[ome-users] Bio-Formats Exporter

[Roger Leigh]

On 10/04/2013 10:18, Mario Novkovic wrote:
> 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)

I can certainly reproduce this problem with the current version of
Bio-Formats.  There's an existing ticket open for BigTIFF (#6589), which
I've CCd you on.  I've also added some additional information to the
ticket along with a similar copy of the above stacktrace.
http://trac.openmicroscopy.org.uk/ome/ticket/6589

> 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.

Currently BigTIFF format has to be explicitly enabled when writing the
TIFF.  It's not enabled automatically when needed (which is what the
ticket above is about).  It does not appear possible to enable it in the
exporter UI.

> 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.

I'm unsure what's happening here.  I'll need a copy of the original LSM
and converted TIFF and details of how you did the concatenation in order
to try to reproduce this.  You can do this here:
http://qa.openmicroscopy.org.uk/qa/upload/


Thanks,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096