I've looked through similar threads to try to resolve this issue, but nothing has really helped so I'm hoping that maybe someone could provide with me a bit of guidance. I've been trying to analyze images using the Color Deconvolution plug-in with ImageJ, but the images are .jp2 so I can't open them in my ImageJ. Instead I downloaded Fiji, which had the BioFormats plug-in, and tried to open the images in there. However, when I imported them using BioFormats, I received this error message:
(Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.6; 1480MB of 4966MB (29%)
java.lang.IllegalArgumentException: Dimensions (width=98688 height=46416) are too large
at java.awt.image.SampleModel.<init>(SampleModel.java:130)
at java.awt.image.ComponentSampleModel.<init>(ComponentSampleModel.java:146)
at java.awt.image.PixelInterleavedSampleModel.<init>(PixelInterleavedSampleModel.java:87)
at java.awt.image.PixelInterleavedSampleModel.createCompatibleSampleModel(PixelInterleavedSampleModel.java:144)
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KReadState.readAsRaster(J2KReadState.java:429)
at com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader.readRaster(J2KImageReader.java:556)
at loci.formats.services.JAIIIOServiceImpl.readRaster(JAIIIOServiceImpl.java:177)
at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:296)
at loci.formats.codec.JPEG2000Codec.decompress(JPEG2000Codec.java:267)
at loci.formats.in.JPEG2000Reader.openBytes(JPEG2000Reader.java:182)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:148)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:198)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
at loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:412)
at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:376)
at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:273)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:234)
at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:212)
at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:107)
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:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:243)
at ij.io.Opener.open(Opener.java:110)
at ij.io.Opener.open(Opener.java:73)
at ij.plugin.Commands.run(Commands.java:27)
at ij.IJ.runPlugIn(IJ.java:187)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)</i>
I know that .jp2 files are big (ranging from 100000 KB to 600000 KB), so I adjusted Fiji's maximum memory to be higher than 5000 MB (via Memory & Threads) but I'm still getting the same error message. For more context about the files, they were obtained from whole slide imaging using Aperio, so they can be opened by Aperio ImageScope but no other program is capable of opening them for preview.
I'm not certain if there's a bug in my program (and even if there were, I'm not quite sure how to report it), if there's an issue with the image file, or if I'm just using the program incorrectly.
Would anybody have advice about how to handle this situation?
Thanks in advance,
H.
