At the Center for Advanced Imaging in the faculty of Mathematics and Natural Sciences of Heinrich Heine University Düsseldorf a post as a Research Associate (f/m/d) is to be occupied at the earliest possible date.
Research Associate (f/m/d) – OMERO Development and Deployment
Extending the functionality of OMERO.figure and developing further plugins for the OMERO ecosystem
Designing and implementing improved organization and documentation of Regions of Interest (ROIs)
Establishing low-threshold channels for user feedback, including triaging bug reports and feature requests and forwarding them to developers
Deployment and benchmarking of OMERO installations
Supporting partner institutions in installing OMERO and integrating it into their local infrastructure
Coordinating with local IT departments on security, access control, and data sharing
Automating server deployments for production and training use with Ansible and Docker
Developing a benchmarking framework: defining key performance indicators (e.g., upload rates, query response times, retrieval performance across formats and image sizes) and building an automated benchmarking toolkit
Analyzing benchmark results, deriving configuration recommendations, and sharing results across sites
Scalable imaging workflows and new image formats
Integrating NGFF (OME-Zarr) into institutional microscopy platforms, including NGFF-based tools such as bioformats2raw and raw2ometiff
Technical deployment of spatial-omics support in OMERO at the pilot sites in coordination with I3D:bio partners with iterative refinement based on feedback
Developing reusable components for Nextflow and Galaxy for staging data from OMERO, writing results back (e.g., segmentation masks), and annotating metadata
Training, documentation, and community work
Further developing training materials and documentation for administrators and data stewards
Contributing to workshops and training courses
Expanding the network of OMERO users and administrators within the GerBI-GMB community
Your Profile
Completed university degree (Master's or equivalent) in computer science, bioinformatics, a natural or life science with a strong IT focus, or a comparable field
Doctorate in a relevant field
Very good programming skills in Python and experience in web development (JavaScript, HTML/CSS)
Experience with collaborative software development (Git, GitHub, continuous integration)
Knowledge of Linux server administration and of working with Docker
Basic understanding of biological image data and its metadata
Ability to work independently on conceptual tasks and to coordinate with partner institutions, IT departments, and users without a technical background
Very good written and spoken English, German language skills
Willingness to travel to partner sites and workshops
Desirable:
Experience with OMERO (administration, use, or plugin development) and the OME data model
Knowledge of Ansible or comparable deployment automation tools
Experience with microscopy image formats, in particular OME-TIFF and NGFF (OME-Zarr), and with Bio-Formats
Experience with workflow systems (Nextflow, Galaxy) and compute clusters
Knowledge of image analysis and AI-assisted segmentation (e.g., napari, Cellpose)
Familiarity with research data management and the FAIR principles
Experience in delivering training and writing documentation
Our Offer
An interdisciplinary working environment at the interface of microscopy, life sciences, software development, and research data management
Close collaboration with the I3D:bio partner sites in Tübingen und Heidelberg, as well as with the GerBI-GMB community
The opportunity to contribute to OMERO, an open-source platform used by research institutions worldwide, and to engage with the international OME developer community
Work with direct, visible impact: your developments will be used by researchers at partner institutions and showcased on a persistent demonstrator instance
A high degree of independence and room to shape technical and conceptual solutions
Opportunities for professional development, including participation in conferences, workshops, and hackathons
The employment is initially limited for a period of 36 months. In accordance with § 2 Abs. 2 of the Act of Academic Fixed-Term Contract (Wissenschaftszeitvertragsgesetz - WissZeitVG), the position is limited to the exercise of a third-party funded project called Information Infrastructure for BioImage Data (I3D:bio), 2nd funding phase.
Our Benefits
Company pension grant
Good transport connection
Free parking
Flexitime
Working from home
Union rates
Part-time possible
Payment of capital-forming benefits
Company pension grant; Good transport connection; Free parking; Flexitime; Working from home; Union rates; Part-time possible; Payment of capital-forming benefits
About us
The Center for Advanced Imaging (CAi) at Heinrich Heine University Düsseldorf is a central microscopy core facility open to researchers from within and outside the university. It offers state-of-the-art light and electron microscopy, with a particular focus on super-resolution microscopy in living cells, correlative imaging methods and fluorescence imaging spectroscopy, together with image analysis and image data management support. The CAi team operates OMERO as the image data management platform for its users and is actively involved in the further development of OMERO, with close ties to the core open source community and OME. The I3D:bio project (Information Infrastructure for BioImage Data) aims to build a community-driven research data management infrastructure for bioimaging in Germany. In the second funding phase of the project we will closely collaborate with the University of Tübingen, the German Cancer Research Center (DKFZ) Heidelberg, and German BioImaging e.V. (GerBI-GMB).
Heinrich Heine University upholds the principle of "Excellence through Diversity". It has signed the "Diversity Charter" and successfully participated in the Stifterverband's audit "Shaping Diversity". It is certified as a family-friendly university and has set itself the goal of promoting diversity among its staff. Applications from people of all genders are expressly welcome. Applications from women will be given preferential consideration in accordance with the State Equal Opportunities Act. The application of severely disabled persons and persons with equivalent disabilities is also welcome. In order for a severe disability or equality to be taken into account, please provide evidence of this with suitable documents.
Contact
Prof. Dr. Stefanie Weidtkamp-Peters, Head of the Center for Advanced Imaging
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