Scientist II, Scaling Lead

Biohub; San Francisco (CA); On-site; USD 138,000 - 172,000; Full time

Benefits offered by this job

401(k) employer match

Paid time off to volunteer

Relocation assistance

Job summary

Biohub is seeking a Scientist II to lead the scaling of our imaging and data-generation pipeline. You will set throughput targets, identify bottlenecks, and work hands-on with sample-prep, imaging, and computation teams to remove them—at the bench, at the microscope, and at the keyboard.

The ideal candidate is curious, dependable, and excited to work at the interface of biology, imaging technology, and collaborative platform science.

Qualifications

• Ph.D. in physics, biophysics, optics/photonics, bioengineering, or a related field.
• 5+ years of end-to-end ownership of a live-imaging pipeline in a developing organism.
• Hands-on design and construction of light-sheet microscopes.
• Experience imaging live embryos or living specimens over time.
• Experience with transgenic reporter lines for live imaging.
• Strong Python-based image processing and software development.
• Quantitative modeling that connects measurements to theory.
• Commitment to robustness, reproducibility, and scalability.
• Systems thinking and collaborative leadership across optics, biology, and computation.

Responsibilities

• Map the full sample-to-data pipeline, define quantitative throughput and quality targets, instrument each stage with metrics and dashboards, and maintain a living view of bottlenecks.
• Spend hands-on time with sample-prep, imaging, and computation teams, diagnosing and fixing obstacles that limit data generation.
• Increase specimens prepared and imaged per session and reduce variability across the sample-handling workflow in collaboration with platform teams.
• Improve multi-specimen acquisition, instrument uptime, and cross-instrument reproducibility on light-sheet microscopes to push throughput toward practical limits.
• Collaborate with the computation team to keep image-processing pace with acquisition (denoising, registration, fusion, segmentation, tracking).
• Establish reproducible SOPs, QC gates, and monitoring as datasets scale to measure throughput.
• Serve as connective tissue between the group and Biohub’s shared platforms, removing cross-team bottlenecks.
• Mentor team members, guide scaling strategy, and assist with recruiting as effort grows.
• Document architectures, protocols, release methods, code, and data for the community.

Skills

Live-imaging

Python

Image analysis

Microscopy design

Leadership

Cross-disciplinary

Quality/reproducibility

System thinking

Communication

Education

PhD in physics/biophysics/optics/biomedical engineering

Tools

Python

GPU computing

HPC/data storage pipelines

Job description

Biohub is the first large-scale initiative bringing frontier AI models, massive compute, and frontier experimental capabilities under one roof. We're building a general-purpose system to accelerate scientific discovery, integrating frontier AI models, biological foundation models, and lab capabilities, with the ultimate goal of curing disease. Our technology powers scientists around the world, translating AI capabilities into tools that accelerate research everywhere.

The Team

The Biohub is a group of nonprofit research institutes that bring together scientists, engineers, and physicians with the goal of pursuing grand scientific challenges on 10- to 15-year time horizons. The Biohub focuses on understanding underlying mechanisms of disease and developing new technologies that will lead to actionable diagnostics and effective therapies.

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 the Biohub facilitate research by scientists and clinicians at our home institutions and beyond
  Diversity of thought, ideas, and perspectives are at the heart of Biohub 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.

This position will work with the team of Dr. Loic Royer to build instruments, AI, and molecular tools to understand how cells self-organize to build, maintain, and repair tissues. The team designs and operates state-of-the-art light-sheet microscopes (including the DaXi platform), develops the Ultrack cell-tracking framework, and produces the Zebrahub atlas of vertebrate development.

The Opportunity

Biohub is seeking a Scientist II to lead the scaling of our imaging and data-generation pipeline. This role will set throughput targets, find the bottlenecks that matter most, and work hands-on with the sample-prep, imaging, and computation teams to remove them — at the bench, at the microscope, and at the keyboard.

We are looking for someone who is curious, dependable, and excited to work at the interface of biology, imaging technology, and collaborative platform science. The ideal candidate is proactive, learns quickly, communicates well across teams, and enjoys contributing to both established workflows and the development of new experimental approaches across a wide range of disciplines, from optics, microscopy, and image processing to developmental, cell, and molecular biology.

This position is well-suited for candidates who have already built a live-imaging pipeline in a developing organism from the ground up — instrument, reporter lines, sample handling, acquisition, and analysis — and are excited to take on the challenge of scaling that pipeline. The strongest candidates will have hands-on experience in microscope design, sample preparation, model-organism husbandry, imaging, and quantitative analysis, with a track record of making methods more robust and reproducible.

