Software Engineer in Image Analysis, Organoid Phenotyping

Roche fosters diversity, equity and inclusion, representing the communities we serve. When dealing with healthcare on a global scale, diversity is an essential ingredient to success. We believe that inclusion is key to understanding people’s varied healthcare needs. Together, we embrace individuality and share a passion for exceptional care. Join Roche, where every voice matters.

The Position

A healthier future. It’s what drives us to innovate. To continuously advance science and ensure everyone has access to the healthcare they need today and for generations to come. Creating a world where we all have more time with the people we love. That’s what makes us Roche.

In Roche’s Pharmaceutical Research and Early Development organization (pRED), we make transformative medicines for patients in order to tackle some of the world’s toughest unmet healthcare needs. At pRED, we are united by our mission to transform science into medicines. Together, we create a culture defined by curiosity, responsibility and humility, where our talented people are empowered and inspired to bring forward extraordinary life-changing innovation at speed.

The Institute of Human Biology (IHB) is a newly established research center in Basel, Switzerland, dedicated to advancing human biology through the use of human model systems for translational research. Our dynamic and interdisciplinary environment fosters collaboration among biologists, engineers, and data scientists, bridging the gap between academic and pharmaceutical research. Closely associated with Roche’s Pharmaceutical Research and Early Development (pRED), we partner with leading academic institutions both locally and globally to address grand challenges with bold, innovative science.

The Opportunity

The Organoid Phenotyping team at the Institute of Human Biology (IHB) is seeking an expert in computational pipelines and frameworks for analyzing 3D imaging data. As a member of our team, you will collaborate with scientists to design and implement state-of-the-art image processing algorithms that enable the processing of terabytes of 3D imaging data using high-performance computing infrastructure. Together with the digital IHB (D-IHB) team you will help shape the digital infrastructure for data integration, processing, visualization, and analysis.

In addition to this primary responsibility, you will collaborate closely with the BioVisionCenter (BVC) at the University of Zurich (UZH) to support the development of a common open-source software project. This initiative strives to advance research in computer vision and promote interdisciplinary collaboration.

• Design and implement analytical workflows in collaboration with scientists at IHB, integrating quantitative imaging with high-dimensional data, such as spatial omics and single-cell sequencing.

• Provide guidance and templates for image analysis best practices (e.g., GitLab repository) to build reproducible processing pipelines.

• Disseminate knowledge to IHB members and host workshops on data analysis topics.

• Implement methods and approaches based on machine learning and mathematical modeling where necessary.

• Stay updated on the latest bioimage analysis tools and methodologies, providing these as well-packaged and tested components of our imaging framework.

Who You Are

• You hold an advanced degree (PhD or MSc with relevant experience) in bioinformatics, computer science, mathematics, or a related field with a validated academic track record in the bioimaging space.

• You have a solid understanding of the bioimage analysis field, are familiar with the latest developments in this space, and bring experience with image processing methods on biological datasets, with an emphasis on microscopy.

• You possess solid knowledge of Python and are familiar with software engineering tools and methods such as source control (GitHub/GitLab), CI/CD, containerization, and software packaging.

• You are experienced in designing scalable solutions leveraging high-performance computing or cloud environments.

• You have a background in exploratory data analysis, statistics methodology and tools and bring knowledge of deep learning and classical machine learning methods.

In addition to your technical expertise, we are looking for customer-focused candidates with a drive for growth and a questioning mindset. You should be skilled in creative problem-solving and organization, and able to implement innovative ideas efficiently in a fast-paced research context. Excellent communication skills with high proficiency in English are needed, as well as the ability to continuously build personal networks and thrive in a dynamic, inclusive environment that offers full accountability for individual contributions and development.

If you embody these qualities, we encourage you to apply and join our team!

Who we are

At Roche, more than 100,000 people across 100 countries are pushing back the frontiers of healthcare. Working together, we’ve become one of the world’s leading research-focused healthcare groups. Our success is built on innovation, curiosity and diversity.

Basel is the headquarters of the Roche Group and one of its most important centres of pharmaceutical research. Over 10,700 employees from over 100 countries come together at our Basel/Kaiseraugst site, which is one of Roche`s largest sites. Read more .

Besides extensive development and training opportunities, we offer flexible working options, 18 weeks of maternity leave and 10 weeks of gender independent partnership leave. Our employees also benefit from multiple services on site such as child-care facilities, medical services, restaurants and cafeterias, as well as various employee events.

We believe in the power of diversity and inclusion, and strive to identify and create opportunities that enable all people to bring their unique selves to Roche.