Setting up a data management infrastructure for bioimaging
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Susanne Kunis
,
Karen Bernhardt
Abstract
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.
Funding source: Deutsche Forschungsgemeinschaft
Award Identifier / Grant number: 180879236
Funding source: Deutsche Forschungsgemeinschaft
Award Identifier / Grant number: 180879236
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Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
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Research funding: This project was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - 180879236 SFB944/INF.
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Conflict of interest statement: The authors declare no conflicts of interest regarding this article.
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Artikel in diesem Heft
- Frontmatter
- Highlight: Physiology and Dynamics of Cellular Microcompartments
- Highlight: on the past and the future of cellular microcompartments
- Nuclear redox processes in land plant development and stress adaptation
- The readily retrievable pool of synaptic vesicles
- Loss of respiratory complex I subunit NDUFB10 affects complex I assembly and supercomplex formation
- Modulation of self-organizing circuits at deforming membranes by intracellular and extracellular factors
- Computational resolution in single molecule localization – impact of noise level and emitter density
- Setting up a data management infrastructure for bioimaging
- Molecular insights into endolysosomal microcompartment formation and maintenance
- The role of lysosomes in lipid homeostasis
- Membrane damage and repair: a thin line between life and death
- Neuronal stress granules as dynamic microcompartments: current concepts and open questions
- Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system
- Neprilysin 4: an essential peptidase with multifaceted physiological relevance
- Determinants of synergistic cell-cell interactions in bacteria
- Drosophila collagens in specialised extracellular matrices
Artikel in diesem Heft
- Frontmatter
- Highlight: Physiology and Dynamics of Cellular Microcompartments
- Highlight: on the past and the future of cellular microcompartments
- Nuclear redox processes in land plant development and stress adaptation
- The readily retrievable pool of synaptic vesicles
- Loss of respiratory complex I subunit NDUFB10 affects complex I assembly and supercomplex formation
- Modulation of self-organizing circuits at deforming membranes by intracellular and extracellular factors
- Computational resolution in single molecule localization – impact of noise level and emitter density
- Setting up a data management infrastructure for bioimaging
- Molecular insights into endolysosomal microcompartment formation and maintenance
- The role of lysosomes in lipid homeostasis
- Membrane damage and repair: a thin line between life and death
- Neuronal stress granules as dynamic microcompartments: current concepts and open questions
- Molecular determinants of protein half-life in chloroplasts with focus on the Clp protease system
- Neprilysin 4: an essential peptidase with multifaceted physiological relevance
- Determinants of synergistic cell-cell interactions in bacteria
- Drosophila collagens in specialised extracellular matrices
