Lead Bioimage Informatics Scientist: Image ML & Cells

Chan Zuckerberg Biohub; San Francisco (CA); On-site; USD 108,000 - 171,000; Full time

Benefits offered by this job

Healthcare coverage

401(k) match

Generous parental leave

Job summary

The Chan Zuckerberg Biohub, Inc. in San Francisco is seeking a Bioimage Informatics Scientist - Image Analysis & Machine Learning to lead quantitative insights from millions of fluorescence microscopy images.

This role blends biology, machine learning, and data science in a collaborative setting. You will design image-processing pipelines, develop deep learning models, and work with biology experts to quantify cellular responses to perturbations.

Qualifications

• PhD in Computational Biology or related field.
• At least 3 years of image processing and scientific Python programming.
• Experience with biological imaging and cell biology.
• Enthusiasm for open-source software and systems biology.
• Familiarity with software development best practices (docs, version control, CI/CD).
• Strong collaboration and communication abilities.

Responsibilities

• Design pipelines for image processing of biological microscopy data
• Conceive novel deep learning-based algorithms to obtain new insights from our unique image datasets
• Partner with biology experts to identify and quantify cellular responses in response to perturbations
• Explain technical concepts to a multi-disciplinary team of biologists, bioengineers, and data scientists at the Biohub
• Author publications & mentor junior colleagues

Skills

PhD required

Python & ML

Biological imaging

Open-source software

Collaborative

CI/CD

Strong communication

Education

PhD in Computational Biology / Bioinformatics / Biophysics

Tools

NumPy

SciPy

scikit-image

TensorFlow

PyTorch

Job description

Come join an interdisciplinary team of biologists, data scientists and engineers! This position is a collaboration between the groups of Loic Royer and Manu Leonetti at the Chan Zuckerberg Biohub (https://www.czbiohub.org/royer, https://www.czbiohub.org/leonetti). We strive to map how the human cell is built by combining CRISPR, fluorescence microscopy, proteomics, robotics, software engineering and data science. We build large datasets and use them to develop new algorithms and analyses. Our tools and data include:

• OpenCell (https://opencell.czbiohub.org/), a large reference of protein localization and interactions that can be mined and re-used by the entire community for discovery.
• innovative self-supervised machine learning algorithms like cytoself to encode protein localization patterns (https://github.com/royerlab/cytoself) or aydin to denoise images (https://github.com/royerlab/aydin). Royer’s team also co-founded napari (https://napari.org/), an interactive and multi-dimensional image viewer for Python with >10,000 users worldwide.

• Our science is fully open-source and published in journals like Science and Nature Methods (https://bit.ly/3T5Fbmf; https://go.nature.com/3rXOSae; https://go.nature.com/3EEf9C9)

Our previous work showed how deep learning can help extract very specific functional information from images of cell morphology and protein localization ((https://bit.ly/3T5Fbmf; https://go.nature.com/3rXOSae). We are seeking a Bioimage Informatics Scientist - Image Analysis & Machine Learning to spearhead our next efforts to extract quantitative biological insights from millions of fluorescence microscopy images. This is an exciting opportunity to work at the leading edge of machine learning and systems biology, supported by experts in a highly collaborative and well-funded scientific environment.

What You’ll Do

• Design pipelines for image processing of biological microscopy data
• Conceive novel deep learning-based algorithms to obtain new insights from our unique image datasets
• Partner with biology experts to identify and quantify cellular responses in response to a variety of perturbations (e.g., CRISPR screens, drug treatments, or viral infection)
• Explain technical concepts to a multi-disciplinary team of biologists, bioengineers, and data scientists at the Biohub
• Author publications & mentor junior colleagues

What You’ll Bring

Essential –

• PhD in Computational Biology, Bioinformatics, Biophysics, or a related discipline. This can be waived if the candidate demonstrates exceptional knowledge and experience.
• At least 3 years of expertise in image processing and scientific programming in Python (e.g. NumPy, SciPy, scikit-image, TensorFlow, PyTorch, etc…)
• Experience with and interest in biological imaging and cell biology
• Enthusiasm for systems biology and open-source software
• Familiarity with professional software development best practices (documentation, version control, CI/CD pipelines)
• Must be highly collaborative, team-oriented, and have excellent written and oral communication skills

Nice to have -

• Experience with fluorescence microscopy
• Experience building and training deep neural networks for computer vision tasks
• Familiarity with relational databases and cloud-based platforms (like AWS)

The Chan Zuckerberg Biohub Network requires all employees, contractors, and interns, regardless of work location or type of role, to provide proof of full COVID-19 vaccination, including a booster vaccine dose, if eligible, by their start date. Those who are unable to get vaccinated or obtain a booster dose because of a disability, or who choose not to be vaccinated due to a sincerely held religious belief, practice, or observance must have an approved exception prior to their start date.

Compensation

• Data Scientist I = $108,000 - $148,500
• Data Scientist II = $124,000 - $170,500

New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. To determine starting pay, we consider multiple job-related factors including a candidate’s skills, education and experience, market demand, business needs, and internal parity. We may also adjust this range in the future based on market data. Your recruiter can share more about the specific pay range during the hiring 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
• Existing collaborations within CZ Biohub: Technology Platforms (Bioengineering, Computational Microscopy, Data Science, Genomic Sequencing, Mass Spectrometry/Proteomics), and Research Group Leaders
• Access to collaborators, resources and facilities at our three partner universities (Stanford, UC Berkeley, and UC San Francisco) and at partner organizations in the Bay Area and beyond
• Competitive compensation and benefits commensurate with experience

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.