Computational Biologist II, CellxState

About the role

The Computational Biologist will play a pivotal role in advancing the state-of-the-art in image analysis for large-scale fluorescent microscopy datasets. This role is part of the CELLxSTATE Program, which aims to decode and control how cells make decisions using cutting-edge technologies.

Responsibilities

• Design, develop, and maintain scalable image analysis pipelines for large-scale fluorescent microscopy datasets, focusing on robust image quality and computational efficiency.
• Integrate emerging multi-modal data types (such as spatial transcriptomics) into unified, AI-ready datasets that support downstream modeling and discovery.
• Advance bio-image analysis capabilities, including segmentation, tracking, image-stitching, and image registration.
• Partner closely with biologists and automation engineers to implement end-to-end quality control metrics, ensuring the fidelity of experimental and computational pipelines.
• Architect modular and reusable processing frameworks that can flexibly support multiple experiment types within a shared infrastructure.
• Publish and disseminate impactful findings through preprints, papers, and software repositories (e.g., GitHub).

Requirements

• PhD in Computational Biology, Biology, or Computer Science, or a MS with relevant job experience.
• At least 4 years of experience in Python-based image analysis or scientific computing.
• Experience with fluorescence microscopy, confocal, or lightsheet is a plus.
• Fluency with computational tools and infrastructure such as Python, Github, and Slurm.
• Experience with modern biological data formats such as OME-Zarr and AnnData.
• Experience designing workflows for large, complex datasets, including scalable storage formats, and reliable metadata and experiment tracking.
• A proven track record of individual innovation, together with a strong ability to work collaboratively.
• A passion for research and understanding how cells work.
• An enthusiasm for team science and open science - this position will be embedded in a large multi-disciplinary team.
• Excellent written and oral communication skills.

Qualifications

• PhD in Computational Biology, Biology, or Computer Science, or a MS with relevant job experience.
• At least 4 years of experience in Python-based image analysis or scientific computing.
• Experience with fluorescence microscopy, confocal, or lightsheet is a plus.
• Fluency with computational tools and infrastructure such as Python, Github, and Slurm.
• Experience with modern biological data formats such as OME-Zarr and AnnData.
• Experience designing workflows for large, complex datasets, including scalable storage formats, and reliable metadata and experiment tracking.
• A proven track record of individual innovation, together with a strong ability to work collaboratively.
• A passion for research and understanding how cells work.
• An enthusiasm for team science and open science - this position will be embedded in a large multi-disciplinary team.
• Excellent written and oral communication skills.

Skills

• Python-based image analysis and scientific computing.
• Experience with fluorescence microscopy, confocal, or lightsheet.
• Modern biological data formats such as OME-Zarr and AnnData.
• Workflow design for large, complex datasets.
• Collaborative and innovative problem-solving skills.
• Strong communication and writing skills.

Benefits

• San Francisco, CA base pay range for a new hire in this role is $153,000 - $210,100.
• This position may be eligible to participate in Biohub's discretionary annual performance bonus program.
• Bonus eligibility and targets are determined in accordance with Biohub's total rewards philosophy and may vary by role.
• The role is a hybrid position requiring you to be onsite for at least 60% of the working month, approximately 3 days a week, with specific in-office days determined by the team’s manager.
• Provides a generous employer match on employee 401(k) contributions to support planning for the future.
• Paid time off to volunteer at an organization of your choice.
• Funding for select family-forming benefits.
• Relocation support for employees who need assistance moving.