Open Microscopy Environment

Dear OME team,

thank you for developing Bioformats and for including msr files from the Imspector software. While it sometimes work, unfortunately many of my .msr files fail to open in Fiji.

When I drag a file on the Fiji window, the Import option window appears just fine but then I am getting the following "Exception":

(Fiji Is Just) ImageJ 1.48s; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 40MB of 18409MB (<1%)

java.lang.ArrayIndexOutOfBoundsException: 21
at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:193)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:479)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
at ij.io.Opener.openImage(Opener.java:311)
at ij.io.Opener.openImage(Opener.java:334)
at ij.io.Opener.open(Opener.java:144)
at ij.io.Opener.openAndAddToRecent(Opener.java:247)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:619)


Unfortunately, this does not give me any clue as to what the problem is.
I have just tried this with the Bioformats Plugin for ImageJ revision c0951f7, built 5 March 2014.

This particular file is 293 MBytes large and thus should not be a problem. It contains 6 color channels of a time series with 100 exposures, each exposure 500x500 pixels. But I also had other files I couldn't open.

It would be great if you could find a solution for this. I'd be more than happy to provide files or other information.

Best regards

Steffen

hello again,

adding to the above problem description, while I got the same error messages with a number of different files, with other files I get the following error, which seems to be different:

(Fiji Is Just) ImageJ 1.48s; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 28MB of 18409MB (<1%)

java.lang.NegativeArraySizeException
at loci.common.RandomAccessInputStream.readString(RandomAccessInputStream.java:401)
at loci.formats.in.ImspectorReader.initFile(ImspectorReader.java:187)
at loci.formats.FormatReader.setId(FormatReader.java:1319)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:479)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:141)
at loci.plugins.in.Importer.run(Importer.java:79)
at loci.plugins.LociImporter.run(LociImporter.java:81)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
at ij.io.Opener.openImage(Opener.java:311)
at ij.io.Opener.openImage(Opener.java:334)
at ij.io.Opener.open(Opener.java:144)
at ij.io.Opener.openAndAddToRecent(Opener.java:247)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:619)

The file in question is only 2.7 MB, 512 px squared in five channels (no z sections or time series).
With yet another file, the following comes up:
(Fiji Is Just) ImageJ 1.48s; Java 1.6.0_20 [64-bit]; Windows 7 6.1; 176MB of 18409MB (<1%)

java.lang.IllegalArgumentException: Array size too large: 2687014 x 1835051 x 2
at loci.common.DataTools.safeMultiply32(DataTools.java:858)
at loci.common.DataTools.allocate(DataTools.java:832)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:317)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:190)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:87)
at loci.plugins.util.ImageProcessorSource.getObject(ImageProcessorSource.java:74)
at loci.formats.cache.Cache.recache(Cache.java:212)
at loci.formats.cache.Cache.recache(Cache.java:232)
at loci.formats.cache.Cache.<init>(Cache.java:96)
at loci.plugins.util.BFVirtualStack.<init>(BFVirtualStack.java:123)
at loci.plugins.in.ImagePlusReader.createVirtualStack(ImagePlusReader.java:331)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:276)
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:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.IJ.runPlugIn(IJ.java:152)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
at ij.io.Opener.openImage(Opener.java:311)
at ij.io.Opener.openImage(Opener.java:334)
at ij.io.Opener.open(Opener.java:144)
at ij.io.Opener.openAndAddToRecent(Opener.java:247)
at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
at java.lang.Thread.run(Thread.java:619)


edit: I have now uploaded three files, one for each of the three error types, to
https://www.openmicroscopy.org/qa2/qa/upload/
Steffen

Thank you for reporting this problem, and for uploading sample files.

There is currently a ticket for this problem on our issue tracking system:

https://trac.openmicroscopy.org.uk/ome/ticket/12035

You have been CC'd, and so you will receive an automated notification each time the ticket is updated. If you prefer not to receive these notifications, please let us know. We currently anticipate having this fixed in time for the 5.0.1 release of Bio-Formats/OMERO.