[ome-devel] Zeiss 710

Tue Oct 12 16:41:11 BST 2010

Hi Rubén & Melissa,

> 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.
>

This could conceivably happen with extremely small image planes. For
example, an 8x8 image at 8-bit resolution only occupies 64 bytes, but the
metadata would be at least ~180 bytes; e.g.:

<Image ID="Image:xxxx" Name="Image xxxx"><Pixels DimensionOrder="XYCZT"
ID="Pixels:xxxx" SizeC="1" SizeT="1" SizeX="8" SizeY="8" SizeZ="1"
Type="uint8"><TiffData/></Pixels></Image>

I can't think of any other case where the metadata size exceeds the pixel
size. Rubén, can you elaborate on what is going on? What are the dimensions
of your images? How many screens, plates, wells, and what is the image
resolution?

-Curtis

On Tue, Oct 12, 2010 at 10:23 AM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> 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
> > >>
> > >>
> > >>
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