[ome-users] zeiss lsm metadata

[Curtis Rueden]

Hi Chris,

We are using OME server and are importing LSM files into OME with
> loci-bioformats.  Maybe I have missed it, but I would like to have as much
> information from the lsm file as possible, i.e., the objective, filters,
> laser power, detector gain, etc. Right now we only get basic image
> information.
>

The metadata conversion within Bio-Formats is a work in progress. There are
a number of reasons why not everything may not be converted.

1) For instrument-related metadata, what is present in third party
acquisition formats such as Zeiss LSM is not a complete specification of the
instrument. The OME data model currently has a serious limitation in that it
does not allow the specification of partial information about many types of
objects. As such, Bio-Formats cannot represent the instrument and its
settings within the OME data model. We have plans to extend the
specification to allow for partial information somehow, but are still
hashing out the details. Once the model has been extended, it will be
possible for Bio-Formats to convert the metadata.

2) Once #1 is taken care of, Bio-Formats still needs to actually recognize
the LSM metadata to be converted to OME, and do so. We do our best to parse
everything from LSM in its original organization, but have probably missed
some fields for the OME conversion step. To address this problem, it would
be very helpful if you had a sample LSM with a list of fields you know are
present, and expect to see represented within OME.

It is also possible that Bio-Formats is converting some of the information
in question, and you just weren't looking in the right place. ;-)
Information about the instrument and other non-Image-specific metadata can
be found by clicking the "Image import" link in the top right box. You
should see a series of tables displaying all the metadata that Bio-Formats
pulled in to the OME system.

Is that possible right now, or would we need get that information from the
> file ourselves.
>

Assuming you check the "Image import" screen and the information is not
present, you would need to access the information some other way. You can
almost certainly use Bio-Formats to do so, by pulling the information out of
its metadata hashtable (which maintains a list of metadata key/value pairs
straight from the file, with no conversion to OME). As a quick test, you can
set up the Bio-Formats command line tools (see <
http://www.loci.wisc.edu/ome/formats.html>) and run from a console:

showinf myData.lsm -nopix

It should dump a whole bunch of information about the file, including all
the metadata it parsed in a big list. If you see what you are looking for,
then you are already most of the way there. If you are a *nix scripter, you
can grep out what you want, or if you are a Java programmer you can use the
Bio-Formats API's loci.formats.IFormatReader.getMetadataValue(String)
method.

You can also see what Bio-Formats is converting to the OME data model:

showinf myData.lsm -nopix -omexml

That will show you a block of OME-XML that represents all your metadata
(without pixels BinData). If you see the information you want in the regular
metadata table, but not within the OME-XML block, then it is a problem with
the OME conversion step as discussed above. Any comments on specific LSM
fields you have that are not converted, but should be, would be very
helpful.

HTH,
Curtis

On Mon, Mar 3, 2008 at 4:36 PM, Wood, Christopher <CJW at stowers-institute.org>
wrote:

> Hello,
>
> We are using OME server and are importing LSM files into OME with
> loci-bioformats.  Maybe I have missed it, but I would like to have as much
> information from the lsm file as possible, i.e., the objective, filters,
> laser power, detector gain, etc. Right now we only get basic image
> information.
>
> Is that possible right now, or would we need get that information from the
> file ourselves.
>
> Thanks
> Chris Wood
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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