[ome-users] bfconvert multi-series LSM file

[Melissa Linkert]

Hi Niko,

> I'm trying to convert a multi-series xyzc LSM file to OME-TIFF.
> Using Bio-Formats via FiJi works for me by ticking the "Open all
> series" and "Concatenate series when compatible" boxes and finally
> exporting the data again.
> 
> So I tried to achieve the same using bfconvert, unfortunately I
> couldn't figure out how to specify the open-all-series and
> concatenate options. Is there a way to do this with bfconvert?

If you just need all of the series from the input file in a single
OME-TIFF, then you actually don't need to specify any options at all -
that's the default behavior.  So just this should work:

$ bfconvert input-file.lsm output-file.ome.tiff

Regards,
-Melissa

On Thu, Sep 13, 2012 at 10:32:53AM +0200, Niko Ehrenfeuchter wrote:
> Dear OME people,
> 
> I'm trying to convert a multi-series xyzc LSM file to OME-TIFF.
> Using Bio-Formats via FiJi works for me by ticking the "Open all
> series" and "Concatenate series when compatible" boxes and finally
> exporting the data again.
> 
> So I tried to achieve the same using bfconvert, unfortunately I
> couldn't figure out how to specify the open-all-series and
> concatenate options. Is there a way to do this with bfconvert?
> 
> Thanks a lot!
> Niko
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