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HI Alex,
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<div class="">thanks for your feedback. The issue below is very similar to the one reported in this ticket [1].</div>
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<div class="">Since Bio-Formats 5.2.0, the support for modern version of Slidebook files is fully delegated</div>
<div class="">to the external native reader developed and maintained by 3i. 3i has also created an update site</div>
<div class="">to simplify their reader distribution for the Fiji users [2].</div>
<div class="">Could you try activating this site and see if it fixes the issue for your files?</div>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://trac.openmicroscopy.org/ome/ticket/12919" class="">https://trac.openmicroscopy.org/ome/ticket/12919</a></div>
<div class="">[2] <a href="https://support.intelligent-imaging.com/techanswers.php#SLDinFiji" class="">https://support.intelligent-imaging.com/techanswers.php#SLDinFiji</a> </div>
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<div class="">NB: the Java8 update site ships the latest release of Bio-Formats which should be 5.3.4 as of today.</div>
<div class="">I suspect an additional update site is enabled which would explains the 5.3.2-SNAPSHOT version you</div>
<div class="">reported. This should not prevent the enabling of the external Slidebook update site.</div>
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<blockquote type="cite" class="">
<div class="">On 15 Mar 2017, at 16:36, Alex Herbert <<a href="mailto:a.herbert@sussex.ac.uk" class="">a.herbert@sussex.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi,<br class="">
<br class="">
I have a bug when trying to open a Slidebook file from version 6 of their software. I have run within Fiji and updated BioFormats; the BioFormats version is 5.3.2-SNAPSHOT.<br class="">
<br class="">
The error is below:<br class="">
<br class="">
(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51j; Java 1.8.0_121 [64-bit]; Linux 4.4.0-66-generic; 91MB of 19341MB (<1%)<br class="">
<br class="">
java.lang.IndexOutOfBoundsException: Index: 0, Size: 0<br class="">
at java.util.ArrayList.rangeCheck(ArrayList.java:653)<br class="">
at java.util.ArrayList.get(ArrayList.java:429)<br class="">
at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)<br class="">
at loci.formats.FormatReader.setId(FormatReader.java:1399)<br class="">
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)<br class="">
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)<br class="">
at loci.plugins.in.Importer.showDialogs(Importer.java:140)<br class="">
at loci.plugins.in.Importer.run(Importer.java:76)<br class="">
at loci.plugins.LociImporter.run(LociImporter.java:78)<br class="">
at ij.IJ.runUserPlugIn(IJ.java:217)<br class="">
at ij.IJ.runPlugIn(IJ.java:181)<br class="">
at ij.Executer.runCommand(Executer.java:137)<br class="">
at ij.Executer.run(Executer.java:66)<br class="">
at java.lang.Thread.run(Thread.java:745)<br class="">
<br class="">
The original image is 145Mb. When exported from Slidebook as OME-TIFF it contains multiple images of 3 channels with 10 z-slices and 1 timepoint. Frames are 512x512 pixels.<br class="">
<br class="">
I have uploaded the file to your QA system. It has QA Bug Id: 17650.<br class="">
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Regards,<br class="">
<br class="">
Alex<br class="">
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