Posted by
Majurski, Michael Paul (Fed) on
Dec 08, 2016; 2:59pm
URL: http://imagej.273.s1.nabble.com/Stitching-output-has-missing-pixels-tp5017714p5017720.html
Mike,
I have run into that missing output tile bug myself a few times and so far I have not seen neither a fix nor speculation as to the cause.
At times I have had the first few tiles end up missing from the output image when I know I am using the plugin correctly. So your bug 1 is not a user error. However, I have never has small blocks of the output image go missing (bug 2 in your email) that were not in the upper left corner (tile 1, tile 1-2). So I cannot comment on that apparent bug.
Another resource (if you have not found it already) would be the Fiji forum:
http://forum.imagej.net/, where there have been a few discussion related to Stephan's stitching plugin.
However, there are other stitching programs to try which might result in less effort for you. The one I was involved in creating (MIST
https://pages.nist.gov/MIST/ ) requires a regular grid of images (basically roughly constant overlap), but it might be worth giving it a try.
Project Page:
https://pages.nist.gov/MIST/
Source:
https://github.com/usnistgov/MISTWiki:
https://github.com/usnistgov/MIST/wikiInstall Guide:
https://github.com/usnistgov/MIST/wiki/Install-GuideBest of luck,
Michael Majurski
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of MChapman
Sent: Wednesday, December 07, 2016 17:14
To:
[hidden email]
Subject: Stitching output has missing pixels
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
--
View this message in context:
http://imagej.1557.x6.nabble.com/Stitching-output-has-missing-pixels-tp5017714.htmlSent from the ImageJ mailing list archive at Nabble.com.
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html