Working with spines

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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MishaZ

Working with spines

Post by MishaZ »

In reading the manuals and posts here, I came across references to spines as something that NEURON can treat different from other parameters. Yet I am having a hard time finding anything specific. Is there anything to this, and if so, once specified (how?), how are the spine compartments treated differently? Sorry for the rudimentary question, I hope someone can point me in the right direction.
ted
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Post by ted »

Read about pt3dadd in the Programmer's Reference. Then forget about it. The only
place you'll find geometry specs with negative diameters is in legacy code. This
may have had some utility back in antediluvian times--imagine that you are manually
entering morphometric data for a cell, and you want to mark some point along a branch
where a particular spine is located. And it doesn't accomplish anything else, i.e. if you
then execute the pt3dadd statements, the resuting model doesn't magically have a
model spine at that location.

If you want to represent the effect of spines on apparent membrane properties, decide
how much "extra surface area" they add per square micron and then scale cm and
conductance densities up by that amount.

If you actually need to represent spine geometry (neck diam and length, head area
and volume) then do it by explicitly creating sections with the required geometry.
And don't forget that changing nseg can change the actual location of anything that is
connected at positions other than the 0 and 1 loci on a section.
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