[ome-devel] Zeiss 710

[Melissa Linkert]

Hi Rubén,

> That's good news. I am amazed by how the project evolves from simpler to more sophisticated needs. Actually bfconvert was designed to convert I guess, but I was trying to transform Leica Matrix Screener multiple OME.TIF to one-big OME.TIF and then enrich the metadata. 

If possible, I would recommend waiting for this ticket to be closed:

http://dev.loci.wisc.edu/trac/software/ticket/563

...at which point you can just do 'bfconvert leica-matrix-file.ome.tiff output.ome.tiff' without any additional magic.

> To give dimensionally to a dataset is my goal. Could one edit the metadata with EditTiffComment for that? Would a tool like EditTiffComment that modifies the metadata of many files accordingly be usefull? 

You could use one of our TIFF comment editing utilities:

 * java loci.formats.tools.TiffComment -edit /path/to/file
 * java loci.formats.tools.EditTiffG /path/to/file

But please be very, very cautious.  Again, the above ticket really is
the best solution, so if you can I would recommend either waiting for
that ticket to be closed or (if you have a lot of free time) helping to implement it.

Regards,
-Melissa

On Wed, Oct 06, 2010 at 02:46:50PM +0200, Rubén Muñoz wrote:
> Hi Melissa, 
> 
> On Oct 6, 2010, at 1:09 AM, Melissa Linkert wrote:
> 
> > Hi Rubén,
> > 
> >> Therefore tried this with bfconvert, even when appending to existing OME.TIF is not supported yet.
> > 
> > Appending to existing OME-TIFF files is, in theory, supported.  However,
> > the MetadataRetrieve object used by OMETiffWriter must be correctly set
> > up, which unfortunately will not happen by repeatedly calling
> > bfconvert.
> 
> That's good news. I am amazed by how the project evolves from simpler to more sophisticated needs. Actually bfconvert was designed to convert I guess, but I was trying to transform Leica Matrix Screener multiple OME.TIF to one-big OME.TIF and then enrich the metadata. 
> 
> > 
> >> However wIth the latest revision of bioformats 7034 when I output the bfconvert to the same file consecutively, the file is always getting bigger in size.
> > 
> > Yes, I see the same behavior.  It is ticketed here:
> > 
> > http://dev.loci.wisc.edu/trac/software/ticket/578
> > 
> > And, as usual, you have been CC'd.  I am a bit curious though: why run
> > bfconvert repeatedly with the same output file?  Are you trying to
> > convert multiple datasets to a single OME-TIFF file?  If I know the use
> > case, then maybe there is a work-around until the above ticket is closed.
> 
> To give dimensionally to a dataset is my goal. Could one edit the metadata with EditTiffComment for that? Would a tool like EditTiffComment that modifies the metadata of many files accordingly be usefull? 
> 
> Another topic, I guess you remember about the Zeiss ZEN software,  multiple positions in the same LSM file are now supported. 
> I recently found out that it also produces multi-file LSM datasets (without .mdb). I am getting one of these. I wonder how these files now about each other, but could be that they don't.
> 
> Best regards,
> 
> Rubén
> 
> 
>