Error upon opening large images on FIJI Image J

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Error upon opening large images on FIJI Image J

Kline, David D.
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

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Re: Error upon opening large images on FIJI Image J

George Patterson
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
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html