Stitching output has missing pixels

Posted by MChapman on Dec 07, 2016; 10:14pm
URL: http://imagej.273.s1.nabble.com/Stitching-output-has-missing-pixels-tp5017714.html

Hello,

I have been fighting Stephan's stitching plugin for a few months now and I just wanted to let you guys know what my issues have been if there is a hope at solving them.  I really like the stitching algorithm, there are just two errors that I have been experiencing.

1) When stitching more than about 50-100 images, the first or first and second tile don't find an adequate alignment and are left out of the stitch and assigned a position of (0,0) in the  TileConfiguration.txt file.

To correct this, I just run a second stitch of the first 2-3 rows of the montage.  Then I use the position of an image in the middle of the bottom row of this stitch as a reference and rewrite the TileConfiguration.txt file positions for the full stitch.  I can then rerun the stitching program without "compute overlap" with the repaired TileConfiguration.txt and this fixes the first error.  A bit of a nuisance, but it works.

2) When I rerun the stitches with the repaired TileConfiguration.txt, some of the pixels (sometimes a single pixel, sometimes a block of 20x300) come back as 0 in the stitch.  There are no gaps in the overlap of the images from the TileConfiguration.txt file, and if I rerun the stitch again the 0 pixels show up in different locations.

My current fix is to just run multiple restitches and then take a max of a stack of the stitches and do that until there are no 0 pixels.  Again this is a nuisance but I can get my data stitched with it.

Is there anything that I am doing wrong or is anybody else having these issues?

Mike

edit* PS...If example images would be helpful, just let me know and I can post them or post a link to them.
I reposted this correctly this time to send it out to the mailing list
MIke