The OME Approach to a Common Interface23 Oct 2014
In the previous entry, we examined the challenges presented by supporting a wide variety of file formats that represent data outputs in the rapidly evolving and innovative field of imaging. We argued that defining a single metadata standard for scientific images is difficult at best and almost certainly impractical. Instead, we have attempted to provide a standardized interface to metadata and pixel data so that we provide a single point of access to many different image files. That point of access is Bio-Formats. In this entry, we discuss the technical foundation for Bio-Formats and how it provides a single metadata description that is both well-defined and extensible.
The OME Data Model
A common interface for accessing image data requires a known specification for that data. When OME started (around 2001) there weren’t any defined specifications available for biological imaging. The most advanced specification available was DICOM (Digital Imaging and Communications in Medicine) but this was very tightly linked to medical imaging and required, for example, a patient’s name to generate a valid file. In OME, we began defining the elements and components of biological imaging systems, illumination devices, objective lenses, detectors, etc. We referred to this specification as the OME Data Model (see Goldberg et al., 2005). For each element of an imaging system, it provides a definition, and, critically, a specific statement of the relationship of that element to others, e.g. numerical aperture is a property of an objective, which is part of an imaging instrument, and so on. The Model was repeatedly updated, improving the specification and matching it to newly developed imaging technologies. When Kevin Eliceiri and Curtis Rueden (LOCI) proposed what became Bio-Formats they realized that the OME Data Model was a useful tool – it was an open, supported and evolving specification into which they could convert any incoming data. Because it was expressed in XML, it could be used to define Bio-Formats’ metadata specifications.
Over the years, the OME Data Model has become the foundation of many different open data solutions. For example, OME–TIFF is an open data format that stores OME-XML metadata in the header of a standard TIFF file. This approach allows anyone to write an open file that includes metadata in a structure that most imaging software tools understand. At the very least, the binary pixel data is accessible, and the image metadata is accessible with little effort.
Bio-Formats uses the OME Data Model as its internal specification, and not only can it read metadata from proprietary files but it can also write OME-XML in an OME-TIFF file. Thus the OME Data Model, via Bio-Formats, is a specification for converting and also writing image data. Any software tool that uses Bio-Formats has access to all the formats Bio-Formats supports.
From its earliest versions, the OME Data Model supported a 5D image, including 3 spatial dimensions, time, and frequency (often referred to as “channel”). Any individual image should have all 5 dimensions but might have a value of 1 in any particular dimension. Thus a standard 2D image plane recorded on a monochrome detector is 5D, but the 3rd spatial dimension (by convention often referred to as “z”), time and channel values are all set to 1.
This representation has proven quite powerful, as it supports many of the most common imaging modalities. However with the appearance of new modalities, e.g. HCS, FLIM, LSFM, and OPT, the need to express even more dimensions has become more and more important. For screening, we extended the OME Data Model to include representations of screens, plates and wells. In our experience, we have seen 6, 7 and 8 dimensional images and anticipate that even higher dimensions will appear as imaging modalities evolve. For the moment, OME has settled on taking the core 5D image model and extending into larger dimensions using a modulo-based approach. This approach keeps the original 5D model intact but gives a simple way to support images with larger dimensionality and avoids writing new individual models for many rapidly evolving domains. This has been successfully used for FLIM and OPT imaging. In the longer term, we anticipate the need to expand OME’s Data Model to a much more extensible approach, and are working with several groups on this problem. In particular, we are following the ImgLib2 project’s work on building an N-dimensional image library.
A least common denominator
As noted in our first entry to this blog, conversion of original metadata into some kind of common model inherently risks data loss. There is a compromise between guaranteeing access to the data and ensuring complete fidelity. In practice, a common specification like the OME Data Model becomes a least common denominator where basic metadata can be reliably stored. For more application-specific metadata, the OME Data Model provides a variety of ways for extending the specification with custom annotations of various types. Full details are provided in the original paper describing how the model works (Goldberg et al., 2005) and in the Data Model specification pages. These custom annotations provide an enormous flexibility but also mean that custom versions of an OME-compliant specification can be generated. We consider this to be a reasonable compromise that allows common metadata to be stored and accessed by any application, while application-specific metadata can be stored and will be accessible to third parties if the appropriate specification is made available.
A frustratingly incomplete, always obsolete, amazingly effective solution
Using a common specification that cannot specify every advanced, cutting edge biological imaging system results in a solution that is always incomplete and very likely unable to support the latest innovations in biological imaging. Moreover, any updates made to the model to support new innovations may become obsolete within a few months as new innovations or updates are added. The OME Data Model also does not provide comprehensive support for all imaging modalities. For example, while fluorescence is well supported, including XML elements ‘Illumination’, ‘Filter Set’, and ‘Detector’, high-end transmitted light techniques such as Differential Interference Contrast are not well supported– there are no elements describing the shear of a Wollaston prism. Addressing such a deficit involves identifying partners who can help define critical data elements and their relationships. This is the approach we used to extend the OME Data Model to support HCS data– OME ScreenPlateWell. Feedback from TDS Dresden, Harvard’s ICCB and others was coalesced into an extension of the OME Data Model. In a rapidly innovating field like imaging, the OME Data Model will always be at least somewhat incomplete, as newly developed modalities mature and can then be included in the specification.
Regardless of these significant limitations, the approach adopted by OME has proven to be reasonably successful and effective. With a fairly rich description of metadata supporting the most popular imaging modalities in biological imaging, the OME Data Model has been adopted by several commercial companies and is used many thousands of times each day via both commercial and open source solutions making use of Bio-Formats. Bio-Formats thus presents a standard interface to scientific image data. This approach can be considered an indirect way of establishing an imaging metadata standard: while accepting all the limitations of a common metadata specification, OME’s approach has allowed many thousands of scientists worldwide easier access to their image data. In OME, we believe this is the pragmatic, user-focused way of developing an imaging standard.