Abstract: The explosion in the volume of biological imaging data challenges the available technologies for data interrogation and its intersection with related published bioinformatics data sets. Moreover, intersection of highly rich and complex datasets from different sources provided as flat csv files requires advanced informatics skills, which is time consuming and not accessible to all. Here, we provide a ?user manual? to our new paradigm for systematically filtering and analysing a dataset with more than 1300 microscopy data figures using Multi-Dimensional Viewer (MDV: https://mdv.molbiol.ox.ac.uk), a solution for interactive multimodal data visualisation and exploration. The primary data we use are derived from our published systematic analysis of 200 YFP gene traps reveals common discordance between mRNA and protein across the nervous system (https://doi.org/10.1083/jcb.202205129). This manual provides the raw image data together with the expert annotations of the mRNA and protein distribution as well as associated bioinformatics data. We provide an explanation, with specific examples, of how to use MDV to make the multiple data types interoperable and explore them together. We also provide the open-source python code (github link) used to annotate the figures, which could be adapted to any other kind of data annotation task

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