What You’ll Do

• Map the full sample-to-data pipeline, define quantitative throughput and quality targets, instrument each stage with metrics and dashboards, and maintain a living view of the true bottlenecks — so effort is always spent on the binding constraint.
• Spend significant hands-on time alongside sample-prep, imaging, and computational scientists, diagnosing and fixing the concrete obstacles — protocol, hardware, software, or logistics — that limit data generation on any given week.
• Increase the number of specimens prepared and imaged per session and reduce variability across the sample-handling workflow — staging, mounting, and quality control — in partnership with the Bioengineering and Zebrafish Transgenesis platforms.
• Improve multi-specimen acquisition, instrument uptime, and cross-instrument reproducibility on the group's light-sheet microscopes, pushing sustained throughput toward the platform's practical limits.
• Work with the computation team to keep the image-processing pipeline (denoising, registration, fusion, deconvolution, segmentation, tracking) keeping pace with acquisition, addressing I/O, compute throughput, storage, and data retention so that raw acquisitions become analysis-ready results without a growing backlog.
• Establish reproducible SOPs, QC gates, and monitoring to ensure improvements persist as the team, instruments, and datasets scale — and to measure throughput, not assume it.
• Serve as the connective tissue between the group and Biohub’s shared platforms, removing cross-team bottlenecks and helping the group hit its shared throughput milestones.
• Mentor and technically guide team members, translate scaling strategy into concrete engineering and experimental plans, and help recruit as the effort grows.
• Document architectures, protocols, release methods, code, and data for the community, in keeping with Biohub’s open-science ethos.

What You’ll Bring

• Ph.D. plus postdoctoral experience in physics, biophysics, optics/photonics, bioengineering, or a related quantitative discipline, with a body of work developing and applying advanced live-imaging methods.
• 5 years of proven experience of end-to-end ownership of a live-imaging pipeline in a developing organism — personally carrying a project from instrument and transgenic reporter lines through sample preparation, acquisition, and image analysis to quantitative, model-ready results. This is the single most important qualification for the role.
• Hands-on design and construction of light-sheet (or comparable custom optical) microscopes — building, aligning, and maintaining instruments, not only operating them.
• Direct experience imaging live embryos or other living specimens over extended time-lapse — ideally zebrafish — including sample preparation, mounting, and the husbandry that sustains long acquisitions.
• Experience developing and working with transgenic reporter lines for live imaging.
• Strong quantitative image processing and analysis, with scientific software development in Python — including building reusable, shareable analysis tools (e.g., segmentation, tracking, or spatial/neighborhood analysis).
• Quantitative or physical-biology modeling that connects measurements to theory.
• A demonstrated commitment to robustness, reproducibility, and scalability — a track record of making instruments or methods simpler, more reliable, more automated, or higher-throughput.
• Systems thinking and hands-on, collaborative leadership — the ability to reason across optics, biology, and computation, locate the binding constraint, and work directly with colleagues to remove it; excellent written and oral communication; and a genuine commitment to interdisciplinary, open science.

Nice to have

• Prior collaboration with the Royer Group, or familiarity with its instrument and software ecosystem (DaXi light-sheet, Ultrack, Zebrahub).
• Experience quantifying fast transcriptional or signaling dynamics in living organisms, particularly in oscillatory systems such as the segmentation clock.
• Authorship of open-source scientific software adopted beyond your own lab.
• Fluorescent-protein, photoconvertible, or biosensor engineering.
• Experience in increasing the throughput of acquisition or sample handling through automation (e.g., liquid handling or robotic sample handling).
• Familiarity with high-performance / GPU computing and large-scale data and storage pipelines.
• Experience with advanced or multimodal light-sheet imaging techniques.
• A record of cross-institutional, multidisciplinary collaboration spanning optics, molecular biology, and computation.

Compensation

The San Francisco, CA base pay range for a new hire in this role is $138,000 - $172,000 . 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.

This position may be eligible to participate in our discretionary annual performance bonus program. Bonus eligibility and targets are determined in accordance with our total rewards philosophy and may vary by role.

Benefits for the Whole You

We’re thankful to have an incredible team behind our work. To honor their commitment, we offer a wide range of benefits to support the people who make all we do possible.

• 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.
• Relocation support for employees who need assistance moving

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.

Voluntary Self Identification

For reporting purposes, we ask candidates to respond to the below self-identification survey. Completion of the form is entirely voluntary. Whatever your decision, it will not be considered in the hiring process or thereafter. Any information that you do provide will be recorded and maintained in a confidential file.

As set forth in the organization’s Equal Employment Opportunity policy, we do not discriminate on the basis of any protected group status under any applicable law.

If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection. Classification of protected categories is as follows:

A "disabled veteran" is one of the following: a veteran of the U.S. military, ground, naval or air service who is entitled to compensation (or who but for the receipt of military retired pay would be entitled to compensation) under laws administered by the Secretary of Veterans Affairs; or a person who was discharged or released from active duty because of a service-connected disability.

A "recently separated veteran" means any veteran during the three-year period beginning on the date of such veteran's discharge or release from active duty in the U.S. military, ground, naval, or air service.

An "active duty wartime or campaign badge veteran" means a veteran who served on active duty in the U.S. military, ground, naval or air service during a war, or in a campaign or expedition for which a campaign badge has been authorized under the laws administered by the Department of Defense.

An "Armed forces service medal veteran" means a veteran who, while serving on active duty in the U.S. military, ground, naval or air service, participated in a United States military operation for which an Armed Forces service medal was awarded pursuant to Executive Order 12985.