Software Developer - Interoperability for Single-Cell and Spatial Omics Methods

Software Developer - Interoperability for Single-Cell and Spatial Omics Methods

Reference number : 2025-0331

Heidelberg

Full-time

Computational Genomics and Systems Genetics

The German Cancer Research Center (DKFZ) is one of Europe’s largest cancer research centers. “Research for a life without cancer" is the mission of our world-class scientists and all our team members.

We investigate how cancer develops, identify cancer risk factors and search for new cancer prevention strategies. We develop new methods with which tumors can be diagnosed more precisely and cancer patients can be treated more successfully. Every contribution counts – whether in research, administration or infrastructure. This is what makes our daily work so meaningful and exciting.

The Division of Computational Genomics and Systems Genetics develops and applies computational approaches to study molecular variations and their phenotypic consequences.

To strengthen our team, we are seeking for the next possible date a

The research group of Prof. Dr. is seeking a software developer to advance interoperability for single-cell and spatial omics across the (Python) and (R) ecosystems. The project focuses on enhancing the FAIR capabilities of , a modern Python framework for spatial omics, across platforms, and on strengthening its language-agnostic file format based on the open standard. You will help ensure seamless cross-language usage, robust data exchange, and clear specifications that serve both communities.

You will be part of a vibrant open-source environment at the interface of software development and biomedical research - specifically within the global scverse community. You will have the opportunity to shape widely used, FAIR-by-design tools that accelerate single-cell and spatial omics research across both Python and R ecosystems. We also offer substantial opportunities for professional growth, learning, and leadership, including mentorship, structured code reviews, participation in conferences and hackathons, and visibility through community calls and cross-consortium initiatives. Recent community events include the Scverse Hackathon in Paris (2025) and the NGFF Hackathon in Zurich (2025); previous hackathons have taken place in Boston, Cambridge, Heidelberg, Innsbruck, and Munich.

The Stegle group is jointly based at DKFZ and EMBL and embedded in Heidelberg’s vibrant ecosystem for data science, machine learning, and computational biology. We collaborate closely with research groups across Germany and worldwide, and we actively engage with open-source communities through coordinated development, cross-consortium events, and hackathons.

Your tasks :

• Expand the bridge between the scverse and R / Bioconductor ecosystems through interoperable software development focused on the OME-Zarr file format and the SpatialData framework
• Build and automate an infrastructure to ensure continued interoperability of SpatialData across R / Python, including robust converters, I / O layers, and validation tests
• Improve the documentation of the SpatialData format with clear tutorials, examples, and contributor guides that lower the barrier to entry
• Contribute to the NGFF specification and help support the incoming versions, in particular and , via updates to the SpatialData codebase, but also by contributing to the NGFF codebase
• Engage with the open-source scverse and NGFF communities : triage issues; review PRs; collaborate in public forums and with the possibility to participate in cross-consortium events, sprints, and hackathons

Your profile :

Required Qualifications :

Preffered Qualifications :

Application process :

If you’re excited about building interoperable, well-documented, and community-aligned software that advances spatial omics, we’d love to hear from you.

Recent relevant publications :

Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData : an open and universal data framework for spatial omics. Nat Methods 22, 58–62 (2025).

Crowell, H. L., Dong Y., Billato I. et al. Orchestrating Spatial Transcriptomics Analysis with Bioconductor. bioRxiv 2025.11.20.688607; doi :

Moore, J., Basurto-Lozada, D., Besson, S. et al. OME-Zarr : a cloud-optimized bioimaging file format with international community support. Histochem Cell Biol 160, 223–251 (2023).

Virshup, I., Bredikhin, D., Heumos, L. et al. The scverse project provides a computational ecosystem for single-cell omics data analysis. Nat Biotechnol 41, 604–606 (2023).

We Offer

Excellent framework conditions : state-of-the-art equipment and opportunities for international networking at the highest level

30 days of vacation per year

Flexible working hours

Remuneration according to TV-L incl. occupational pension plan and capital-forming payments

Possibility of mobile work and part-time work

Family-friendly working environment

Sustainable travel to work : subsidized Germany job ticket

Unleash your full potential : targeted offers for your personal development to further develop your talents

Our Corporate Health Management Program offers a holistic approach to your well-being