[ome-users] Fwd: ImageJ LOCI Bio-Formats Exporter

[Curtis Rueden]

---------- Forwarded message ----------
From: Mario Novkovic <novkovic.mario at gmail.com>
Date: Tue, Apr 9, 2013 at 9:14 AM
Subject: ImageJ LOCI Bio-Formats Exporter

I have a problem using the Bio-Formats Exporter in ImageJ.

When I load several dozen .lsm files and concatenate them in ImageJ, I try
to export this concatenated image using the Bio-Formats Exporter. I get the
following error message:
loci.formats.FormatException: File is too large; call setBigTiff(true)
        at loci.formats.out.TiffWriter.**prepareToWriteImage(**
TiffWriter.java:294)
        at loci.formats.out.TiffWriter.**saveBytes(TiffWriter.java:184)
        at loci.formats.out.**OMETiffWriter.saveBytes(**
OMETiffWriter.java:201)
        at loci.formats.out.**OMETiffWriter.saveBytes(**
OMETiffWriter.java:187)
        at loci.formats.FormatWriter.**saveBytes(FormatWriter.java:**136)
        at loci.plugins.out.Exporter.run(**Exporter.java:571)
        at loci.plugins.LociExporter.run(**LociExporter.java:77)
        at ij.plugin.filter.**PlugInFilterRunner.**processOneImage(**
PlugInFilterRunner.java:256)
        at ij.plugin.filter.**PlugInFilterRunner.<init>(**
PlugInFilterRunner.java:105)
        at ij.IJ.runUserPlugIn(IJ.java:**187)
        at ij.IJ.runPlugIn(IJ.java:152)
        at ij.Executer.runCommand(**Executer.java:127)
        at ij.Executer.run(Executer.java:**64)
        at java.lang.Thread.run(Thread.**java:619)

This is because the concatenated image reaches a file size greater than 4
GB. Isn't the exporter supposed to set the bigTIFF format in case this
happens? It does export the image in the end, but not the whole image, only
the stacks up to 4 GB size. So I am missing the rest of the stacks.

When I try to do this with a multi-TIFF image created from the .lsm files,
I get another error message:
java.lang.**IllegalArgumentException: ZCT size vs image count mismatch
(sizeZ=169, sizeC=3, sizeT=1, total=169)
        at loci.formats.FormatTools.**getZCTCoords(FormatTools.java:**424)
        at loci.plugins.out.Exporter.run(**Exporter.java:544)
        at loci.plugins.LociExporter.run(**LociExporter.java:77)
        at ij.plugin.filter.**PlugInFilterRunner.**processOneImage(**
PlugInFilterRunner.java:256)
        at ij.plugin.filter.**PlugInFilterRunner.<init>(**
PlugInFilterRunner.java:105)
        at ij.IJ.runUserPlugIn(IJ.java:**187)
        at ij.IJ.runPlugIn(IJ.java:152)
        at ij.Executer.runCommand(**Executer.java:127)
        at ij.Executer.run(Executer.java:**64)
        at java.lang.Thread.run(Thread.**java:619)

When I open Image/Properties in ImageJ, it clearly states that number of Z
is 169, time series is 1 and number of channels is 1. So I do not know why
is the exporter reading this information wrongly.

Overall, what I want to do is export the large microscopy stacks image
(over 4 GB) into OME-TIFF format so I can load it into Imaris software.

Kind regards
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