Extended Data Fig. 4: The Micro-Meta App is designed to aid in the collection of 4DN-BINA-OME sanctioned Microscope Hardware Specifications metadata.

Micro-Meta App can be used as a stand-alone desktop application. Alternatively, it can be launched from a third-party portal such as the 4DN-Data Portal (Extended Data Fig. 10), where Microscope files can be stored as image-dataset attachments. In either situation: Α) After selecting the desired location for saving Microscope.JSON files for later use (not shown), before creating a new microscope file it is first necessary to select the desired Tier for the experiment at hand. Β) The Manage Instrument workflow in Micro-Meta App. The App can be used to create a structured Microscope.JSON file containing a description of the hardware components of a given microscopy Instrument based on the 4DN-BINA-OME ontology <Instrument> class model. C) A new microscope can be created totally from scratch by selecting either an Inverted or an Upright Microscope Stand. D) Alternatively, a previously saved Microscope.JSON file can be selected among those saved on an available repository and opened for further editing, such as in the depicted example. E) In this example, the “Magnification” drop- down menu is opened [1] and an “Objective” is dragged and snapped-in-place in the designated position [2] on the workspace. F) In this example, an additional “Objective” [3] is dragged onto the workspace and relevant metadata fields are entered using the designated metadata entry form [4]. G) Once all changes are entered, the microscope file can be saved to file or to the desired repository.