[ome-users] Bio-Formats Exporter

[Roger Leigh]

On 10/04/2013 10:18, Mario Novkovic wrote:
  information wrongly.
>
> So whichever file format I use, .lsm, normal TIFF or OME-TIFF microscopy
> files, I can't seem to export them into one concatenated OME-TIFF file.
> Any help with this would be greatly appreciated.

As a workaround, you can do this outside of FiJi using the Bio-Formats
"bfconvert" command-line tool.

As an example, I ran
   bfconvert -bigtiff -stitch tmp_Z0.ome.tiff tmp_Z1.ome.tiff big.ome.tiff

and this concatenated two files with x/y/z/c = 1024/1024/828/2
to give a file with 1024/1024/1656/2 (~7GB).  You can do this directly
with your original LSM files so long as the dimensions are compatible,
and you can stitch different dimensions using different suffixes; here
I've just used Z.  You'll get a "big" OME TIFF as the result, which you
can then load into ImageJ using the LOCI importer.


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096