Fig. 1: An overview of MoBIE.

a, MoBIE user interface. Image data, tables and views can be accessed from local and/or cloud storage. The image viewer (BigDataViewer) shows the image data and the interactive tables display features associated with segmented objects, image regions or spot data. Scatter plots visualize table columns; segmented objects can be rendered in 3D. Navigation and selection are synchronized between all four viewer elements. Here, we show gene clustering on top of the electron microscopy data from the Platynereis atlas³. The cells corresponding to a cluster are selected in each viewer element. b, MoBIE workflow. After data collection users can create a MoBIE project with the Fiji plugin or the python library. More data can be added continuously after the project is created. The MoBIE Fiji plugin can access this data either through the file system or object storage. Users can save any viewer configuration as a view and share the saved views with collaborators or use them to build interactive and reproducible figures. c, Example applications. MoBIE can represent data from many different modalities, including published data from correlative light-electron microscopy, high throughput screening microscopy⁴, light microscopy time series and spatial transcriptomics⁵. The panels from a and c are available as views within MoBIE and can be opened via the “Open Published MoBIE View” command in Fiji.