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

[Curtis Rueden]

Hi Guenter,

I am just starting to implement OME-TIFF/XML storage of files obtained from
> a new microscope. I did not check yet if there is some overlap between TIFF
> tags and OME-TIFF (XML moiety) tags (OME scheme).
>
> Is there some overlap? If yes, is there a comparison list of general and of
> microscopy-related TIFF tags and OME-TIFF tags  (stored in the XML header)
> available?
>

Since TIFF is a very general image format, there is not much overlap aside
from core metadata fields:

TIFF ImageWidth = OME Pixels SizeX
TIFF ImageLength = OME Pixels SizeY
TIFF endianness signature (II / MM) = OME Pixels LittleEndian
TIFF SamplesPerPixel = OME Pixels SizeC (mostly)
TIFF number of IFDs = OME Pixels SizeT
TIFF BitsPerSample maps to OME Pixels PixelType
TIFF DateTime = OME Image CreationDate
TIFF XResolution = OME Pixels PhysicalSizeX
TIFF YResolution = OME Pixels PhysicalSizeY
TIFF ImageDescription = OME Image Description

You can see these expressed in code in the Bio-Formats base TIFF reader's
initMetadataStore() method:

https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/src/loci/formats/in/BaseTiffReader.java#L490

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.

For a full list of supported OME metadata fields in each file format, see
the big table on the Bio-Formats web site:
  http://www.loci.wisc.edu/ome/formats.html

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

-Curtis

On Wed, Mar 11, 2009 at 12:28 PM, Guenter Giese <
Guenter.Giese at mpimf-heidelberg.mpg.de> wrote:

> Dear list members,
>
> I am just starting to implement OME-TIFF/XML storage of files obtained from
> a new microscope. I did not check yet if there is some overlap between TIFF
> tags and OME-TIFF (XML moiety) tags (OME scheme).
>
> Is there some overlap? If yes, is there a comparison list of general and of
> microscopy-related TIFF tags and OME-TIFF tags  (stored in the XML header)
> available?
>
> 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
>
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