Batch converting Simple Neurite Tracer files to images

[Straub, Volko A. (Dr.)]

Dear All,

I have been using the Simple Neurite Tracer in Fiji and know have a
large collection of trace files that I would like to convert to images.
I know that I can load the trace files within the Simple Neurite Tracer
and then use the 'Make Line Stack' command to create a b/w image of the
traces. I was just wondering whether anybody knows a convenient way to
do this automatically for a whole folder of trace files rather than
having to manually load each trace file and create the image.

Thanks for your help,
Volko

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[Tiago Ferreira-2]

Dear Volko,

On Apr 28, 2016, at 15:40, Volko Straub <[hidden email]> wrote:
> I was just wondering whether anybody knows a convenient way to do this automatically for a whole folder of trace files rather than having to manually load each trace file and create the image.


The Neuroanatomy update site[1] implements the "File>Import>Tracings (SWC/Traces)..." command that is macro recordable and should do just that.

NB: Some of the options in the "Render as" drop down menu, may not work as they require SNT v3.0.3, yet to be released.
    However, "Untagged skeleton" (equivalent to 'Make Line Stack' in SNT's UI), should work without issues.

[1] http://imagej.net/User:Neuroanatomy

-tiago
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[Straub, Volko A. (Dr.)]

On 29/04/2016 04:46, Tiago Ferreira wrote:

> Dear Volko,
>
> On Apr 28, 2016, at 15:40, Volko Straub <[hidden email]> wrote:
>> I was just wondering whether anybody knows a convenient way to do this automatically for a whole folder of trace files rather than having to manually load each trace file and create the image.
>
> The Neuroanatomy update site[1] implements the "File>Import>Tracings (SWC/Traces)..." command that is macro recordable and should do just that.
>
> NB: Some of the options in the "Render as" drop down menu, may not work as they require SNT v3.0.3, yet to be released.
>      However, "Untagged skeleton" (equivalent to 'Make Line Stack' in SNT's UI), should work without issues.
>
> [1] http://imagej.net/User:Neuroanatomy
>
> -tiago

Thanks Tiago,
This is exactly what I was looking for.
I'm intrigued to hear about an updated version of SNT. Any idea when
this will be released and what new/additional features it will include?
Volko

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