Software Engineer, Computational Microscopy Platform (Biohub SF)

The Chan Zuckerberg Biohub San Francisco (CZ Biohub SF) (https://www.czbiohub.org/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.

Our Vision

• We pursue large scientific challenges that cannot be pursued in conventional environments
• We enable individual investigators to pursue their riskiest and most innovative ideas
• The technologies developed at CZ Biohub San Francisco facilitate research by scientists and clinicians at our home institutions and beyond

Diversity of thought, ideas, and perspectives are at the heart of CZ Biohub Network and enable disruptive innovation and scholarly excellence. We are committed to cultivating an organization where all colleagues feel inspired and know their work makes an important contribution.

The Opportunity

The Computational Microscopy Platform (www.czbiohub.org/comp-micro/) 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. 

You will

• Lead the development and maintenance of a high-performance image i/o library (https://github.com/czbiohub-sf/iohub) used for managing and processing petabytes of datasets
• Use and adapt a high-performance image processing framework (https://github.com/czbiohub-sf/biahub) 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

Please include a cover letter with your application describing:

• Your interest in this role, the contributions you are excited to make, and the skills you want to strengthen on the job
• Your professional goals and the alignment with this role
• Course and hobby projects relevant to this role

We seek to recruit individuals with foundational skills, the ability to learn quickly, and the ability to pursue ambitious projects through collaborations. Prior experience related to the projects mentioned above is nice to have, but optional. Candidates with a Master’s degree are also welcome to apply, but the role is not suitable for candidates with a doctoral degree.

Essential –

• 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.

Benefits

We offer a robust benefits program that enables the important work Biohubbers do everyday. Our benefits include healthcare coverage, life and disability insurance, commuter subsidies, family planning services with fertility care, childcare stipend, 401(k) match, flexible time off and a generous parental leave policy. In addition, we honor our commitment to career development and our value of scholarly excellence through regular onsite opportunities to learn from the world's leading scientists.

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. Therefore, we provide employment opportunities without regard to age, race, color, ancestry, national origin, religion, disability, sex, gender identity or expression, sexual orientation, or any other protected status in accordance with applicable law.

Pursuant to the California Fair Chance Act, we will consider for employment qualified applicants with arrest and conviction records.

Headhunters and recruitment agencies may not submit resumes/CVs through this website or directly to managers. The CZ Biohub Network does not accept unsolicited headhunter and agency resumes. The CZ Biohub Network will not pay fees to any third-party agency or company that does not have a signed agreement with the CZ Biohub Network.