Journal Article

DKFZ-2024-01866

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users.

Jannasch, A. ; Tulok, S. ; Okafornta, C. W. ; Kugel, T. ; Bortolomeazzi, M.DKFZ* ; Boissonnet, T. ; Schmidt, C.DKFZ* ; Vogelsang, A. ; Dittfeld, C. ; Tugtekin, S.-M. ; Matschke, K. ; Paliulis, L. ; Thomas, C. ; Lindemann, D. ; Fabig, G. ; Müller-Reichert, T.

2025
Wiley-Blackwell Oxford [u.a.]

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Please use a persistent id in citations: doi:10.1111/jmi.13360

Abstract: Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multidimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universität Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardised group-specific naming convention, metadata curation with tagging and Key-Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.

Keyword(s): FAIR principles ; OMERO ; bioimaging data ; imaging facility ; research data management (RDM)

Note: 2025 Jan;297(1):105-119

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Contributing Institute(s):

1. Single-cell Open Lab (W192)
2. Enabling Technology (W650)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2024

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DEAL Wiley ; Ebsco Academic Search ; Essential Science Indicators ; IF < 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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