[ome-devel] Proposal for 4D Nucleome Microscopy Metadata Guidelines based on the OME data model

[Joshua Moore (Staff)]

A week ago[1], Caterina kindly organized a (very early US-morning!) call for users and developers who had responded with interest to this proposal, including individuals from the 4D Nucleome Imaging Standards Working Group, German BioImaging, RIKEN, and the University of Dundee. A number of uses & benefits of the distinctive features she listed were discussed with the general consensus being that having a way to flexibly capture more metadata about image acquisition would support a large number of different groups, from vendors to bench scientists.

The primary issue raised, however, was the speed of the OME-XML schema release cycle as well as the necessary related code changes and database upgrades for developers and sysadmins. Norio presented his work on translating the OME-Model into RDF/OWL[2]. The “open world assumption” of RDF/OWL means that a schema update is not needed for someone to make new and interesting statements about an experiment.

With this type of extension mechanism, the community (i.e. *you*) should be able to propose terms and values that you would like to capture within OME-XML / OME-TIFF, while still having the guarantee that as the model evolves, we will keep your data up-to-date. Developers should be able to build flexible GUIs for parsing, displaying, and editing these values. Curators and standards bodies should be able to cooperate to manage this expanding vocabulary.

At the moment, Caterina, Norio, & Co. are investigating revising the proposal to make use of RDF & OWL. At the same time, the extension framework will need to be specified for allowing the import and export of extended metadata within the OME ecosystem.

Various parts of this work will soon start showing up in the ome-model repository[3], but we look forward to your thoughts -- from what elements other than <Instrument/> you would like to extended to what vocabularies you could imagine yourself using.

All the best,

~Josh


[1] https://docs.google.com/document/d/1mSd6BRF-82Usgsda9DNYUdmDMIR5cDoTzgiHLVXkcPU/edit#

[2] https://gitlab.com/openmicroscopy/incubator/ome-owl/issues/1#note_81349655

[3] https://github.com/ome/ome-model


On Thu, Apr 18, 2019 at 11:00 AM Jason Swedlow (Staff) <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>> wrote:
Hi Caterina and David-

Thanks much for this communication and in particular for all the work on this.  We first discussed this work with David at our 2018 Annual Users Meeting and it’s great to see the ideas mature into working specs.

Overall , we like the idea of a tiered approach to the spec—this provides the flexibility required for real-world scientific environments (we couldn’t help wondering if you are going to provide an award for the first validated “Virtuoso” implementation 😉).  In addition, it’s very clear that the original modelling OME published in 2005 (Goldberg et al, https://doi.org/10.1186/gb-2005-6-5-r47) has to be expanded to over other critical concepts around optical and illumination calibration that are required for transmitting and interpreting modern imaging modalities.  We have been considering how to evolve the Instrument model for some time—there are now many implementations of “light microscopy” in the just the biological sciences, so modelling becomes quite challenging. Regardless, intensity calibration seemed less important in 2005, it’s now quite critical. We appreciate the effort you’ve put into this and your willingness to open the discussion on how we capture the diversity and details required for modern quantitative light microscopy.

Just so everyone is up to date, the work from Caterina and David dovetails with work from Norio Kobayashi (https://gitlab.com/openmicroscopy/incubator/ome-owl/) and a few others.  If at all possible, we want to ensure all these efforts are at least are aware of each other and if possible, align.

We’re working towards a major OMERO release, so must focus on that over the next few weeks.  We’ll follow up with more detailed comments in the next couple of weeks.

Thanks again for the great work.

Cheers,

Jason



From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>> On Behalf Of Strambio, Caterina
Sent: 11 April 2019 22:48
To: ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
Subject: [ome-devel] Proposal for 4D Nucleome Microscopy Metadata Guidelines based on the OME data model

Dear All

the 4D Nucleome Imaging Standards Working Group would like to solicit feedback on proposed guidelines we are putting forwards for a metadata standard for describing:

1) MICROSCOPE HARDWARE Specifications
2) IMAGE ACQUISITION Settings
3) OPTICAL, FIELD, EXCITATION POWER and WAVELENGTH, and DETECTOR CALIBRATION Procedures

used to document imaging experiments and foster their reproducibility.

The guidelines incorporate and update the OME data model and aim at increasing data fidelity, easing future analysis and facilitating objective comparison of different imaging datasets and imaging experiments setups.

The proposed 4DN-OME guidelines have the following distinctive features:

1) Based on the premise that not all imaging experiments are “created equal” and that different reporting guidelines might be required depending upon the experimental intent, we propose a Tiered system of  guidelines that specify what kind of metadata is required for different kind of imaging experiments.

2) Attempt to transition the OME data model towards a clear set of community standards that could serve as a basis for an “Encode”-like standard for imaging.

3) Help to guide different stake holders, including manufacturers, experimental and computational biologists, peer reviewers, publishers and funding agencies in evaluating of the performance,  quality and uncertainty associated with specific microscope setups.

The current version of the metadata model and tier system description can be found on GitHub at the following address:

https://github.com/WU-BIMAC/MicroscopyMetadata4DNGuidelines

Please feel free to contact us for any question, concern, comment, (constructive) criticism.

Cheers

Caterina Strambio De Castillia and David Grunwald

The University of Dundee is a registered Scottish Charity, No: SC015096
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