2021: A turning point for the advancement of reporting and reproducibility in microscopy metadata

Published: 2022-01-18

Amazing progress has been made in 2021 towards establishing community-approved guidelines and tools for improving reporting and reproducibility of microscopy metadata, as well as supporting FAIR microscopy data sharing and re-use. The December Issue of Nature Methods provides a “Focus” on Reporting and Reproducibility in Microscopy, bringing together a series of papers that provide guidelines and solutions for collecting and reporting microscopy metadata.

Image copyright: Thao Do, Allen Institute, Seattle, WA, USA

Together, these community-driven initiatives represent a true revolution in the microscopy world. The grass-roots momentum behind improving reporting and reproducibility of metadata is truly inspiring. We strongly encourage our community to check out the December issue of Nature Methods to learn more about the imaging communities, recommendations and tools that are changing the way we work. Congratulations to all involved in these fantastic community initiatives!

To learn more about these tools and initiatives, we spoke to some of the authors whose work is featured in the Nature Methods December issue.

Caterina Strambio-De Castillia on Micro Micro-Meta App:

Want to know more about how Micro-Meta App can help with microscopy metadata reporting and why it’s important to use it? We spoke to Caterina Strambio-De Castillia, part of Quarep-LiMi, and lead of the BINA Working Group on Quality Control and Management. You can watch the video below:

For more information, read the full paper: "Micro-Meta App: an interactive tool for collecting microscopy metadata based on community specifications"

Claire Brown on MethodsJ2:

How does MethodsJ2 help collect hardware and software metadata for publications? We spoke to Claire Brown to find out how imaging scientists and core facility staff can use this tool to automatically include metadata and add acknowledgements text to publications. Watch the video below:

For more information, read the full paper: "MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text"

Stefanie Weidtkamp-Peters and Susanne Kunis on MDEmic:

What is MDEmic and how does it help simplify complex metadata capture? Stefanie Weidtkamp-Peters and Susanne Kunis  explain how this tool will contribute to the evolution of FAIR data sharing in this short video below:

For more information, read the full paper: "MDEmic: a metadata annotation tool to facilitate management of FAIR image data in the bioimaging community"

Josh Moore on Next Generation File Formats (NGFFs):

The big data & cloud computing revolution is coming to the microscopy world. Are we ready? Josh Moore provides some insight on what file formats will help optimise image data for multiple use cases, including cloud computing, bringing the microscopy community one step closer to FAIR data exchange.

For more information, read the full paper: "OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies“"

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