Re: Trakem2- importing sequence as a grid

Posted by Saalfeld, Stephan on Nov 18, 2016; 4:07pm
URL: http://imagej.273.s1.nabble.com/Trakem2-importing-sequence-as-a-grid-tp5017596p5017603.html

Hi,

the easiest way to import custom acquisition patterns is to generate an
import file and use "Import from text file".  It is very easy to
generate such import file with e.g. Excel, OpenOffice Calc, or the
scripting language of your choice if your pattern is moderately
regular.  If it's not, you have to do it anyways.  This question has
been answered multiple times at various mailing lists but Web-Search is
hard if you do not know the terms yet ;)

Here they are: "import text file TrakEM2"

Documentation is here

https://www.ini.uzh.ch/~acardona/trakem2_manual.html#importing_list

Cheers,
Stephan

On Fri, 2016-11-18 at 14:12 +0200, Stoyan Pavlov wrote:

> Dear friends,
> I recently started using TRAKEM2 for the stitching of microscopic
> mosaics.
> The thing I like the most is that it allows to export flattened
> (stitched
> and blended) image of any size. However I hit a bump and I hope
> someone can
> help:
> When I import sequence of images the tiles in every other row in the
> resulting grid are in reverse order. I guess the reason for this is
> that
> the plugin is importing the tiles in comb-like fashion. Is there a
> way to
> modify this behaviour in order to load the images in meander-like
> order,
> similarly to the sequential-continuous import in the MIST plugin (I
> like
> this plugin very much also, but unfortunately it doesn't allow the
> export
> of images >2 GPx).
> In other words TrakEM2 imports sequences now like this:
> 123
> 456
> 789
>
> Is there a way to force it to import them like this:
> 123
> 654
> 789
>
> Thank you in advance
>
> Stoyan
> ---
> Dr. Stoyan P. Pavlov, MD, PhD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
>  Bulgaria
> Tel: +359 (0) 52 - 677 - 052
> e-mail: [hidden email]
>            [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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