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Licensed Unlicensed Requires Authentication Published by De Gruyter March 1, 2023

Setting up a data management infrastructure for bioimaging

  • Susanne Kunis ORCID logo EMAIL logo , Karen Bernhardt and Michael Hensel
From the journal Biological Chemistry


While the FAIR (Findable, Accessible, Interoperable, and Re-usable) principles are well accepted in the scientific community, there are still many challenges in implementing them in the day-to-day scientific process. Data management of microscopy images poses special challenges due to the volume, variety, and many proprietary formats. In particular, appropriate metadata collection, a basic requirement for FAIR data, is a real challenge for scientists due to the technical and content-related aspects. Researchers benefit here from interdisciplinary research network with centralized data management. The typically multimodal structure requires generalized data management and the corresponding acquisition of metadata. Here we report on the establishment of an appropriate infrastructure for the research network by a Core Facility and the development and integration of a software tool MDEmic that allows easy and convenient processing of metadata of microscopy images while providing high flexibility in terms of customization of metadata sets. Since it is also in the interest of the core facility to apply standards regarding the scope and serialization formats to realize successful and sustainable data management for bioimaging, we report on our efforts within the community to define standards in metadata, interfaces, and to reduce the barriers of daily data management.

Corresponding author: Susanne Kunis, Department of Biology/Chemistry, Center of Cellular Nanoanalytics, Integrated Bioimaging Facility iBiOs, Osnabrück University, Babarastrasse 11, D-49076 Osnabrück, Germany, E-mail:

Funding source: Deutsche Forschungsgemeinschaft

Award Identifier / Grant number: 180879236

Funding source: Deutsche Forschungsgemeinschaft

Award Identifier / Grant number: 180879236

  1. Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

  2. Research funding: This project was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 180879236 SFB944/INF.

  3. Conflict of interest statement: The authors declare no conflicts of interest regarding this article.


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Received: 2022-09-30
Accepted: 2023-01-27
Published Online: 2023-03-01
Published in Print: 2023-04-25

© 2023 Walter de Gruyter GmbH, Berlin/Boston

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