[ome-users] bfconvert multi-series LSM file

[Melissa Linkert]

Hi Niko,

> >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
> 
> thanks for the suggestion. That's what I tried already, but it
> results in one big TIFF where all the channels and z-slices are in
> consecutive order. At least this is what FiJi shows when I'm opening
> the resulting file, but I rather need to be able to distinguish the
> channels, Z slices and stacks (like the 5D-variant displayed by FiJi
> showing the sliders for C, Z and t).
> 
> Is there a way to do this? Or is bfconvert just behaving strangely
> on my data?

Hmm.  So there is just a single slider when you open the converted file
in Fiji?  I would expect that behavior if the "View stack with" option
was set to "Standard ImageJ" when the file is opened, or if the file was
converted like this:

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

instead of like this:

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

(Note that the .ome.tiff extension is very much required to get an
OME-TIFF.)

If neither of those things is the culprit, then could you please send
the output of:

$ bfconvert -version

Regards,
-Melissa

On Thu, Sep 13, 2012 at 04:16:00PM +0200, Niko Ehrenfeuchter wrote:
> Dear Melissa,
> 
> On 13.09.2012 15:54, Melissa Linkert wrote:
> >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
> 
> thanks for the suggestion. That's what I tried already, but it
> results in one big TIFF where all the channels and z-slices are in
> consecutive order. At least this is what FiJi shows when I'm opening
> the resulting file, but I rather need to be able to distinguish the
> channels, Z slices and stacks (like the 5D-variant displayed by FiJi
> showing the sliders for C, Z and t).
> 
> Is there a way to do this? Or is bfconvert just behaving strangely
> on my data?
> 
> Cheers,
> Niko
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