Import neuronstudio swc. files to Fiji

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Import neuronstudio swc. files to Fiji

Corisjo Schroevers
 Dear developers and users of ImageJ,

Currently in our department we are trying to find a standardized method of
tracing neurons received from stacks. We generate the stacks and any
substacks within Fiji and once we have a target neuron we import the stacks
into Neuronstudio to trace it, as Neuronstudio can automatically trace.
After saving these traces in an swc file we try to reload it into Fiji
Simple Neurite tracer, however we always encounter an issue with scaling.
We always have the correct offset coordinates at hand, previously saved
from the original stacks in Fiji, but the offset scaling is always off,
sometimes really off. The tracings always appear smaller than the original.
With trial and error we can come as close as possible to the correct
scaling but this is rather time consuming and the endgoal is to fully
automate the whole process via standard procedures for a protocol, that
will be used in the lab. Would anybody know if what the precise error is or
how to work around it?

With kind regards,

Concerned Master internees

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Re: Import neuronstudio swc. files to Fiji

Curtis Rueden
Hi Corisjo,

Since this is a question about Simple Neurite Tracer, I filed an issue in
the SNT issue tracker for it:

  https://github.com/fiji/Simple_Neurite_Tracer/issues/36

I recommend you create a GitHub account and comment there with more
details, such as a small attached non-working SWC file, so that the issue
can be investigated further.

Regards,
Curtis

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Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, May 23, 2018 at 7:21 AM, Corisjo Schroevers <
[hidden email]> wrote:

>  Dear developers and users of ImageJ,
>
> Currently in our department we are trying to find a standardized method of
> tracing neurons received from stacks. We generate the stacks and any
> substacks within Fiji and once we have a target neuron we import the stacks
> into Neuronstudio to trace it, as Neuronstudio can automatically trace.
> After saving these traces in an swc file we try to reload it into Fiji
> Simple Neurite tracer, however we always encounter an issue with scaling.
> We always have the correct offset coordinates at hand, previously saved
> from the original stacks in Fiji, but the offset scaling is always off,
> sometimes really off. The tracings always appear smaller than the original.
> With trial and error we can come as close as possible to the correct
> scaling but this is rather time consuming and the endgoal is to fully
> automate the whole process via standard procedures for a protocol, that
> will be used in the lab. Would anybody know if what the precise error is or
> how to work around it?
>
> With kind regards,
>
> Concerned Master internees
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html