Re: Stitching together multiple images within a series of folders

Posted by on May 09, 2018; 5:45am
URL: http://imagej.273.s1.nabble.com/Stitching-together-multiple-images-within-a-series-of-folders-tp5020586p5020637.html

Hi Ben,

It’s great to hear that the BigStitcher works for you. Did you try to put all tiles on top of each other and maybe it’ll be able to figure it out itself using quite aggressive, high thresholds?

If that works, you can easily automate it using the ImageJ Macro Recording function with BigStitcher (Plugins > BigStitcher > Batch Processing & Plugins > Multiview Reconstruction > Batch Processing). It might also work well using interest point detection and Precise Descriptor-based registration in the Multiview Reconstruction instead of the correlation-based stitching. Depends on the marker in your C. elegans.

All the best,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b
Robert-Rössle-Str. 10
13125 Berlin

email: [hidden email]<mailto:[hidden email]>
web: http://preibischlab.mdc-berlin.de
twitter: http://twitter.com/preibischs

On May 4, 2018, at 10:38 PM, nebenb <[hidden email]<mailto:[hidden email]>> wrote:

Hi Curtis,

If I'm remembering correctly, ImageJ/FIJI weren't wanting to update because
they couldn't connect to a server? Regardless, I have the BigStitcher beta
now and its GREAT its so easy and straightforward and does a remarkable job
stitching my files together.

I'm still working on understanding how to script the stitching process to be
automated, since I can use the same stitch-settings for each group of files.
Ideally, FIJI would move from folder to folder stitching together the files
in each. I don't see a clear way to do this with BigStitcher but also have
close to zero coding experience and might be missing something obvious.


Dr. Preibisch,

Thank you again for the tip on BigStitcher, it works wonders! As i mentioned
above I'm trying to script the image stitching to be automated. Since the
worms i'm trying to stitch are arbitrarily oriented, I can't define a
tiling-orientation ahead of time, but the stitcher does a good job orienting
the tiles.


Thanks again for all the input,

Ben





--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html