Bug report for grid/collection stitching and version 2012-06 OME-XML

There appears to be a bug for the grid/collection stitching plugin from a recent update. 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


Perhaps you should file a bug report via Bio-Formats?

As @ctrueden said in this other thread here


Thank you, I will do so. I wasn’t sure if it applied or note, because the plugin is not bioformats. This does seem to include the bioformats reader though so maybe it is appropriate.

For the archives: Michael started a thread on ome-users about this issue.