Scientist II, Scaling Lead

About the role

The Biohub is seeking a Scientist II to lead the scaling of our imaging and data-generation pipeline. This role will map the full sample-to-data pipeline, define throughput and quality targets, instrument each stage with metrics and dashboards, and diagnose and fix concrete obstacles in the sample-handling workflow.

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 the true bottlenecks.
• 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.

Requirements

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.

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.

Qualifications

• 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.

Skills

• Expertise in live-imaging methods and pipelines.
• Strong quantitative image processing and analysis skills.
• Experience with Python and scientific software development.
• Ability to work collaboratively across multiple disciplines.
• Experience with high-performance computing and large-scale data management.
• Knowledge of advanced light-sheet imaging techniques.

Benefits

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.