Projects

NFDI4BIOIMAGE is a consortium of the  Nationale Forschungsdateninfrastruktur (NFDI) e.V. in Germany. Our focus is on all steps of the life cycle of research data for microscopy and bioimage analysis.

Project goals:

• Standardization: data acquisition, metadata, file formats, (meta-)data models, ontologies, annotation tools, data provenance
• Storage concepts and open repositories: access and transfer requirements, capacity, long-term vs. short-term, distributed vs. centralized, data flows
• Data integration: combination with -omics data and other discipline-specific data types, integrative dataset queries, interoperability, interfaces
• Development of bioimage informatics tools: Bioimage analysis, automated AI-based bioimage analysis pipelines, workflow management and reproducibility, interoperability of analysis tools, statistics and modeling
• Training: training courses, workshops, online tools, open training formats
• Networking: international harmonization, knowledge exchange, connection to other NFDI consortia and non-NFDI RDM initiatives

Projects in the  CRC 1557 lead to complex, multidimensional data sets. They require storage, metadata annotation and complete documentation of the experimental conditions in order to meet the standards of the  FAIR principles.

In continuation of the image database  OMERO introduced in the  CRC 944, this INF project aims to establish data management for additional data formats. Furthermore, an electronic lab notebook (ELN) system will be established for the requirements of the CRC 1557 to enable the digitization of instrumental and experimental metadata in parallel to data generation in experiments and analyses.

Project goals:

• Implementation of a standard ELN and database system for the projects of the CRC 1557
• Data preparation for the transfer of data to public repositories and big data analyses
• Training in data handling and management as well as training of researchers

The group initiated by Susanne Kunis (CellNanOs, Osnabrück), Stefanie Weidtkamp-Peters (CAi, Düsseldorf) and Astrid Strauss (CECAD, Cologne) began its work in 2019 and focuses on the topic of research data management for microscopy ( RDM4mic overview (PDF)). The group currently has 76 members from various institutions.

Thematic focus:

• Strategies for image data management
• Requirements and resources for setting up a local image data repository
• Available software, tools, workflows and standards
• Dealing with change management

I3D:bio aims to facilitate the management of microscopy research data in Germany. The project is organized into three work packages (deployment, communication and training, technical infrastructure) to create and iteratively refine project deliverables based on community needs.

I3D:bio is based on the open source image data management platform  OMERO (OME remote objects). OMERO was developed by the  Open Microscopy Environment (OME) consortium.

Project goals:

• Support an easy installation of OMERO according to local needs
• Development of new solutions for editing metadata in OMERO
• Facilitate the storage of microscopy data in suitable public repositories
• Creation of a public, open database for quality control measurements (metrology database)