Re: Bio-formats export of hyperstack

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/Bio-formats-export-of-hyperstack-tp3692658p3692659.html

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]
>
>
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