Hi,
it's unfortunately not possible with the included import tools.
TrakEM2's convention to reference slices of stacks as patches is to add
-----#slice=1
-----#slice=2
...
to the filename. Unfortunately, this gets rejected when used in the
import file which probably treats # as the beginning of a comment?
So you will have to script it, either within TrakEM2 or outside
generating the XML.
On another note. TrakEM2 does not perform very well when working with
TIFF stacks. Whenever it needs access to an original pixel value, it
loads the entire stack. This happens whenever you hover over a patch,
or during montaging alignment. I'd therefore explore options to
generate 2d-tiff series of the stacks, and may be archive the real
stacks away.
Best,
Stephan
On Thu, 2015-02-12 at 14:52 -0500, Albert Cardona wrote:
> Hi Oli,
>
> I would do this with a script that reads each multi-TIFF file and positions
> a tile at the right place.
>
> Albert
>
> 2015-02-12 8:32 GMT-05:00 Burri Olivier <
[hidden email]>:
>
> > Hi all,
> >
> > We were asked the following question by one of our users who has a couple
> > of TB of tiled stacks that he would like to import into TrakEM.
> >
> > > I would like to import stacks into trackEM and place them at the right
> > position.
> > > therefore i generate the textfile of the xyz position of the origin of
> > the stack.
> > > the files are compressed 3d Tiff files of 100 slices each.
> > > The files gets placed at the right xy coordinate but z is not
> > distributed onto the different layers.
> > > However one single 3d tiff file stack gets imported just fine.
> > >
> > > Is there something to be done or do i have to reconvert all the stacks
> > into single files ?
> > > Converting the 3dtiffs into single plane tiff would be very time
> > consuming as the compound datasize is very high.
> > >
> > >
> > >thank you
> >
> > So far the only solution I could think of based on the Tutorials was to
> > export each stack as a series of TIFFs then import those into TrackEM.
> >
> > Is there another way to import a tiling of TIFF stacks?
> >
> > Thanks for any feedback you might have,
> >
> >
> > Oli
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
>
>
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