Scanning Electron Microscopy (SEM) - Metadata extraction tool and schema mapper

The management of research data should follow the guidelines provided by the FAIR (Findable, Accessible, Interoperable and Reusable) principles. In particular, data should be described by rich metadata following community standards and schemas in order to be reused. Collecting a plurality of metadata attributes can be demanding for the user, if manually performed. Thus, this task should be automated whenever possible, and tools need to be developed to fulfil it.
As an example of application, we focused on the image data generated from Scanning Electron Microscopy (SEM) measurements in the TIFF file format. We developed a Python tool which extracts the metadata attributes enclosed in the file and maps them to a metadata schema we published in 2021, which reached a consensus within the user community of the projects we are involved in (NFFA-Europe Pilot, Joint Lab MDMC "Integrated Model and Data-driven Materials Characterization", NFDI-MatWerk).
The tool is provided with a web Graphical User Interface (GUI), which enables the users to access and use it without any prior programming knowledge. The final output is a downloadable JSON metadata document containing the extracted attributes. ... mehrThe document can be further enriched manually in order to provide the attributes of the schema which are not available in the TIFF file. This task can be performed by using an Electronic Laboratory Notebook (ELN), if JSON import is supported. To ease the user, we also offered a custom JavaScript interface to be employed as an alternative to ELNs to edit the metadata document according to the schema.
Once the metadata document has been filled in, it can be stored in a metadata repository and linked to the persistent identifier of the repository where the data it describes is deposited. The MetaStore provided by the Karlsruhe Institute of Technology-Steinbuch Centre for computing (KIT-SCC) is an example of such a metadata repository, offering schema registration and metadata validation.
The current version of the SEM extraction and mapping tool is limited to TIFF files generated by Zeiss microscopes. It would be extended to other vendors and third party acquisition softwares in future.