[ome-users] bug opening tiled Zeiss 710 image?

[Melissa Linkert]

Hi Michael,

> We just uploaded a file to your server via ftp that will not open using Loci in ImageJ.  The error messages are below.  Help woith this would be appreciated.

Thank you for the bug report.

> Drag & drop file error:
> java.lang.NegativeArraySizeException
>                 at ij.io.ImageReader.read8bitImage(ImageReader.java:47)
>                 at ij.io.ImageReader.readPixels(ImageReader.java:768)
>                 at LSM_Reader.readStack(LSM_Reader.java:682)

This is a problem in the LSM_Reader plugin, not Bio-Formats.

> Open from Plugins menu with menu error:
> java.lang.NegativeArraySizeException
>                 at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:263)
>                 at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:308)
>                 at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:308)
>                 at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)

This is a result of there being more than 2 GB of pixel data in a single
plane (i.e. each plane is very, very large).  You will need to open
smaller tiles of the image by selecting the "Crop on import" option in
the "Bio-Formats Import Options" window.

Regards,
-Melissa


On Fri, Mar 01, 2013 at 07:53:40PM +0000, Cammer, Michael wrote:
> We just uploaded a file to your server via ftp that will not open using Loci in ImageJ.  The error messages are below.  Help woith this would be appreciated.
> 
> Thank you,
> 
> Michael
> 
> Drag & drop file error:
> java.lang.NegativeArraySizeException
>                 at ij.io.ImageReader.read8bitImage(ImageReader.java:47)
>                 at ij.io.ImageReader.readPixels(ImageReader.java:768)
>                 at LSM_Reader.readStack(LSM_Reader.java:682)
>                 at LSM_Reader.open(LSM_Reader.java:551)
>                 at LSM_Reader.open(LSM_Reader.java:139)
>                 at LSM_Reader.open(LSM_Reader.java:111)
>                 at LSM_Reader.run(LSM_Reader.java:95)
>                 at ij.IJ.runUserPlugIn(IJ.java:193)
>                 at ij.IJ.runPlugIn(IJ.java:160)
>                 at ij.IJ.runPlugIn(IJ.java:149)
>                 at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:272)
>                 at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:152)
>                 at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:236)
>                 at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
>                 at ij.IJ.runUserPlugIn(IJ.java:193)
>                 at ij.IJ.runPlugIn(IJ.java:160)
>                 at ij.IJ.runPlugIn(IJ.java:149)
>                 at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:434)
>                 at ij.io.Opener.openImage(Opener.java:306)
>                 at ij.io.Opener.openImage(Opener.java:329)
>                 at ij.io.Opener.open(Opener.java:142)
>                 at ij.io.Opener.openAndAddToRecent(Opener.java:242)
>                 at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
>                 at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
>                 at java.lang.Thread.run(Unknown Source)
> 
> Open from Plugins menu with menu error:
> java.lang.NegativeArraySizeException
>                 at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:263)
>                 at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:308)
>                 at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:308)
>                 at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
>                 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:114)
>                 at loci.plugins.in.Importer.readPixels(Importer.java:150)
>                 at loci.plugins.in.Importer.run(Importer.java:89)
>                 at loci.plugins.LociImporter.run(LociImporter.java:81)
>                 at ij.IJ.runUserPlugIn(IJ.java:193)
>                 at ij.IJ.runPlugIn(IJ.java:160)
>                 at ij.Executer.runCommand(Executer.java:127)
>                 at ij.Executer.run(Executer.java:64)
>                 at java.lang.Thread.run(Unknown Source)
> 
> 
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: (212) 263-3208  Cell: (914) 309-3270
> 

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