Bio-formats export of hyperstack

[Glen MacDonald-2]

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
[phone]
[hidden email]

******************************************************************************
The box said "Requires WindowsXP or better", so I bought a Macintosh.
******************************************************************************

[ctrueden]

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
> [phone]
> [hidden email]
>
>
> ******************************************************************************
> The box said "Requires WindowsXP or better", so I bought a Macintosh.
>
> ******************************************************************************
>

[Glen MacDonald-2]

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
>> [phone]
>> [hidden email]
>>
>>
>> ******************************************************************************
>> The box said "Requires WindowsXP or better", so I bought a Macintosh.
>>
>> ******************************************************************************
>>