Extended Data Fig. 1: Quality, rigor, reproducibility and sharing value for imaging experiments require the definition of community-driven Microscopy Metadata specifications and the adoption of easy-to-use metadata collection tools to facilitate the documentation and quality control tasks for experimental scientists.

The establishment of FAIR¹, community-driven Microscopy image data Standards implies parallel development on three interrelated fronts: 1) WHERE: Next-Generation File Formats (NGFF) where the ever-increasing scale and complexity of image data and metadata would be contained for exchange⁵⁵ (blue bubble). 2) WHAT: Community-driven specifications for what ‘data provenance’ information (microscope hardware specifications, image acquisition settings and image structure metadata) and quality control metrics are essential for rigor, reproducibility, and reuse and should therefore be captured in Microscopy Metadata (magenta bubble). 3) HOW: Shared rules for how the (ideally) automated capture, representation and storage of Microscopy Metadata should be implemented in practice (yellow bubble). Micro-Meta App, MethodsJ2 and OMERO.mde^{14,15,16,17,63} are three highly interoperable tools and complementary that function to: 1) train users on the importance of documentation and quality control; 2) facilitate metadata extraction, collection, and storage; 3) automatically write Methods sections; and 4) facilitate the development of experimental metadata specifications in connection with local core facilities. The different tools leverage different use- styles and preferences and are based on different software platforms in order to appeal to the broadest community including microscope builders, imaging scientists working in core facilities and experimental scientists. Thus: Micro-Meta App is used as a stand- alone app and can be integrated in third-party data portals^2,59,60,62. MethodsJ2 works as an ImageJ plugin. OMERO.mde works in the context of the OMERO image data repository. The concept is to bring the tools to software platforms people are already using and lower the bar to enable broad uptake.