserting channels (some distribution) after loading SWC

Post by ted » Fri Apr 10, 2015 10:27 am

The easiest way to do this is with the CellBuilder--see the
CellBuilder tutorials
link at http://www.neuron.yale.edu/neuron/docs
especially the tutorial on parameterized variation of biophysical properties.

One nice feature of the CellBuilder is that it can export reusable hoc code. This means you can implement a strategy using a toy model (stick figure cell), then generalize the exported hoc code for use with any morphology.

dilawar
Posts: 13
Joined: Mon May 26, 2014 9:12 am
Location: NCBS Bangalore

Re: Inserting channels (some distribution) after loading SWC

Post by dilawar » Mon Jul 06, 2015 4:52 am

Thanks,

I managed to load the SWC file using python interface. Then I inserted few ion-channels into the model. To be sure, I want to count the number of channels to check my mechanism is getting inserted or not. How to get the number of compartment and channels using nrnpython?

best,
Dilawar

ted
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Location: Yale University School of Medicine
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Re: Inserting channels (some distribution) after loading SWC

Post by ted » Mon Jul 06, 2015 11:06 am

The GUI's ModelView tool is the best way to discover what is present in a model cell. Works with models whose properties were specified by any combination of hoc and/or Python. Just make sure that you start NEURON by
nrngui -python
or that you
from neuron import h, gui

If you prefer to read railroad timetables,
h('forall psection()')
may produce something more to your liking. However, that will not tell you about parameter values at section centers, so it's not very useful for assessing parameters that vary along the length of a section.

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