Metadata and Performance Tracking for Fluorescent Microscopes - Towards a Shared Microscopy Ontology - The 4DN-OME ontology: an OME-OWL extension with emphasis on usability, minimum information guidelines, and quality control for super-resolution fluorescence microscopy

One of the central goals of the 4D Nucleome consists of mapping the localization of single genomic loci obtained by fluorescence microscopy onto global chromatin folding maps obtained by Chromatin Conformation Capture (CCC) experiments. A significant challenge with the reproducibility of microscopy data and with its integration with multi-modality ‘omics’ data lies in the large variability of what is recorded by different microscopes, the absence of quality control standards and the lack of shared guidelines. The Open Microscopy Environment (OME) model, is a specification for sharing biological imaging data which stores metadata part as OME-XML. The OME Consortium recently introduced the OME Core Ontology as a basis to facilitate the introduction of domain- specific extensions. In synergy with this effort, the 4DN IWG has proposed an extension of the OME model, which is tailored at enhancing the comparability of single-molecule super-resolution fluorescence microscopy experiments. Here we present the current status of development of the 4DN-OME ontology prototype. This semantic extension of the OME Core Ontology has the following features: 1) a tiered-system of reporting guidelines that scales required metadata content with experimental complexity. 2) A metadata model designed to better capture the technical complexity of high-resolution single- molecule localization and single-particle tracking experiments. 3) The introduction of standards for fluorescence microscope calibration and quantitative instrument performance assessment. Specifically, the 4DN-OME proposal extends the existing OME core-classes `Instrument’ and `Image’ to reflect the technological advances and the quality control requirements associated with single-molecule super- resolution microscopy. To this aim, the proposal puts forth several types of modifications, including the creation of additional classes and attributes to capture the complexity of microscope hardware commonly encountered in the field and their calibration requirements. This work is accompanied by other contributions describing the proposed 4DN standards for optical and performance calibration and the development of a software tool termed Micro-Meta App that facilitates the collection of microscopy metadata.