OME Compliant Specification

The full text is available at:

http://jcb.rupress.org/content/189/5/777

The article represents OME's position on the continued explosion of file formats in biological imaging. As we move towards more complex data, greater opportunities for data sharing and collaboration, and rapidly developing image repositories, we strongly contend that the current situation must evolve. New file formats should not be created with every new software release. At the very least, the option of writing data to open, standardized file formats must be supported in all software, whether open or proprietary. We understand that exceptional cases exists where specialized image data or metadata requires proprietary, custom formats. However, our experience with OME-XML and Bio-Formats suggests that the great majority of metadata can be supported in open data formats. For this reason, we believe that the option of writing image data to an open file format that includes support for image acquisition metadata should be mandatory in all imaging software.

Our article contains a number of recommendations for driving use of standardized file formats. Most importantly, we believe that those who decide on which platforms to invest in should use their purchasing power to demand support for open file formats. Realistically, this is the only way these file formats will be universally used and supported.

In this article, we have announced a new spec, the OME Compliant Specification. This simply uses standard OME-XML, and requires that all components of the Image Element are filled in. We see this as a first step towards a more complete set of metadata for imaging. The documentation for the OME Compliant Specification is at:

http://www.ome-xml.org/wiki/CompliantSpecification

A key point is that an 'OME Compliant' file is as complete as possible, but only contains metadata relevant to a specific imaging experiment. The expectation is not that every field is filled out regardless of the experiment, but that all fields that are relevant to an experiment are completed. As an example, PockelCellSetting would not be used in most wide-field microscopy experiments, but would be mandatory for many multi-photon imaging experiments. The goal of that 'best-effort' should be to document an experiment as completely as possible, so another person could, with the same sample and microscope, reproduce the data recorded in the file.

OME's own file formats, OME-XML and OME-TIFF are well exercised and supported by a number of commercial vendors (http://www.openmicroscopy.org/site/support/about/partners). We continue to work to develop and support these formats, and welcome any and all feedback on their design, use, and documentation. However, we recognize that OME-XML and OME-TIFF do not fulfill all requirements for all imaging experiments. Many others (ICS, DICOM, NifTI) are available and will be more or less appropriate, depending on a specific experiment. Individual scientists should decide which of these formats must be supported, and which they will use. The critical point is that image data and metadata are complete and openly available for viewing and analysis.

We appreciate any and all feedback on this issue.

As always, thanks for your support.