Posted by
Glen MacDonald-2 on
URL: http://imagej.273.s1.nabble.com/Bio-formats-export-of-hyperstack-tp3692658p3692660.html
Hi Curtis,
I was using the LOCI daily builds from yesterday and today (5081).
The trunk build (5086) works to export! thanks.
ImageJ 1.42.n 64-bit on unibody MacBookPro and Mac Pro,2009.
For what its worth, here is a sample error message from the daily
builds -
SamplesPerPixel #0 is null:
loci.formats.FormatException: SamplesPerPixel #0 is null
at
loci.formats.MetadataTools.verifyMinimumPopulated(MetadataTools.java:
334)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:104)
at loci.formats.out.TiffWriter.saveBytes(TiffWriter.java:183)
at loci.formats.out.OMETiffWriter.saveBytes(OMETiffWriter.java:161)
at loci.formats.FormatWriter.saveImage(FormatWriter.java:129)
at loci.formats.FormatWriter.saveImage(FormatWriter.java:94)
at loci.plugins.exporter.Exporter.run(exporter.java:340)
at loci.plugins.exporter.LociExporter.run(LociExporter.java:70)
at
ij
.plugin
.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:245)
at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:
102)
at ij.IJ.runUserPlugIn(IJ.java:179)
at ij.IJ.runPlugIn(IJ.java:143)
at ij.Executer.runCommand(Executer.java:121)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(thread.java:637)
Thanks again, I will stick with the trunk builds from now on.
Glen
On May 6, 2009, at 4:23 PM, Curtis Rueden wrote:
> Hi Glen,
>
> Thanks for the bug report. However, I am unable to duplicate your
> problem
> with the latest trunk build of loci_tools.jar (revision 5085, built
> 6 May
> 2009, with ImageJ 1.42l).
>
> I tested using your 4205basal106072.oif dataset, both with separated
> channels, as well as merged into a hyperstack in both Composite and
> Color
> display modes. I did run into some trouble when using virtual stacks
> -- we
> are looking into that -- but I'm guessing you were not using that
> feature?
>
> So, I'm hoping the bug was fixed in a recent build. Would you please
> verify
> that you are using r5085 or newer? If you still have problems,
> please let me
> know the exact series of steps you performed, and the exact error
> message.
>
> Thanks,
> Curtis
>
> On Wed, May 6, 2009 at 2:59 PM, Glen MacDonald <
[hidden email]
> >wrote:
>
>> Hello,
>> I've written a simple macro that provides the user a means to
>> choose the
>> order in which confocal channels are merged, then uses the Loci
>> plugin to
>> import an Olympus OIF file as separate channels and merge them into a
>> hyperstack. Attempting to use the Bio-Formats exporter to save the
>> 16-bit,
>> 3 channel Hyperstack as ICS or ome.tiff freezes with an error
>> message. this
>> also occurs if the hyperstack is converted to RGB and attempted to
>> export as
>> TIFF. However the RGB stack will save with 'File/Save as...'/ TIFF.
>>
>> the error message begins with
>> "SamplesPerPixel #0 is null:
>> loci.formats.FormatException: SamplesPerPixel #0 is null
>> ........."
>>
>> any suggestions on how to avoid this?
>>
>> Thanks,
>> Glen
>>
>>
>> Glen MacDonald
>> Core for Communication Research
>> Virginia Merrill Bloedel Hearing Research Center
>> Box 357923
>> University of Washington
>> Seattle, WA 98195-7923 USA
>> (206) 616-4156
>>
[hidden email]
>>
>>
>> ******************************************************************************
>> The box said "Requires WindowsXP or better", so I bought a Macintosh.
>>
>> ******************************************************************************
>>