Computational Biologist, Bioimage Analysis (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

Come develop multidisciplinary skills in a collegial non-profit environment that brings together biologists, engineers, and data scientists! This position is a collaboration between the groups of Manu Leonetti and Loic Royer. We strive to map how human cells are organized in space and time as a dynamic ecosystem of biomolecules and pathways. Our science spans multiple disciplines, from CRISPR, imaging, and proteomics, to data science and AI/ML (see Cho et al. Science 2022; Kobayashi et al. Nature Methods 2022; Lange et al Cell 2025; Hein et al. Cell 2025). We build large open-source datasets like OpenCell and Zebrahub, and use them to drive biological discoveries.

In current projects, we are asking how to decode live-cell image data into defined cellular states. We seek a Computational Biologist to help translate imaging data into biological insights. This role is ideal for a biologist or microscopist with significant coding experience. This is an in-person position to maximize interactions between biologists and data analysts.

You will

• Collaborate closely with Biologists, Computer Scientists, and Optical Engineers to quantify observations from large-scale phenotypic screens and discover new biology
• Manage the creation of and analysis pipelines for large-scale imaging datasets (100s TB)
• Generate and test hypotheses using imaging data
• Identify statistically significant observations from complex biological phenotypes
• Lead innovative research and contribute to top-tier publications and conference presentations
• Mentor junior scientists and foster a collaborative, continuous-learning environment

You have

Essential –

• Recent (< 2 years) PhD. in Biology, Biophysics, Computer Science, Engineering, or related technical field
• 4+ years of experience in Python and relevant image processing libraries (e.g. numpy, scipy, skimage, napari)
• 4+ years experience in microscopy applied to biological systems (fluorescence and/or label-free modalities
• Experience deploying advanced methods for segmentation and quantification of biological images (e.g. Cellpose, Segment Anything, Cellprofiler, etc.)
• A track record of impactful publications demonstrating experience with extracting biological insights from imaging data
• Excellent problem-solving skills and ability to work in an interdisciplinary environment;
• Excellent written and verbal communication skills
• Excellent documentation skills

Nice to have -

• Experience deploying code on high-performance computing and distributed systems
• Familiarity with Next-Generation-File-Formats (e.g. OME-ZARR)
• Experience with pipelining packages (snakemake / nextflow) or pipelining automation
• Familiarity with image acquisition pipeline (µManager)
• Familiarity with fundamental cell biology, such as signaling pathways or organelles
• Experience with high-throughput phenotypic assays (e.g. CRISPR screening, multiplexed imaging, spatial omics)

Compensation

The San Francisco, CA base pay range for this role is  $138,000.00 - $148,500.00. 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.