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<p style="margin-top:0in;background:white"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">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.<o:p></o:p></span></p>
<p style="margin-top:0in;background:white"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">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<o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Type: Positions from File<br>
Order: Defined by Image Metadata<o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">And everything unchecked in the next screen. When I try to run the algorithm it gives the following warning<o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">[WARN] Could not transform version 2012-06 OME-XML.<o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">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.<o:p></o:p></span></p>
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<span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">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.<o:p></o:p></span></p>
<p style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222"><o:p> </o:p></span></p>
<p style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Best regards,<o:p></o:p></span></p>
<p style="background:white"><span style="font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#222222">Michael Pinkert<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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