Grid/Collection Stitch

Posted by Cheuk Tam-2 on Oct 16, 2015; 5:46pm
URL: http://imagej.273.s1.nabble.com/Grid-Collection-Stitch-tp5014667.html

Hi All,

I'm new to FIJI, and I was troubleshooting the Grid stitching plugin.  It was able to produce a stitched image, but some areas are aligned incorrectly.  For example, the nuclei from overlapping constituent images are juxtaposed in the fused image instead of merged together (upper right part of the neurosphere, adjacent to the 2 bubbles).  

The images are in the following folder:
https://www.dropbox.com/sh/8idzyd0rh3qt3in/AADUA93Kd-31bK-pzzwCgt50a?dl=0

"C3-08C6 _A_comp 10x Fused" is the stitched image
"08C6 _A_Hoechst_10x_13" is the corresponding original

I've tried to increase the regression threshold and decrease the displacement threshold, but without any luck.  Is there anything I can change in the way I take the pictures or stitch them together?  Is there such a thing as too much overlap in the individual pictures?

Thank you for your help.

Sincerely,
Cheuk

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