Identifying whether a branch is dendrite or axon in .swc files

Technical
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1

Hello!
Wondering if there is any way to identify whether a branch is dendrite or axon in .swc files that have 3d reconstruction data?
We’ve noticed that there seems to be an ID ranging between 1 and 3; but what these numbers mean is rather unclear.
Thank you!
Eric

2

Hello Eric, in SWC format the second column identifies structure or compartment of the cell as such;

1 - soma
2 - axon
3 - basal dendrite
4 - apical dendrite

Hope this helps,
-Rachel

3

Hi Rachel,
this does help! I appreciate the input!
my apologies for the delay in responding!
thank you,
Eric

4

Hi Rachel,
I was wondering how each structure was identified? Was this based on the thickness of each neurite or some other metric? Thanks.

  • Curt
5

Hello @curt.johnson, we use thickness, texture (presences of spines or putative boutons), origination point and topology to differentiate axon and dendrite in morphologies generated with the patch clamp or -seq process.

-Rachel