Machine Learning Engineer

About Katana Labs

Katana Labs is a
software engineering and AI startup
building the next-generation AI- and cloud-native software platform for
spatial multi-omics
. Our
mission
is to empower R&D teams in translational and clinical research to
advance precision medicine
. The next frontier in healthcare is decoding biology in health and disease. This will facilitate a more comprehensive understanding of complex diseases, enable early diagnosis, and, ultimately, contribute to their cure. The overall objective of Katana Labs is to build one AI platform that provides
biological intelligence at scale
, enabling coherent and actionable insights from the molecular to cell and tissue levels.

Our
flagship product
,
Katana Edge
, is a cloud-native, no-code and AI-powered platform optimized for the advanced analysis of large biological image datasets with single-cell resolution. R&D teams in Life Sciences and Biopharma use Katana Edge to
accelerate
their
research
by improving workflow efficiency, reducing costs, and generating novel insights in their daily work. Our product vision is to expand Katana Edge into a
comprehensive platform for spatial multi-omics
, seamlessly integrating proteomics, transcriptomics, and other modalities to accelerate clinical research and therapy development in precision medicine.

The Role

We are seeking a
Machine Learning Engineer
to join our product development team with a strong emphasis on technical expertise in ML engineering and software development. You will split your time between:

• Developing, deploying, and optimizing machine learning and deep learning workflows tailored to histopathological and spatial multi-omics image data.
• Collaborating on projects with third-party partners (academia, CROs, biotech, pharma) to process, analyze, and deliver actionable insights from complex image and spatial datasets.
• Enhancing the Katana Edge platform by architecting scalable ML pipelines, agentic AI components, and automated data processing systems.

This role is ideal for someone passionate about building robust, production-grade ML systems that advance cancer research and next-level therapies for precision medicine.

We invite highly motivated applicants with a registered residence in Germany to apply for this position.

Your Responsibilities

• Design, implement, and maintain scalable ML and deep learning pipelines (e.g., using PyTorch, TensorFlow) for image data in histopathology, multiplex immunofluorescence and spatial omics.
• Develop custom image analysis modules, including cell segmentation, feature extraction, and spatial data integration, optimizing for performance and reproducibility.
• Collaborate closely with software engineers and data scientists to integrate ML models into cloud-native applications and intuitive user interfaces.
• Automate data processing workflows and ensure robust versioning, testing, and deployment of ML components.
• Participate in code reviews, continuous integration, and documentation to promote software quality and team collaboration.
• Present technical findings and project outcomes to internal teams and external partners at scientific and industry forums.

Your Profile

• Degree in computer science, bioinformatics, computational biology, or a related quantitative discipline.
• Proven hands-on experience (2+ years) designing and deploying ML and deep learning models, preferably in biomedical imaging or related fields.
• Proficiency in Python and ML frameworks such as PyTorch or TensorFlow; familiarity with cloud platforms and containerization (Docker, Kubernetes) is a plus.
• Background in computer vision or bioimage analysis (cell segmentation, microscopy/spatial data processing) is desired; experience in (geo)spatial analysis is a strong plus.
• Experience building production-level ML pipelines, including data ingestion, preprocessing, model training, validation, and deployment.
• Solid software engineering skills, including version control (Git), testing, and collaborative development practices.
• Excellent communication skills to effectively share complex technical information with interdisciplinary teams and external stakeholders.
• Ability to work independently while thriving in a multidisciplinary startup environment.
• Fluent in English; German language skills are a plus.

What We Offer

• Competitive salary
• Amazing team
• A technical role with direct impact on product innovation and advancing the field of precision oncology.
• Collaboration with an international network of research institutes, biotech, and pharma partners.
• A dynamic startup environment with flat hierarchies, a culture of learning, and continuous growth.
• Flexible working hours and remote-friendly policies, anchored by our office in Dresden-Neustadt.
• The opportunity to grow at the intersection of AI, spatial biology, and oncology.

If this role interests you, kindly submit your application and comprehensive CV to:

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