NDPI BioFormats Error

[nellypledge]

Hi guys, I hope all goes well.

Can I please ask if anybody is having troubles with their NDPI files when using the BioFormats plugin.  I get the option to select one of the images from the different sizes, and then after it takes while to scratch at the disk and grab a load of memory it gives the below error.

Any thoughts would be appreciated.
Thanks
Neil


(Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 2666MB of 6095MB (43%)
 
java.lang.ArrayIndexOutOfBoundsException
        at java.lang.System.arraycopy(Native Method)
        at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:213)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
        at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
        at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
        at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
        at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
        at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
        at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
        at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
        at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
        at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
        at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
        at loci.plugins.in.Importer.readPixels(Importer.java:149)
        at loci.plugins.in.Importer.run(Importer.java:86)
        at loci.plugins.LociImporter.run(LociImporter.java:78)
        at ij.IJ.runUserPlugIn(IJ.java:212)
        at ij.IJ.runPlugIn(IJ.java:176)
        at ij.Executer.runCommand(Executer.java:136)
        at ij.Executer.run(Executer.java:65)
        at java.lang.Thread.run(Thread.java:662)

[ctrueden]

Hi Neil,

That looks like a probable bug in Bio-Formats.

Best to report to the Bio-Formats team:
http://openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html

Regards,
Curtis

On Fri, Dec 18, 2015 at 9:23 AM, nellypledge <[hidden email]> wrote:

> Hi guys, I hope all goes well.
>
> Can I please ask if anybody is having troubles with their NDPI files when
> using the BioFormats plugin.  I get the option to select one of the images
> from the different sizes, and then after it takes while to scratch at the
> disk and grab a load of memory it gives the below error.
>
> Any thoughts would be appreciated.
> Thanks
> Neil
>
> /
> (Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 2666MB of 6095MB (43%)
>
> java.lang.ArrayIndexOutOfBoundsException
>         at java.lang.System.arraycopy(Native Method)
>         at
> loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:213)
>         at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
>         at
> loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
>         at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:349)
>         at
> loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
>         at
> loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
>         at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>         at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>         at
>
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
>         at
> loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
>         at
> loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
>         at
> loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
>         at
> loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
>         at
> loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
>         at
> loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
>         at loci.plugins.in.Importer.readPixels(Importer.java:149)
>         at loci.plugins.in.Importer.run(Importer.java:86)
>         at loci.plugins.LociImporter.run(LociImporter.java:78)
>         at ij.IJ.runUserPlugIn(IJ.java:212)
>         at ij.IJ.runPlugIn(IJ.java:176)
>         at ij.Executer.runCommand(Executer.java:136)
>         at ij.Executer.run(Executer.java:65)
>         at java.lang.Thread.run(Thread.java:662)/
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/NDPI-BioFormats-Error-tp5015254.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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