[ome-users] comparison list of TIFF tags and OME-TIFF (XML moiety) tags available?

Mon Mar 16 16:26:34 GMT 2009

Hi Guenter,

Sorry, I should have been more precise: My microscope is a home-built light
> sheet microscope (optically a type of wide field microscope) with different
> mechanical, electronic  and optical components, controlled by a PC. Some of
> the components obviously are addressed neither by TIFF tags nor by OME-XML
> scheme tags.
>
> Basically, I want to store as many microscope and recording parameters as
> possible in appropriate TIFF tags, and additional metadata (plus copies of
> the TIFF tags) in a format which is not proprietary but open and expandable
> (OME-TIFF / XML seems quite a good candidate).
>
> First I want to evaluate the metadata tags already addressed by TIFF as
> well as by the OME XML scheme (trying to avoid "private" data tags).
>

Since TIFF is not a microscopy format, I doubt many of the fields you need
will be available. However, most of the microscopy-specific fields you need
should be available in the OME schema. If not, we are enthusiastic about
expanding the specification to accommodate additional needs; just let us
know which specific fields you are considering. For extremely niche metadata
fields, you can use a feature of OME-XML called structured annotations to
represent the information in a semi-structured way.

Other metadata (many still to be defined) may then in addition be stored as
> (preliminary) XML tags (sometimes hopefully making it into a common, open
> scheme, or finding their equivalent in it).
>

Indeed, the goal is for OME-XML to be able to express the majority of
people's use cases for microscopy metadata.

Did I miss something, or is there a better way to proceed?

What my group did (LOCI) with our home-built systems is to add support for
OME-TIFF to our internal acquisition software. To accomplish this, we use
Bio-Formats (http://www.loci.wisc.edu/ome/formats.html) with Ice, to harness
the Bio-Formats metadata API, and embed OME-XML into our TIFFs using
libtiff. There is a brief, somewhat out of date overview at:

  http://www.loci.wisc.edu/ome/wiscscan.html

Did you also create your own acquisition package, or are you using an
off-the-shelf program?

Lastly, we are almost finished with a C++ wrapper that should make
Bio-Formats easier to use from within acquisition software.

>   https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader
>
> Thanks, this is exactly the stuff I was looking for. I will check in more
> detail tomorrow.
>

Let me know if you have any questions.

To caution you, the fields listed on that wiki are a subset of all available
OME-XML fields. They represent only those currently mapped by Bio-Formats
into our flat metadata API. However, it is quite easy for us to map in
additional fields from the XML schema into Bio-Formats. I can elaborate
further on this process if you are interested.

For a full list of all available OME metadata, see:

  https://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd

And for further documentation:
  https://openmicroscopy.org/Schemas/
  http://ome-xml.org/browser/Documentation
  http://ome-xml.org/

There are other diagrams as well but I don't have the URLs handy at the
moment.

I am not a programmer (others are in charge of this), but highly concerned
> about proper metadata storage handling, and retrieval of course. I have been
> struggling, as a microscopy facility manager, with the mess of proprietary
> (or simply non-existing) metadata since years. I hope an open standard (like
> OME-TIFF /  XML) will meet my demands.
>

Join the club. :-)  The OME data model exists for people in positions like
yours, so please let us know if it does not meet your needs!

Regards,
-Curtis

On Wed, Mar 11, 2009 at 4:21 PM, Guenter Giese <
Guenter.Giese at mpimf-heidelberg.mpg.de> wrote:

> Hi Curtis,
>
> thank you for your rapid answer! It addresses my questions almost
> perfectly.
>
> > I am not sure what you mean by "microscopy-related TIFF tags." There are
> many proprietary microscopy-specific variants of TIFF (e.g.: Flex, Olympus
> Fluoview, Molecular Dynamics GEL, Imaris, Improvision, Metamorph, Nikon,
> Image-Pro Sequence, SVS, Zeiss LSM) that contain extra information, but
> these are not OME-TIFFs. However, Bio-Formats parses each format's
> proprietary metadata and converts what it can into OME-XML.
>
>
> Sorry, I should have been more precise: My microscope is a home-built light
> sheet microscope (optically a type of wide field microscope) with different
> mechanical, electronic  and optical components, controlled by a PC. Some of
> the components obviously are addressed neither by TIFF tags nor by OME-XML
> scheme tags.
>
> Basically, I want to store as many microscope and recording parameters as
> possible in appropriate TIFF tags, and additional metadata (plus copies of
> the TIFF tags) in a format which is not proprietary but open and expandable
> (OME-TIFF / XML seems quite a good candidate).
>
> First I want to evaluate the metadata tags already addressed by TIFF as
> well as by the OME XML scheme (trying to avoid "private" data tags).
>
> Other metadata (many still to be defined) may then in addition be stored as
> (preliminary) XML tags (sometimes hopefully making it into a common, open
> scheme, or finding their equivalent in it).
>
>
> Did I miss something, or is there a better way to proceed?
>
>
> > For example, if you mouse over the entry for TIFF, at the bottom of the
> pop-up you will see a link to "Supported metadata fields":
> >   https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader
>
> Thanks, this is exactly the stuff I was looking for. I will check in more
> detail tomorrow.
>
>
> I am not a programmer (others are in charge of this), but highly concerned
> about proper metadata storage handling, and retrieval of course. I have been
> struggling, as a microscopy facility manager, with the mess of proprietary
> (or simply non-existing) metadata since years. I hope an open standard (like
> OME-TIFF /  XML) will meet my demands.
>
>
> Best,
>
> Guenter
>
> > ------------------------------------------
>> > Dr. Guenter Giese
>> > Light Microscopy Facility Manager
>> > Dept. of Biomedical Optics
>> > MPI fuer Medizinische Forschung Jahnstr. 29
>> > D-69120 Heidelberg, Germany
>> > Phone (+49) 6221-486-360 (Fax: -325)
>> > e-mail: guenter.giese at mpimf-heidelberg.mpg.de
>>
>> > _______________________________________________
>> > ome-users mailing list
>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>
>>
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
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>
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