Morphology import error

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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shyam_u2
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Joined: Sun Feb 20, 2011 7:15 pm

Morphology import error

Post by shyam_u2 » Tue Jul 02, 2019 10:07 am

I am trying to import a morphology (from an .swc file) through cell builder. NEURON says that there are file translation problems. The terminal emits an error message saying that there is more than one tree. Any information on this appreciated.

Thanks in advance

ted
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Re: Morphology import error

Post by ted » Wed Jul 03, 2019 2:24 pm

If two or more intact cell morphologies are present, Import3d will just launch multiple CellBuilders (one for each cell morphology), and will not generate an error message. You got an error message, so most likely you have a morphology file in which at least one neurite is not connected to its parent. Tell the person who gave you the data.

shyam_u2
Posts: 77
Joined: Sun Feb 20, 2011 7:15 pm

Re: Morphology import error

Post by shyam_u2 » Tue Jul 09, 2019 4:32 pm

Thanks so much for taking the time to explain me the problem. The morphology as viewed using Neurolucida/HBP Neuron Morphology viewer looks good without any issues. I don't see any point which is not connected to the parent. Only when I import it in NEURON, there are a few points without any parent. Is there any way to solve this issue?

Thanks in advance,
Shyam

ted
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Re: Morphology import error

Post by ted » Thu Jul 11, 2019 10:07 am

Can you send me ted dot carnevale at yale dot edu the morphology file?

ted
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Re: Morphology import error

Post by ted » Mon Jul 15, 2019 3:30 pm

It's a bad file. Look at the error messages that NEURON prints to the interpreter window.

Code: Select all

oc>warning ./morphology.swc: more than one tree:
   root at line 35
   root at line 36
   root at line 76
   root at line 120
   root at line 164
   root at line 208
   root at line 258
etc.
for more than 20 lines.
Open the file with a text editor and you'll see that the messages are correct (the last item in each referenced line ends with -1, which is SWC's way of saying that the line is the first coordinate of a branch that is the root of a tree.

The problem lies either with the software that was used to generate or capture the swc data, or with the person who used the hardware and software that was employed to generate or capture the swc data (who would have failed to use it properly). I can't help you with this.

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