help > Issues with parent ID in .swc files
Showing 1-3 of 3 posts
Display:
Results per page:
Jun 8, 2022  04:06 PM | Meha Pravin Jadhav - NCBS Bangalore
Issues with parent ID in .swc files
Hello,
I am a novice with Vaa3d. I am trying to use it to trace morphologies of neurons to ultimately import them into NEURON simulator. When I load the swc file into NEURON, I was getting an error saying it is unable to read the file.
I finally realized that the error is due to inconsistencies in parent ID numbers. I don't know what I am doing wrong with the tracing.

Here is how I trace the 3d structure:
 1. I add markers on the morphology (one at soma and one each at all the terminals)
2. label the marker at soma as the starting point
3. choose 'trace from starting point to all markers'.
4. I finally choose 'join all segments' option
5. save the traced neuron as an .swc file.

Could someone please tell me what the issue could be?

I have attached the .swc file (note the -1 parent ID at segment 196):
Attachment: Neuron_1.swc
Jun 17, 2022  06:06 AM | Lingli Zhang
RE: Issues with parent ID in .swc files
Hello,

     You can use the sort swc plugin in Vaa3D,which will help you to solve the inconsistencies in parent ID problems. I have also attached the sorted swc of your file below.
      if there has any other problems, i will be glad to help to solve it.
Jun 19, 2022  02:06 PM | Meha Pravin Jadhav - NCBS Bangalore
RE: Issues with parent ID in .swc files
Thank you! Yes, the plugin solves the issue.