[ome-devel] Zeiss 710

[Melissa Linkert]

Hi Rubén,

> Is there a way of excluding the image/pixel list in all the OME.TIF with bfconvert?

Perhaps I am misunderstanding the question, but are you asking about
excluding the Image and Pixels elements from the OME-XML metadata?  If
so, then I'm afraid that that is really not possible - both elements
provide critical metadata for reading the pixel data.

> For large multi-file sets the metadata is bigger than the pixel values and this prevents us to use OME.TIF in High Throughput Screens. 

That is a bit strange, but I have a few ideas as to what might be
happening there.  I imagine the OME-TIFF file is prohibitively large,
but if you could send just the OME-XML metadata that would be a huge
help.  You can extract the metadata like this:

 # if all of the Bio-Formats command-line tools are installed
 $ tiffcomment /path/to/file.ome.tiff

 # if 'tiffcomment' is not installed
 $ java loci.formats.tools.TiffComment /path/to/file.ome.tiff

> I'd like to help with the Leica Matrix Screener and ZEN importers as much as possible.

Thank you for the offer.  At the moment, there is not much that can be
done with the Zeiss LSM/Zen reader.  It will be at least a few weeks
before I can do anything with the Leica Matrix reader, but you are more
than welcome to start on a reader in the meantime if you like.  There
are three main pieces of work to be done for this reader:

 1) Make sure that all of the files are grouped together correctly, no
 matter which file in the dataset is selected by the user.

 2) Make sure that all of the pixel data and 'core' metadata is read
 correctly.

 3) Make sure that all of the OME-XML metadata from each of the
 constituent OME-TIFFs is parsed and unified.

My plan is to roughtly model the Leica Matrix reader after
loci.formats.in.MIASReader and loci.formats.in.InCellReader, with an
internal loci.formats.in.OMETiffReader doing much of the work for (2)
and (3).

Alternatively, you can wait a bit until I've had time to write an initial
version, and then help with the testing and polishing.

Regards,
-Melissa

On Mon, Oct 11, 2010 at 09:51:56PM +0200, Rubén Muñoz wrote:
> Hi Melissa,
> Is there a way of excluding the image/pixel list in all the OME.TIF with bfconvert?
> For large multi-file sets the metadata is bigger than the pixel values and this prevents us to use OME.TIF in High Throughput Screens. I'd like to help with the Leica Matrix Screener and ZEN importers as much as possible.
> Best regards,
> Rubén
> 
> On Oct 11, 2010, at 8:22 PM, Melissa Linkert <melissa at glencoesoftware.com> wrote:
> 
> > 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
> >> 
> >> 
> >>