SynthImmune Research Data Scientist/Research Data Manager

• Design, implement and refine automated image analysis workflows, including machine learning-based methods for segmentation, feature extraction and multidimensional molecular and morphological feature-based classification in complex datasets
• Collaborate closely with experimental scientists to develop scalable, robust and automated data pipelines and flexible toolsets to support diverse microscopy-based research projects, including the integration of multimodal datasets (e. g., imaging, omics and spatial omics)
• Serve as the primary point of contact for planning, coordinating and advising on image analysis projects within IDIP and the SynthImmune consortium
• Work in close partnership with leading AI-based data analysis research groups on campus to co-develop and implement innovative computational approaches for consortium-wide challenges
• Lead the implementation of data management practices across the SynthImmune consortium, promoting standardization and best practices
• Ensure compliance with FAIR (Findable, Accessible, Interoperable, Reproducible) data principles in collaboration with IT teams
• Foster interdisciplinary collaboration by actively engaging with researchers across biology, bioinformatics and data science
• Train and support scientists in coding, automated workflows and image analysis best practices to build sustainable in-house expertise

• PhD in any field with strong bioimage analysis component, computer science, data science, computational biology or a related field
• Several years of relevant professional experience in a research environment (e. g., academic research group, core facility, company)
• Strong programming and data analysis skills, with demonstrated expertise in Python and scientific computing ecosystems
• Proven experience in developing and applying deep learning methods for image analysis, such as convolutional neural networks (CNNs) for segmentation and classification
• Practical experience with deep learning frameworks (e. g., PyTorch, TensorFlow) and model training, evaluation and optimization on large-scale datasets
• Experience with bioimage analysis tools and environments (e. g., FIJI/ImageJ, Jupyter, CellProfiler, Napari), and the ability to adapt and extend them for complex workflows
• Experience in developing automated, scalable, and reproducible data analysis pipelines
• Experience with research data management, including handling large datasets and implementing FAIR data principles, is an asset
• Collaboration-oriented mindset with high self-motivation, reliability and the ability to manage and prioritize multiple projects
• Excellent ability to communicate complex computational and analytical concepts in a clear and accessible manner, particularly in training and teaching contexts
• Strong analytical thinking and creativity in problem-solving, * Familiarity with multimodal data integration (e. g., combining imaging and omics)
• Experience with high-performance computing (HPC) environments and/or cloud-based data processing infrastructures
• Familiarity with workflow management systems (e. g. Nextflow) and workflow orchestration
• Experience with large-scale data handling
• Hands-on experience with advanced light microscopy instrumentation (e. g., confocal, light-sheet, super-resolution microscopy)
• Prior experience working in core facilities or shared research infrastructures
• Exposure to biosafety level environments (BSL-2/3) or infectious disease research settings

Application:

If you are excited about contributing to cutting-edge research at the interface of bioimaging, data science, and synthetic immunology, we would be delighted to hear from you.

Applications should be submitted as a single PDF file including:

• PhD transcript/certificate
• A letter of motivation

The SynthImmune Cluster of Excellence (synthimmune.de/) is seeking a highly motivated Research Data Scientist/Research Data Manager to strengthen its Infectious Diseases Imaging Platform (IDIP, www.idip-heidelberg.org/) at the Center for Integrative Infectious Disease Research (CIID, ciid-heidelberg.de/), Heidelberg, Germany, and to serve as the primary contact point for all SynthImmune members. The SynthImmune Research Data Scientist/Research Data Manager will be also associated with the Research Data Unit of Heidelberg University (www.data.uni-heidelberg.de/en). SynthImmune brings together leading researchers to pioneer the emerging field of synthetic immunology, aiming to develop transformative strategies to combat infectious diseases and cancer by understanding and engineering elite immune responses. Within this collaborative framework, IDIP provides state-of-the-art high-containment microscopy infrastructure (BSL-2 and BSL-3) and advanced imaging technologies spanning molecular to whole-organism scales. The successful candidate will contribute to cutting-edge research at the interface of bioimaging, data science, infection biology and immunology, supporting the quantitative analysis of complex biological systems and helping to translate imaging data into new insights for therapeutic innovation., The position is remunerated according to TV-L E 13, it is available immediately and is limited to 3 years. The position can be filled in part-time. We offer the opportunity to work in a highly interdisciplinary and collaborative environment at the forefront of infectious disease research and synthetic immunology, with access to state-of-the-art imaging infrastructure and strong connections to leading computational and AI research groups. Join us in shaping innovative approaches to understand and combat infectious diseases and cancer.