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Agent guide: [/agents.md](https://www.wearedevelopers.com/agents.md). --- # Scientist II, Scaling Lead - **Company:** BIOHUB LLC - **Location:** San Francisco, CA, United States - **Experience:** Expert - **Salary:** $138,000.0 - $172,000.0 - **Contract:** Permanent contract - **Skills:** Big Data, Image Analysis, Data Retention, General-Purpose Computing on Graphics Processing Units, Imaging Technology, Python (Programming Language), Open Source Technology, Software Engineering, Data Pipelines, Data Generation - **Published:** September 4, 2026 - **Apply:** https://startup.jobs/scientist-ii-scaling-lead-biohub-9793300 ## About the Role * 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., * 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. ## Description 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. ## Related Videos - [Alibaba Big Data and Machine Learning Technology](https://www.wearedevelopers.com/videos/37-alibaba-big-data-and-machine-learning-technology) - [Geometric deep learning for drug discovery](https://www.wearedevelopers.com/videos/264-geometric-deep-learning-for-drug-discovery) - [Generate AI in the Browser with Chrome AI - Raymond Camden](https://www.wearedevelopers.com/videos/1770-generate-ai-in-the-browser-with-chrome-ai-raymond-camden) - [Architecting the Future: Leveraging AI, Cloud, and Data for Business Success](https://www.wearedevelopers.com/videos/1096-architecting-the-future-leveraging-ai-cloud-and-data-for-business-success) - [Unboxing the DeepFace](https://www.wearedevelopers.com/videos/335-unboxing-the-deepface) - [Strange New Worlds: shaping the future of the digital age](https://www.wearedevelopers.com/videos/677-strange-new-worlds-shaping-the-future-of-the-digital-age) ## Related Articles - [How We Built a Worry-Free System That Runs for 10+ Years – And What We’d Do Again](https://www.wearedevelopers.com/magazine/751-how-we-built-a-worry-free-system-that-runs-for-10-years-and-what-we-d-do-again) - [The Biggest German Tech Companies](https://www.wearedevelopers.com/magazine/424-the-biggest-german-tech-companies) - [Résumé-Driven Development: How IT trends affect the job market for software developers](https://www.wearedevelopers.com/magazine/59-resume-driven-development-how-it-trends-affect-the-job-market-for-software-developers) - [The Fastest-Growing Tech Sectors to Look Out for in 2025](https://www.wearedevelopers.com/magazine/373-the-fastest-growing-tech-sectors-to-look-out-for-in-2025) - [Highest Paying Tech Companies for Developers](https://www.wearedevelopers.com/magazine/220-highest-paying-tech-companies-for-developers) - [Dev Digest 121 - AI goes offline](https://www.wearedevelopers.com/magazine/456-dev-digest-121-ai-goes-offline)