Stitching problem

Posted by Ed Siefker on
URL: http://imagej.273.s1.nabble.com/Stitching-problem-tp5019063.html

I take tiled images in Zeiss Zen.  I would like to move them to ImageJ
for analysis.  I cannot get the stitching plugin to work for me.

I'm using Grid/Collection stitching with Positions from file, and
Defined by image metadata. When I use the simple stitching option
in the Bio-Formats importer, it puts the tiles in the correct order.
So the positions and order in the .czi should be correct.

If I allow ImageJ to compute the overlaps it finds none.

If I stitch the file in Zen and tell the plugin to trust the coordinates in the
file, it opens but puts a large gap between the tiles. e.g. a file with two
tiles that are 968x728 becomes a fused image at 968x2176.

I don't know how to troubleshoot this further.  Is there something I'm
doing wrong?
-Ed

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