[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 #6 from suzel at g.harvard.edu ---
(In reply to Jan Eglinger from comment #4)
> (In reply to suzel from comment #3)
> > If I stitch the entire set of images using the 'position from files'
> > sub-routine, the stitching work fine,
> 
> In 'positions from file', do you use the 'Defined by TileConfiguration' or
> the 'Defined by image metadata' mode?
> 
> If using a TileConfiguration.txt file worked for you, you can edit that file
> to include only the files of interest.
> If using image metadata (which more likely if understood you correctly), a
> workaround might be to re-save the files to tiff *without* their metadata
> and then use row-by-row as you tried.
> 
> What format are you using? OME-Tiff?

Also, and interestingly, the bio-format importer doesn't seem capable of
generating a hyperstack when I loaded the original stacks (which I thought
could be convenient to resave the entire set of images in one go instead of
resaving them one by one). However, once resaved separately, bio-format
importedd has no trouble grouping the stacks into a hyperstack. There seems to
be some incompatibility between the image/stack format spitted out by
Micromanager and the imageJ plugins for handling those stacks (which is odd
considering that micromanager runs on imageJ).

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