[ome-users] Bio-Formats Exporter

[Mario Novkovic]

Dear Bio-Formats Team,

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 has 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. The same
error message appears when I use OME-TIFF files converted (in ZEN2011) from
.lsm files.

I also converted the .lsm files to normal TIFFs, concatenated them into one
file and tried to use the exporter. I got a different 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 for this image, 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.

So whichever file format I use, .lsm, normal TIFF or OME-TIFF microscopy
files, I can't seem to export them into one concatenated OME-TIFF file. Any
help with this would be greatly appreciated.

Kind regards,
Mario
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