Grid/Collection stitching z-stack

[Jakob M]

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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[Stephan Preibisch]

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regarding the side-note: On top of the wiki page it says that this is an outdated version that is not supported any more and it links to the current version: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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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Jakob M]

Hi Stephan,

thanks for you reply, good to know it should be possible. However, I still don’t know how, maybe I didn’t explain well enough. I have the following two problems:

1. If I give the plugin a number of z-stacks to stitch, it doesn’t work because it assumes that the z-stacks are different time points. Is it possible to merge z-stacks? If so, how?

2. Once I have a TileConfiguration.txt (I currently can get it for the individual z-slices), how do I apply that to other files? I assume I have to choose "Position from files", but then there is no option to give a different directory or other files to be used with the positions in that file. I could modify TileConfiguration.txt to include different file names, but that seems rather clumsy.

Thanks again for you help!
Jakob

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