neuromau wrote:ted wrote:If such swc files are common, I would expect Import3D to already have a policy for dealing with them. Have you such a file, and what did Import3D do?
Yes, I downloaded the file from
http://neuromorpho.org/neuroMorpho/dabl ... 61.CNG.swc. The first two data lines of it look like:
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1 1 -3. -0.5714 -0.60710 5.808 -1
2 2 -3. 9.5 -3.5 0.4 1
where the numbers in the second column refer to compartment type (1=soma, 2=axon). So you can see that only the first line refers to the soma (there are no other soma lines later on). NEURON's response is the same as sgratiy got, which is to reassign the second line, which refers to the axon, to the soma so that it defines a cylinder. I can give the exact wording tomorrow if you need it.
You got the morphology in question from NeuroMorpo.org? I'd like to see it.
Yes, it is from NeuroMorpho.org. Here is the link
http://neuromorpho.org/neuroMorpho/neur ... ame=c10261 for CA1 pyramidal cell #c10261 from the Amaral lab, and the standardized SWC file for this cell is the one I mentioned above. Should I be using a different model, with a more detailed soma specification?
I want to resurrect this thread because I don't think this issue has been resolved, because I want to give a better answer to Ted's first question above, and because I want to echo his thought that Import3D should have a policy for dealing with this scenario.
I can verify that there are multiple files on neuromorpho.org that have only a single line for the soma. That's not my problem, however. I'm using L-NEURON (
http://krasnow.gmu.edu/cn3/L-Neuron/index.htm) to generate unique cells within a certain morphological class, and any SWC file that it outputs only has a single line for the soma, like so:
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1 1 0.000000 0.000000 0.000000 5.000000 -1
2 3 -2.883534 7.320411 -19.991474 0.568317 1
3 3 -5.146981 13.066614 -35.683907 0.568317 2
4 3 -7.410429 18.812817 -51.376339 0.039782 3
In this case, the soma is a sphere with a radius of 5 micrometers. The second line is the first section of one of the dendritic trees, which connects to the soma.
When you try to import this file (called "output.swc") using Import3D, Neuron returns the following message:
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Notice: ./output.swc:
The first two points have different types (1 and 3) but
a single point root section is not allowed.
Changing point id 2 so that it is type 1.
If this is an incorrect repair, then change the file.
When you look at the generated HOC code, you get the following code after all the sections get connected together:
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proc shape3d_1() {
soma {pt3dclear()
pt3dadd(0, 0, 0, 10)
pt3dadd(-2.88353, 7.32041, -19.9915, 1.13663)
}
dend {pt3dclear()
pt3dadd(-2.88353, 7.32041, -19.9915, 1.13663)
pt3dadd(-5.14698, 13.0666, -35.6839, 1.13663)
pt3dadd(-7.41043, 18.8128, -51.3763, 0.079564)
pt3dadd(-9.67388, 24.559, -67.0688, 0.079564)
pt3dadd(-9.7437, 24.7363, -70.0627, 0.07975)
pt3dadd(-10.4404, 26.5051, -72.3835, 0.07975)
pt3dadd(-10.8431, 27.5273, -75.1751, 0.07975)
pt3dadd(-11.2457, 28.5494, -77.9667, 0.07975)
}
Why is the same 3D point being added to both the soma and the first dendritic section?
So it looks like NEURON is basically turning the first dendritic section into an extension of the soma, which could have problematic results for the morphology of the cell, though what's actually happening in the code is not clear to me.
What should Import3D do in this case? And what should users of NEURON do to fix what's actually happening? NEURON explicitly tells us to change the file, but how?
Phillip