[ome-users] zeiss lsm metadata

[Wood, Christopher]

Curtis,
Thanks for the info. I will try that out.

Chris
-----Original Message-----
From: ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] On Behalf Of Curtis Rueden
Sent: Wednesday, March 05, 2008 11:38 AM
To: Wood, Christopher
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] zeiss lsm metadata

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<mailto: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
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