Re: Grid/Collection stitching z-stack
Posted by
Stephan Preibisch on
Aug 04, 2015; 8:45am
URL: http://imagej.273.s1.nabble.com/Grid-Collection-stitching-z-stack-tp5013880p5013881.html
Hi Jakob,
you can just stitch one timepoint and then apply the same coordinates to images in a different directory, for example. That should work ...
regarding the side-note: On top of the wiki page it says that this is an outdated version that is not supported any more and it links to the current version:
http://fiji.sc/Image_Stitching <
http://fiji.sc/Image_Stitching> <
http://fiji.sc/Image_Stitching <
http://fiji.sc/Image_Stitching>>
All the best,
Stephan
---
Dr. Stephan Preibisch
Group Leader
Berlin Institute of Medical Systems Biology of the MDC
email:
[hidden email] <mailto:
[hidden email]>
web:
http://www.preibisch.net/ <
http://fly.mpi-cbg.de/preibisch>
> On 03 Aug 2015, at 20:22, Jakob M <
[hidden email]> wrote:
>
> Hi,
>
> I am trying to find an optimal way of stitching a number of z-stacks for different time points using the Fiji Grid/Collection stitching plugin.
> I would like to stitch one z-stack corresponding to one time-point, and then apply that to all other z-stacks. So far, it works if I do it on individual z-slices, and then apply the resulting TileConfiguration.txt to other slices. Is there a way I can give the full tif-stack to the plugin? Currently, it assumes that the different images in the stack are different time points, so that doesn’t work.
>
> Or would it be better to make a large time-z-stack and stitch that? How does the plugin know which is the z-index and which is the time index?
>
> Sidenote: This tutorial
http://fiji.sc/Stitch_and_Align_a_sequence_of_grid_images_Tutorial and also the help site
http://fiji.sc/Stitching_2D/3D mention some options like "Stitch Image Grid Sequence” that do not show up in my current Fiji version.
>
> Thanks
> Jakob
>
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