[ome-devel] Slidebook sld file open error in Fiji

[Anthony, Neil]

Hi Sebastien, thanks for the speedy reply.

I got it to open up the files in the end.  It turns out that it's super slow, taking around 10 mins to 7.4GB.  I've contacted 3i to request some speed ups.


Thanks

Neil



________________________________
From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of Sebastien Besson (Staff) <s.besson at dundee.ac.uk>
Sent: Friday, February 9, 2018 12:06:51 PM
To: devel OME
Subject: Re: [ome-devel] Slidebook sld file open error in Fiji

Hi Neil,

for recent SlideBook files, a native reader is developed and maintained
by 3i [1] which is recognized by Bio-Formats.
In Fiji, 3i also maintains a dedicated update site that you might want to
activate in order to open the file. See the 3i support page for more information [2].

Best,
Sebastien


[1] http://docs.openmicroscopy.org/bio-formats/5.7.3/formats/3i-slidebook.html
[2] https://www.intelligent-imaging.com/technical-answers

On 9 Feb 2018, at 16:15, Anthony, Neil <nantho2 at emory.edu<mailto:nantho2 at emory.edu>> wrote:

Hi all, I hope the data treats you well.

I can't seem to get my slidebook file open with BF in Fiji.  I get the below error.  I've added Bioformats to my update site list and made sure all is up to date.  I'll also post this to the ImageJ list too, in case I have the wrong direction.

Here is the sld file for reference:
https://www.amazon.com/clouddrive/share/WBCXFTxSfyR4w2087RexdSYa8RJ8Eteg0S8q1lWfH3a

Any pointers are much appreciated.  Please let me know if you need anything further from me to figure things out.

Thanks
Neil

(Fiji Is Just) ImageJ 2.0.0-rc-65/1.51s; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 263MB of 392934MB (<1%)

java.lang.ArrayIndexOutOfBoundsException: 0
    at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:558)
    at loci.formats.FormatReader.setId(FormatReader.java:1397)
    at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:499)
    at loci.plugins.in.ImportProcess.execute(ImportProcess.java:142)
    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:221)
    at ij.IJ.runPlugIn(IJ.java:185)
    at ij.Executer.runCommand(Executer.java:137)
    at ij.Executer.run(Executer.java:66)
    at java.lang.Thread.run(Thread.java:745)



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