Grid/Collection stitching z-stack

Posted by Jakob M on Aug 03, 2015; 6:22pm
URL: http://imagej.273.s1.nabble.com/Grid-Collection-stitching-z-stack-tp5013880.html

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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