Job Description

Software Engineer, Computational Microscopy Platform (Biohub SF)

The Chan Zuckerberg Biohub San Francisco ( CZ Biohub SF ) is an independent nonprofit research institute that brings together three powerhouse universities - Stanford, UC Berkeley, and UC San Francisco - into a single collaborative technology and discovery engine. CZ Biohub SF itself supports some of the brightest, boldest engineers, data scientists, and biomedical researchers to investigate the fundamental mechanisms underlying disease and develop new technologies that will lead to actionable diagnostics and effective therapies. We are guided by our values of scholarly excellence; disruptive innovation; hands-on engineering/hacking/building; partnership and collaboration; open communication and respect; inclusiveness; and opportunity for all.

The Opportunity

The Computational Microscopy Platform ( led by Shalin Mehta builds imaging technologies to analyze the dynamics of cells across biological scales ranging from organelles to zebrafish larvae. We develop computational imaging methods to visualize the physical and molecular properties of live cells and zebrafish with increased accuracy, resolution, and throughput. We develop deep learning methods to analyze dynamic cell states from the high-dimensional image data. We collaborate with groups within the CZ Biohub Network and university collaborators to discover biological mechanisms and pursue therapeutic opportunities using these technology platforms.

Reporting to a Senior Machine Learning Engineer on the team, the Associate Software engineer will build open source software tools for managing and processing 10-100 terabyte-scale datasets. The individual will collaborate with an interdisciplinary group of biologists, imaging scientists, and computational scientists. Successful candidates will have prior experience with large code bases and an interest in imaging and biology.

• Use and adapt a high-performance image processing framework ( for one high-throughput imaging screen at a time, e.g., mapping changes in organelles during differentiation of stem cells and dynamics of infection in zebrafish. This project will require working on microscopes in a BSL-2 imaging laboratory after appropriate safety training.
• Organize and curate datasets contributed by multiple collaborators for training image-based phenotyping models.
• Package the above pipelines via docker/singularity containers that can be used across platforms, including the HPC cluster.

You have

• Bachelor’s degree in physics, engineering, bioengineering, or computer science.
• 4+ years of coding experience with multiple languages (at minimum, Python, shell, and C++/C/Rust).
• Experience using and producing different types of application programming interfaces.
• Exposure to the development of image visualization tools.
• Ability to write clean, maintainable, and well-documented code, adhering to modern software engineering standards.
• Prior research experience (internship experience is considered).
• Strong verbal and written communication skills.
• Team player who can also work independently.

Nice to have -

• Prior experience with image analysis tools and libraries (e.g. scikit-image, OpenCV, PyTorch, ImageJ).
• Prior experience with biological research.

Compensation

The San Francisco, CA base pay range for this role is $96,000.00 - $132,000.00. New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. Actual placement in range is based on job-related skills and experience, as evaluated throughout the interview process.

What We Provide

• Resources to disrupt and innovate at the frontiers of our knowledge of biology and disease.
• A collegial and collaborative environment consisting of diverse expertise.
• Access to collaborators, resources and facilities at our three partner universities (Stanford University, UC Berkeley, and UC San Francisco) and at partner organizations in the SF Bay Area and beyond.
• Competitive compensation and benefits commensurate with the experience.

If you’re interested in a role but your previous experience doesn’t perfectly align with each qualification in the job description, we still encourage you to apply as you may be the perfect fit for this or another role.

The CZ Biohub Network is an equal opportunity employer committed to diversity of thought, ideas and perspectives. We are committed to cultivating an inclusive organization where all Biohubbers feel inspired and know their work makes an important contribution.

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