selecting frames from multiple zstacks and stitching in sequence

Posted by wustlmed on Sep 10, 2014; 8:36am
URL: http://imagej.273.s1.nabble.com/selecting-frames-from-multiple-zstacks-and-stitching-in-sequence-tp5009564.html

Hi,

Still new to ImageJ so I was wondering if anyone might have some experience with this.

I have a series of zstacks covering overlapping volume. Each successive stack is offset from the previous by a few microns in the z direction but xy coordinates are the same. I would like to select a limited number of frames from each stack  of 100 planes and combine into one master stack (say z planes 5-10 from stack 1 and planes 10-15 from stack 2 ...) and then combine them into one "master" z stack. To be clear, I don't want to simply place one z stack after another as they cover overlapping volumes, rather I need to select a subset of frames from one stack and combine it with another subset from the following z stack.

Best,
Ben

University of Pennsylvania