[ome-users] Import metadata from lif image

[Curtis Rueden]

Hi Mario,

The behavior you describe is both an incomplete implementation within
Bio-Formats, and a limitation of the OME data model itself. The Bio-Formats
metadata conversion to the OME data model is a work in progress, and we do
not yet convert the Objective information from Leica LIF files.

In addition, the OME data model often requires certain metadata fields to be
populated -- in the case of Objective, it requires Model, Manufacturer,
Correction, Immersion, LensNA, NominalMagnification,
CalibratedMagnification, and WorkingDistance. However, no third party format
actually stores all of that information, which means that it is currently
impossible for Bio-Formats to fully convert objective-related information
into an OME-compliant document. A solution to this problem is under
discussion, and we hope to have a solution by the end of March.

In the meantime, Bio-Formats does preserve all the metadata in its original
form when importing to an OME database. You can see it by clicking on the
"Image import" module execution link from the image detail page, scrolling
down and looking at the "OriginalMetadata" entries. Please let me know if
this does not work.

-Curtis

On Jan 31, 2008 8:10 AM, Mario Valle <mvalle at cscs.ch> wrote:

> If I understand correctly, the metadata are loaded from an imported image
> into OME.
>
> Take for example the 2007-11-12_L15_AF001.lif Leica image you find under
> ftp.cscs.ch/out/mvalle/
>
> For example the loci tool shoinf extracts from this image the following
> data about the
> instrument:
>
> AF_405ex_001 - DMI6000 Turret - Dummy Name (Obj.) - DUMMYNAME: Dummy5
> AF_405ex_001 - DMI6000 Turret - Numerical aperture (Obj.) -
> NumericalAperture: 1.4
> AF_405ex_001 - DMI6000 Turret - Objective - Objective: HCX PL APO lambda
> blue  63.0x1.40
> OIL  UV
> AF_405ex_001 - DMI6000 Turret - Order number (Obj.) - OrderNumber:
> 11506192
> AF_405ex_001 - DMI6000 Turret - Refraction index - RefractionIndex: 1.518
>
> But inside OME we were not able to find those values anywhere.
> Also executing a: select * from objectives;
> from inside the database reveals no metadata about objectives has been
> loaded from all our
> tests.
>
> Is this a bug or a limitation of OME?
> Thanks for clarifying!
>                                mario
>
>
> --
> Ing. Mario Valle
> Visualization Group                              |
> http://www.cscs.ch/~mvalle <http://www.cscs.ch/%7Emvalle>
> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)
> 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)
> 610.82.82
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>
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