[ome-users] Bug report for version 2012-06 OME-XML in Fiji, seen in grid/collection stitching

[Michael Pinkert]

There appears to be a bug concerning the OME-XML reading implementation in Fiji.  I apologize if this is an inappropriate place to submit the bug report, but it was recommended I submit here.

I first saw the bug in the grid/collection stitching plugin after a recent update to Fiji. I have several sets of images obtained using WiscScan on one of the scopes at LOCI. I've tried to use the stitching algorithm, with

Type: Positions from File
Order: Defined by Image Metadata

And everything unchecked in the next screen. When I try to run the algorithm it gives the following warning

[WARN] Could not transform version 2012-06 OME-XML.

It returns a single image that has no Z-stack. It is blank, but this may be due to the location of the starting image. I was able to stitch images a few weeks ago, before I updated ImageJ. I checked on my previously-stitched images and it receives the same problem.

I tested the bioformats reader plugin, and it spat out the same warning. It did seem to recognize all the file names though, and with the appropriate options checked it saw all the right files.



Best regards,

Michael Pinkert

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