6.2 - List of standards and ontologies in mouse image data sets

The WP6 use case addresses interoperability of large-scale image data sets, which is required for reusing and analysing data sets generated by different sources.--- The following aspects of image data sets significantly influence their interoperability: 1. File formats 2. Accessibility of the data 3. Image annotation--- Image datasets within the mouse scientist community consist mainly of proprietary raw image formats provided by the proprietary software running the slide scanning machines. This high diversity contributes to the low interoperability of the data coming from different sources. Especially the international mouse phenotyping consortium (IMPC) provides harmonisation approaches regarding the data sources and file formats. Here, the most commonly used file formats are ndpi-files as raw format which can be converted into jpg or tiff files. These image will be made visible within a public accessible database in an annotated form.--- Finally, consistent annotation of mouse tissue image data sets is required for their interoperability. Although some ontologies for mouse anatomy and mouse pathology are available, none of them covers comprehensively the histological or the cytological phenotype. Therefore, image data sets are normally annotated using free text or a diverse set of ontologies. To bridge the gap between existing ontologies, WP6 partners are currently developing the cellular microscopy phenotype ontology (CMPO).