[ome-users] BioFormats bug : SlideBook Version 6

[Sebastien Besson (Staff)]

HI Alex,

thanks for your feedback. The issue below is very similar to the one reported in this ticket [1].

Since Bio-Formats 5.2.0, the support for modern version of Slidebook files is fully delegated
to the external native reader developed and maintained by 3i. 3i has also created an update site
to simplify their reader distribution for the Fiji users [2].
Could you try activating this site and see if it fixes the issue for your files?

Best,
Sebastien

[1] https://trac.openmicroscopy.org/ome/ticket/12919
[2] https://support.intelligent-imaging.com/techanswers.php#SLDinFiji

NB: the Java8 update site ships the latest release of Bio-Formats which should be 5.3.4 as of today.
I suspect an additional update site is enabled which would explains the 5.3.2-SNAPSHOT version you
reported. This should not prevent the enabling of the external Slidebook update site.

On 15 Mar 2017, at 16:36, Alex Herbert <a.herbert at sussex.ac.uk<mailto:a.herbert at sussex.ac.uk>> wrote:

Hi,

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.

The error is below:

(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%)

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
   at java.util.ArrayList.rangeCheck(ArrayList.java:653)
   at java.util.ArrayList.get(ArrayList.java:429)
   at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
   at loci.formats.FormatReader.setId(FormatReader.java:1399)
   at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
   at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
   at loci.plugins.in.Importer.showDialogs(Importer.java:140)
   at loci.plugins.in.Importer.run(Importer.java:76)
   at loci.plugins.LociImporter.run(LociImporter.java:78)
   at ij.IJ.runUserPlugIn(IJ.java:217)
   at ij.IJ.runPlugIn(IJ.java:181)
   at ij.Executer.runCommand(Executer.java:137)
   at ij.Executer.run(Executer.java:66)
   at java.lang.Thread.run(Thread.java:745)

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.

I have uploaded the file to your QA system. It has QA Bug Id: 17650.

Regards,

Alex

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