[ome-users] bfconvert multi-series LSM file

[Niko Ehrenfeuchter]

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