Hyperstack manipulations

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Hyperstack manipulations

Philippe CARL
Dear all,

I have an hyperstack (1-channels, 48-slices, 14-frames) on which I would
like to apply the same Kang Li Image Stabilizer plugin
(http://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html) values for all 14

Thus I choose a given slice position (the goal being to iterate this on all
14 frames) for example with:
Stack.setPosition(1, 1, 5);

I reduce the dimensionality:
run("Reduce Dimensionality...", "slices keep");

I apply the previously generated "StabRef.log" on the given reduced stack
run("Image Stabilizer Log Applier", " ");

And then I would like to replace the stabilized pictures back into the
hyperstack which is where I got stuck and didn’t find any solution (even by
surfing on previous forum postings on the web).

Also I performed a reduce dimensionality before applying the previously
generated "StabRef.log" given that the Image Stabilizer plugin can only be
applied on stacks (i.e. not hyperstacks).

Is there a "good" or easy way to perform what I’m looking for?

I thank you very much in advance for your ideas and hints.

My best regards,



Philippe CARL

Laboratoire de Biophotonique et Pharmacologie

UMR 7213 CNRS - Université de Strasbourg

Faculté de Pharmacie

74 route du Rhin


Tel : +33(0)3 68 85 41 84

ImageJ mailing list: http://imagej.nih.gov/ij/list.html