Re: NBLAST with SWC file format

[Dr Gregory Jefferis]

Dear Evan,

Thanks for your interest in NBLAST. The NBLAST algorithm is of course not tied to a particular input file format. The natverse function read.neurons can read in a set of SWC files (and a number of other file formats) to which you can then carry out NBLAST all by all clustering or other analyses:

library(natverse)
nl=read.neurons("/folder/of/swcs")

Then you need to convert to dotprops i.e. vector cloud format, minimally by doing:

nld=dotprops(nl)

And then you can follow the remaining steps of this tutorial:

http://natverse.org/nat.nblast/articles/NBLAST-Clustering.html

All the best,

Greg.

PS I have taken the liberty of ccing this message to the nat-user google group since the answer may be of interest to others.

On 24 Mar 2021, at 10:47, Evan Cresswell wrote:

Hello Dr. Jefferis,

I am a researcher at the Basque Center for Applied Mathematics
investigating the effect of Astrocyte cell morphology on intracellular
calcium dynamics. We are trying to characterize morphological traits and
morphologically similar cells using morphology files in swc format.

I came across NBLAST while looking for software to compare cell
morphologies. I am very impressed with the functionality and setup of
NBLAST but it is unclear whether I can utilize it for my investigation. *Does
the software work with the SWC file format?* I checked the documentation
and it doesn't appear so, but I wanted to verify with you since the
software seems quite powerful.

Best regards,
Evan Cresswell-Clay

--
Gregory Jefferis, PhD
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
https://www.zoo.cam.ac.uk/research/groups/connectomics
http://jefferislab.org