Fig. 2: Light microscopy metadata are essential for the assessment, interpretation, reproducibility, comparison and reuse of the results of microscopy experiments.

a, A schematic representation of a typical bioimaging experiment and the image metadata that must be collected to ensure the quality, reproducibility and scientific value of the resulting pixel image data (blue box). Specifically, imaging experiments and the associated metadata can be subdivided as follows: (1) sample preparation documented by experimental and sample metadata; (2) image data acquisition documented by microscopy metadata; and (3) image analysis documented by analysis metadata. In turn, microscopy metadata (pink boxes) can be subdivided in two categories as indicated: (1) provenance metadata include information that documents microscope hardware specifications, image acquisition settings and image structure and (2) quality-control metadata include metrics that quantitatively assess the performance of the microscope and the quality of image data and are obtained through the execution of specifically designed optical, intensity and mechanical calibration procedures. b, In order to capture and store microscopy metadata, the 4DN-BINA-OME Specifications presented here take advantage of the structure of the OME Data Model^8,9, which serves as the de facto specification for the exchange of image data and metadata. Specifically, provenance metadata are stored into revised and extended versions of the <Instrument> and <Image> elements of the OME Data Model. On the other hand, quality-control metadata are stored using a newly designed Calibration and Performance extension of the same model.