[ome-users] error converting to .ids

[Melissa Linkert]

Hi Harri,

> we're trying to use bfconvert to convert a stack of images (OME-TIFs
> written by Leica Matrix Screener), and we run into an
> ArrayIndexOutOfBoundsException.
> 
> Here you can find a sample dataset and the exact output:
> https://wiki.helsinki.fi/display/LMUISA/Leica+HCS-A+OME-TIFs

Thank you for the report and corresponding example files.

The problem has to do with usage of the '-merge' flag.  We have a fix
under review here:

https://github.com/openmicroscopy/bioformats/pull/373

You're welcome to try building that and see if it helps; otherwise,
omitting the '-merge' flag should allow the files to convert in the
meantime (and you can always merge the channels after the fact when opening
the .ics/.ids files).

Regards,
-Melissa

On Fri, Feb 08, 2013 at 04:15:24PM +0200, Harri Jäälinoja wrote:
> Hi all,
> we're trying to use bfconvert to convert a stack of images (OME-TIFs
> written by Leica Matrix Screener), and we run into an
> ArrayIndexOutOfBoundsException.
> 
> Here you can find a sample dataset and the exact output:
> https://wiki.helsinki.fi/display/LMUISA/Leica+HCS-A+OME-TIFs
> 
> Thanks for your help in sorting this out.
> 
> Best,
> Harri
> -- 
> __________________________________________________
> Harri Jäälinoja
> Light Microscopy Unit
> Institute of Biotechnology, University of Helsinki
> http://www.biocenter.helsinki.fi/bi/lmu/
> +358 9 191 59370 fax +358 9 191 59366
> 
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