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NFDI4BIOIMAGE - An Initiative for a National Research Data Infrastructure for Microscopy Data

Schmidt, Christian ; Ferrando-May, Elisa

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Abstract

The National Research Data Infrastructure (NFDI) paves the way for community-driven, closely connected RDM measures in all areas of science. Microscopy is a versatile research technique widely used throughout the natural and biomedical sciences. Bioimaging data generated by modern microscopes ranging from conventional, confocal, and super-resolution light microscopes to high-resolution electron microscopes are of vital importance to gain insight into the microverse of cells, tissues, and materials. The acquired data is often stored only locally, not systematically annotated, and comparability is hampered by proprietary software and heterogeneous file formats. These issues demand better harmonized practices of image data management and extensive training and education of users. At the same time, bioimaging is an active research area in itself, leading to advancements in instrumentation and data acquisition speed that has not been achieved before. Microscopy has long changed from an observational qualitative method to a big-data quantitative approach used, e.g., in automated high-content and high-throughput screenings. Huge amounts of data from increased acquisition speed and increased information density per image file demand coordinated measures to handle and preserve data and require strategies for future-proof secure storage and re-usability. Integration with multimodal data sets and subject-specific (meta)data standards and formats are further issues to be addressed. Leveraging on our extensive experience within German Bioimaging – Society for Microscopy and Image Analysis in bringing together researchers, IT-service and –infrastructure providers, image analysts, and application specialists at core facilities in Germany, we aim to tackle these challenges. We intend to submit our proposal for a consortium for microcopy data within the NFDI in September 2021. Our network builds on experience and best practices in image data management, including the installation of OMERO-instances at local institutions as well as extending metadata annotation tools and usability standards. We have established and further seek collaborations with international activities in the field of bioimage analysis and data management, e.g., the Open Microscopy Environment (OME) community, the Network of European BioImage Analysts (NEUBIAS), the BioImage Archive (BIA), and more. In this fertile environment, we aim at becoming the national reference entity for FAIR management of microscopy data in Germany. RDM strategies need to remain adaptable, as future advancements in computing, storage solutions, machine learning methods, and more will demand novel measures so that today can comply with tomorrow without slowing innovation and progress. We aim to promote sustainable RDM throughout every step of the image data life cycle, engage in training and education, and closely connect with all interested user groups, consortia, and national as well as international RDM initiatives.

Item Type: Conference Item
Place of Publication: Heidelberg
Date Deposited: 29 Apr 2021 15:35
Date: 2021
Number of Pages: 1
Event Dates: 04.03. - 05.03.2021
Event Location: Heidelberg
Event Title: E-Science-Tage 2021: Share Your Research Data
Faculties / Institutes: Service facilities > Computing Centre
Subjects: 000 Generalities, Science
004 Data processing Computer science
Collection: E-Science Days 2021
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