stitching troubleshoot

Posted by Suleiman on Jun 20, 2012; 2:50pm
URL: http://imagej.273.s1.nabble.com/stitching-troubleshoot-tp4999134.html

Hi ImageJ users,

I am having some trouble stitching time lapse videos using the pairwise and 3d pluggins. Some of the images stitch, some of them don't and am not sure why that is the case.

My initial images were acquired on a spinning disc microscope using volocity. I have different Z stacks  taken of up to 30 different (XY) regions over a 6-10h period. I am exporting the individual stacks from volocity as tiffs and importing to imageJ as hyperstacks. I take Z projections and  then attempt to stitch them using the Pairwise Stitching/3D pluggins. I would like to see the stacks stitched so that neighbouring XY regions are next to each other, with some overlap. However, this does not always happen. Some stacks stitch with some overlap, others overlap completely and look like 1 stack, and others do not stitch at all.

all stacks have the same XYZT parameters,they are all 8 bit. Original video saved as .mvd2 on volocity, in the raw data files all are .atsf  

Any advice/tips would be appreciated

Thanks,
Suleiman