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Re: Import neuronstudio swc. files to Fiji

Posted by Curtis Rueden on May 23, 2018; 7:43pm
URL: http://imagej.273.s1.nabble.com/Import-neuronstudio-swc-files-to-Fiji-tp5020710p5020716.html

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
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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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