Error upon opening large images on FIJI Image J
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Error upon opening large images on FIJI Image J
 
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All,
We are attempting to image large sections of a slide for neurite growth analysis. Images are acquired at 20X with Neurolucida, stitched together and saved as a jp2 file. However, when attempting to open in FIJI Image J we receive the following error. (Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 77MB of 12119MB (<1%) java.lang.IllegalArgumentException: Array size too large: 29128 x 55220 x 2 at loci.common.DataTools.safeMultiply32(DataTools.java:1286) at loci.common.DataTools.allocate(DataTools.java:1259) at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:158) at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233) 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:422) at loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:387) at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:282) at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:243) at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:221) at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:116) 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:228) at ij.IJ.runPlugIn(IJ.java:192) at ij.IJ.runPlugIn(IJ.java:181) at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499) at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72) at ij.IJ.runUserPlugIn(IJ.java:228) at ij.IJ.runPlugIn(IJ.java:192) at ij.IJ.runPlugIn(IJ.java:181) at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:516) at ij.io.Opener.openImage(Opener.java:370) at ij.io.Opener.openImage(Opener.java:242) at ij.io.Opener.open(Opener.java:109) at ij.io.Opener.openAndAddToRecent(Opener.java:291) at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192) at ij.plugin.DragAndDrop.run(DragAndDrop.java:159) at java.lang.Thread.run(Thread.java:745) Can anyone suggest another method or work-around to open these very large files in Image J? Or, is the image size a limitation of Image J? Thanks, Dave -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Error upon opening large images on FIJI Image J
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David,
While I am not really the best person to answer your question, I believe you are encountering the array size limit in Java. However, the link below has some suggestions to help get around your problem of opening your large file. http://imagej.1557.x6.nabble.com/Large-image-td5015380.html George On Tue, Jan 8, 2019 at 10:36 AM Kline, David D. <[hidden email]> wrote: > All, > > We are attempting to image large sections of a slide for neurite growth > analysis. Images are acquired at 20X with Neurolucida, stitched together > and saved as a jp2 file. However, when attempting to open in FIJI Image J > we receive the following error. > > (Fiji Is Just) ImageJ 2.0.0-rc-69/1.52i; Java 1.8.0_66 [64-bit]; Windows > 10 10.0; 77MB of 12119MB (<1%) > java.lang.IllegalArgumentException: Array size too large: 29128 x 55220 x 2 > at loci.common.DataTools.safeMultiply32(DataTools.java:1286) > at loci.common.DataTools.allocate(DataTools.java:1259) > at > loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:158) > at > loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334) > at > loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233) > 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:422) > at loci.plugins.in > .ImagePlusReader.readPlanes(ImagePlusReader.java:387) > at loci.plugins.in > .ImagePlusReader.readImage(ImagePlusReader.java:282) > at loci.plugins.in > .ImagePlusReader.readImages(ImagePlusReader.java:243) > at loci.plugins.in > .ImagePlusReader.readImages(ImagePlusReader.java:221) > at loci.plugins.in > .ImagePlusReader.openImagePlus(ImagePlusReader.java:116) > 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:228) > at ij.IJ.runPlugIn(IJ.java:192) > at ij.IJ.runPlugIn(IJ.java:181) > at > HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499) > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72) > at ij.IJ.runUserPlugIn(IJ.java:228) > at ij.IJ.runPlugIn(IJ.java:192) > at ij.IJ.runPlugIn(IJ.java:181) > at > ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:516) > at ij.io.Opener.openImage(Opener.java:370) > at ij.io.Opener.openImage(Opener.java:242) > at ij.io.Opener.open(Opener.java:109) > at ij.io.Opener.openAndAddToRecent(Opener.java:291) > at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:192) > at ij.plugin.DragAndDrop.run(DragAndDrop.java:159) > at java.lang.Thread.run(Thread.java:745) > > > Can anyone suggest another method or work-around to open these very large > files in Image J? Or, is the image size a limitation of Image J? > > Thanks, > > Dave > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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