Research Associate (f/m/d) – OMERO Development and Deployment

Heinrich-Heine-Universität Düsseldorf; Düsseldorf; On-site; EUR 55,000 - 75,000; Full time

Benefits offered by this job

Interdisciplinary environment

Collaboration with I3D:bio partners

Open-source OMERO community

Impactful research deployments

Independent project shaping

Professional development & conferences

Job summary

The Center for Advanced Imaging at Heinrich Heine University Düsseldorf invites applications for a Research Associate (f/m/d) in OMERO development and deployment. You will drive user-focused plugin development, extend OMERO.figure, and enhance ROI organization within a collaborative environment.

Ideal candidates hold a Master’s or Doctorate in IT-focused sciences, possess strong Python and web skills, Docker/Linux experience, and good English/German.

Qualifications

• Master's degree (or equivalent) in computer science, bioinformatics, a natural/life science with IT focus, or related field.
• Doctorate in a relevant field.
• Strong Python programming skills; web development experience (JavaScript, HTML/CSS).
• Experience with collaborative software development (Git, GitHub, CI).
• Linux server administration knowledge; Docker experience.
• Basic understanding of biological image data and metadata.
• Ability to work independently and coordinate with partners and non-technical stakeholders.
• Excellent English and German language skills.

Responsibilities

• Develop OMERO plugins driven by user needs.
• Extend OMERO.figure functionality and build plugins for OMERO ecosystem.
• Improve organization and documentation of Regions of Interest (ROIs).
• Deploy and benchmark OMERO installations; automate server deployments with Ansible and Docker.
• Support partner institutions in OMERO deployment and integration.
• Coordinate with local IT for security and access control.
• Develop benchmarking framework and KPI metrics; build automation tools.
• Integrate NGFF (OME-Zarr) into institutional microscopy platforms.
• Contribute to Nextflow and Galaxy for data staging and results annotation.
• Create training materials and contribute to community documentation.

Skills

Python

JavaScript

HTML/CSS

Git

GitHub

CI/CD

Linux administration

Docker

English (written & spoken)

German language skills

Travel willingness

Education

Master's degree

Doctorate

Tools

OMERO

Ansible

NGFF/OME-Zarr

Nextflow

Galaxy

Job description

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 earliestpossible date.

Research Associate (f/m/d) – OMERO Development and Deployment

Main tasks:

• User-driven development of OMERO plugins
• 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 capitalforming 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 communitydriven 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. Applications from 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.