[ome-users] problem importing large tiled & stitched CZI format from Zen Blue 2.3

[Cammer, Michael]

Last week we posted about a problem we were having opening large tiled filed from Zen Blue to the ImageJ mailing list (apologies for posting to the wrong listserv) and since then a new version of BioFormats was released.  We tested with ImageJ 1.52f47 with Java1.8 bundled with it and BioFormats 5.9.2 3 Sept.  The version of Zen that saved the CZI file is 2.3.69.01000 and it is saving CZI files in a different format than the previous version we had.  Specifically, it now saves multiple scaled versions of the image in the file.


The original files are 3 channels, 16 bits, stitched with "Fuse Tiles" checked.  Large stitched areas that  are less than 6 GB open fine.  Also, these were all taken as simple grids.


The file that does not open is 13 GB.  Also, it was taken using the convex hull tiling method, but the resulting file was stitched using "Fuse Tiles" which, in the previous version of Zen we had, created a single large image.  We do not know whether this has changed with the new version of Zen or if the problem we are having is simply a file size issue.


Regardless, we would greatly appreciate help with this and are happy to upload raw data (files that work and the one that doesn't work), screen snaps, etc.  The error log is pasted below the signature line.


Most of the images here are processed in ImageJ and BioFormats is essential to our work, so having this fixed would be wonderful.


Thank you!


Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

Michael.Cammer at med.nyu.edu<mailto:Michael.Cammer at med.nyu.edu>  http://nyulmc.org/micros  http://microscopynotes.com/

Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567




ImageJ 1.52f47; Java 1.8.0_112 [64-bit]; Windows 7 6.1; 164MB of 28000MB (<1%)

java.lang.NegativeArraySizeException

at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:259)

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.Executer.runCommand(Executer.java:137)

at ij.Executer.run(Executer.java:66)

at java.lang.Thread.run(Thread.java:745)




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