[ImageJ-bugs] [Bug 1234] Issue with the Stitching plugin (Grid/collection stitching)

[bugzilla at fiji.sc]

http://fiji.sc/bugzilla/show_bug.cgi?id=1234

--- Comment #3 from suzel at g.harvard.edu ---
(In reply to Jan Eglinger from comment #1)
> Do you try to stitch tiles from a series of files that Bio-Formats would
> recognize as a multi-series dataset?
> I've observed that when working with a multi-file dataset, Bio-Formats tries
> to be smart and always opens the whole dataset. The Stitching plugin uses
> Bio-Formats in the backend, and will see the first series of the dataset
> even if any other file name from the dataset is provided in the
> TileConfiguration.txt file.
> 
> If you provide more details about the file format you're trying to stitch, I
> can try to give more specific advice how to work around the issue.

Hi Jan,

Thank you for responding to my post.

The set of images I'm working with is generated by the Multi-D acquisition
module from micromanager. Specifically, the set of images consists of a total
of 96 2-image stacks, corresponding to 12 separate regions for which I generate
a 8 image (4x2) local 10% overlap coverage.
If I stitch the entire set of images using the 'position from files'
sub-routine, the stitching work fine, except that it generates a massive
montage image where the 12 separate regions are displayed on the same huge
image and it quickly runs out of memory. That's why I was hoping to use the
'row-by-row' module to only select the few images that I'm interested in.
Alternatively, I tried to copy the few images I was interested in into a
separate folder and run the 'position from file' module, except that each image
contains the metadata from the entire 12 region stack, and that seems to cause
troubles when trying to stitch and assemble only a subset of images.
I hope this makes sense.

Thanks again to taking the time to help out with this issue! Much appreciated!

Seb

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