Adequate record keeping is essential for most experiments as it is necessary in order to evaluate results, share data and allow experiments to be repeated. Keeping notes on microscopy experiments should be relatively unchallenging in this regard, as the microscope is a machine equipped with a limited number of known parts and settings.
Metadata automatically recorded by microscopes from different companies vary widely and pose a substantial challenge for microscope users to create a good faith record of their work. Similarly, the complexity and aim of experiments using microscopes varies leading to different reporting requirements from the simple description of a sample to the need to document the complexities of sub-diffraction resolution imaging in living cells and beyond.
In 2005 the Open Microscopy Environment (OME) initiative defined the OME data model "to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results." (verbatim from: Goldberg et al., 2005). The OME model forms the basis of the BioFormats library and is implemented in the OME-TIFF file format and in the OMERO image data repository.
Despite the this very successful efforts, there remains a substantial gap between the OME data model and its wide adoption by the wide bio-imaging community as a bona fide Microscopy Data and Metadata Standard, dictating the set of metadata descriptors to be recorded or published with imaging datasets.
Here we present Microscopy Metadata 4DN Guidelines (4DN-Micro-Meta), which is a tiered system of guidelines that was developed by the 4D Nucleome (4DN) initiative Imaging Standards Working Group for calibrating, and documenting microscopy experiments. In particular the proposal describes standards for:
- MICROSCOPE HARDWARE Specifications
- IMAGE ACQUISITION Settings
- OPTICAL, FIELD, EXCITATION POWER and WAVELENGTH, and DETECTOR CALIBRATION Procedures
In addition to extending the OME data model and maintaining full-compatibility with it, the main advance provided by the 4DN-Micro-Meta guidelines is to posit the subdivision of imaging experiments among a set of five Tiers representing increasing imaging and analytical complexity levels. As a consequence, these guidelines not only provide an OME-based comprehensive list of metadata key-value pairs that should be recorded, but also details which subset of the full list should be recorded depending on the specific Tier the experiment belongs to. In so doing the guidelines lie the foundation for the birth of a microscopy data standard that could serve the same purpose the Encode guidelines serve in the genomic community.
In order to foster the wide usability of the guidelines, the proposal aim at providing detailed explanations of why these values matter. Finally, in order to aide their adoption by software developers, the guidelines are expressed in the Extensible Markup Language (XML) Schema Definition (XSD) format that can be utilized to generate code for both traditional databases and other software utilizing the data model.
The proposed Microscopy Metadata guidelines are available as follows:
- An .xsd file providing the XML-schema for the proposed OME extension.
- A .graphml providing an rendering of the INSTRUMENT Specifications and IMAGE ACQUISITION Settings sections of the model using the Entity-Relationship (ER) formalism. In order to open the file you can use the yED application.
- A PDF version of the same ER schema.
- A .xsl worksheet providing a comprehensive list of metadata key-value pairs that should be recorded for each tier, which can be found here -->