Utilizing morphology from IMARIS: help classifying "filaments" as basal/apical dendrites, etc
Posted: Tue Jul 17, 2018 12:46 pm
Hello all (my first post here!),
I am currently "taking over" a project in my new lab that involves utilizing NEURON to create a detailed multi-compartment cell model. The existing code that was handed off to me included the cell's morphology taken utilizing the IMARIS program. While I'm not familiar with this particular program, one of its limitations seems to be that, in creating the morphology in a fashion that NEURON can utilize, it does not differentiate between soma, dendrite, and axon; instead, all portions of the cell are simply classified as "filaments". For example, the morphology file looks like the following (with details redacted):
I am currently working on putting various ion channels into the model, and am evaluating the pros and cons of doing so uniformly across all of the "filaments" or doing so differently for the soma, dendrites, and axon. However, the later option, at present, would involve me manually going through all of the filaments and classifying them by hand (which I'm also mildly concerned could lead to some unintended consequences to the code if, say, I change 200 of the filaments to be instead be objects of the form dendrite[]). So, my primary question is this: is there any way that, utilizing NEURON, I can programmatically classify and rename the various filaments that currently make up my morphology, or am I restricted by the way the morphology was taken to doing this manually? Any other thoughts/suggestions on anything brought up in this lengthy post would also be appreciated, as this project is my first major foray into utilizing NEURON in my research!
Thanks in advance for any help you all can provide.
I am currently "taking over" a project in my new lab that involves utilizing NEURON to create a detailed multi-compartment cell model. The existing code that was handed off to me included the cell's morphology taken utilizing the IMARIS program. While I'm not familiar with this particular program, one of its limitations seems to be that, in creating the morphology in a fashion that NEURON can utilize, it does not differentiate between soma, dendrite, and axon; instead, all portions of the cell are simply classified as "filaments". For example, the morphology file looks like the following (with details redacted):
Code: Select all
strdef neuron_name
neuron_name = "Filaments 1"
create filament_100000042[211]
filament_100000042[0]{
pt3dclear()
pt3dadd(...)
pt3dadd(...)
}
filament_100000042[1]{
...
}
...
connect filament_100000042[1](0.0), filament_100000042[0](1.0)
...
define_shape()
access filament_100000042[0]
Thanks in advance for any help you all can provide.