I have a very large bigTiff file (~162GB uncompressed) created by exporting from Zeiss' Zen software. I had hoped to import this image into ImageJ (Fiji). However, when I try to import/open the image in Fiji (using the Bio-Formats plugin), I get the error message (see below): "Array size too large". I think that the Bio-Formats (Release 5.1.9, build date 14 April 2016, Revision c3065feb775a7ac0cc2cf6e35979331cca2418b) is installed and working since I can use the plugin to import cropped regions of the image, provided that the region is 24,000x18,000 pixels or smaller. Any thoughts as to whether my inability to import the bigTiff file is:
1) a limitation imposed by Bio-Formats? I think that the bigTiff specification theoretically can handle unrealistically large files, but there probably will be more realistic limits as to size of the file that the software can handle. Does Bio-Formats have its own cut-off size for the bigTiff files it can handle?
2) a limitation with my implementation of Fiji? The computer has 32GB RAM, of which Fiji can use up to ~23.7GB (24,473MB), so Fiji/Bio-Formats probably would need to use the hard-drive as virtual RAM to import the image. Is this the problem, or can Fiji/Bio-Format spool to the hard-drive?
3) some other problem with my installation of Fiji or the Bio-Source plugin? I just loaded Fiji onto a new computer and I haven't played with bigTiff files before, so I could have done something wrong/something could have gotten corrupted during installation.
As an aside, if I try to import a cropped region with dimensions of 32,000x24,000 pixels or 40,000x30,000 pixels, Fiji displays an image but it is corrupted. If I try to import a cropped region from the bigTiff file of 80,000x60,000 pixels, I get the same error message as if I try to import or open the entire bigTiff file.
The error message that we get when we try to open the bigTiff file is:
(Fiji Is Just) ImageJ 2.0.0-rc-47/1.50i; Java 1.8.0_66 [64-bit]; Windows 7 6.1; 66MB of 24473MB (<1%)
java.lang.IllegalArgumentException: Array size too large: 331197 x 174340 x 1
at loci.common.DataTools.safeMultiply32(DataTools.java:850)
at loci.common.DataTools.allocate(DataTools.java:824)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:155)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
at loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:83)
at loci.plugins.util.ImageProcessorSource.getObject(ImageProcessorSource.java:72)
at loci.formats.cache.Cache.recache(Cache.java:204)
at loci.formats.cache.Cache.recache(Cache.java:224)
at loci.formats.cache.Cache.<init>(Cache.java:88)
at loci.plugins.util.BFVirtualStack.<init>(BFVirtualStack.java:126)
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:111)
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:216)
at ij.IJ.runPlugIn(IJ.java:180)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)
Thanks for your help & ideas!
- - Jim
