[ome-users] bfconvert multi-series LSM file

[Niko Ehrenfeuchter]

Hi Melissa,

On 13.09.2012 16:27, Melissa Linkert wrote:
> 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.)

sorry for the delay. Actually I checked again and in fact you're right - 
the sliders are there when opening the file in FiJi. I probably got this 
wrong because my initial reason for converting them was to use the 
OME-TIFF as input for the XuvTools stitcher - which currently doesn't 
read my LSM files properly, but those being converted via FiJi to 
OME-TIFF work fine.

So I opened the file resulting from the bfconvert with XuvTools and just 
saw one tile - whereas the OME-TIFF exported from FiJi correctly showed 
with the many different tiles. Yes, I'm aware this is an issue of 
XuvTools (unfortunately we don't have the time to fix it right now), but 
still this means the file generated by bfconvert differs somehow from 
the one exported by FiJi even though they look the same when you open 
them in FiJi. Don't get me wrong, that's not a complaint, just an 
observation that I thought is worth sharing :)

Cheers & thanks
Niko