Senior Microscope Engineer

Eon Systems PBC; San Francisco (CA); On-site; USD 140,000 - 200,000; Full time

Benefits offered by this job

Equity and benefits

Cutting-edge field exposure

Collaborative team culture

Job summary

Eon Systems PBC in San Francisco seeks a Senior Microscope Engineer to design, build, and scale high-throughput optical microscopes for expanded brain tissue imaging. You\u2019ll lead the transition from prototype to production, enabling replication into a small fleet for large-scale acquisition.

This hands-on role requires deep optics, optomechanics, illumination, and control expertise, with a focus on robust imaging hardware and practical problem solving in a fast-paced research environment.

Qualifications

• 5+ years designing and building optical microscopy instruments, including high-throughput systems.
• Hands-on optomechanical build experience and CAD proficiency.
• Practical command of illumination sources, objectives/optics, and cameras/detectors.
• Ability to code for instrument control, automation, and image processing.
• Strong collaboration in dynamic research environments.

Responsibilities

• Design and build custom high-throughput optical microscopes for expanded tissue.
• Turn prototype into production-ready instrument with motorized staging and validated performance.
• Operate microscopes to acquire high-quality 3D image volumes with high uptime.
• Produce complete build documentation and lead replication to a small fleet.
• Troubleshoot imaging issues and perform routine maintenance.

Skills

Spinning-disk confocal

High-throughput microscopy

Optomechanics

CAD & rapid prototyping

Instrument control programming

Team collaboration

Optical design

Tools

CAD

Prototyping hardware

Imaging hardware integration

Job description

About Us

Eon is building the infrastructure for large-scale connectomics data collection, reconstruction, and brain simulation. Our mission is to enable the safe and scalable development of brain emulation technology, beginning with digital twins of model organisms.

We are developing an end‑to‑end platform that spans tissue preparation, high‑throughput microscopy, large‑scale image processing, neural reconstruction, connectome-based modeling, and embodied simulation. We are looking for exceptional engineers and scientists who can help turn biological brain data into usable computational systems.

Role

We are seeking a Senior Microscope Engineer to build and scale the imaging systems at the heart of our connectomics pipeline. You will design, build, and bring up custom high‑throughput optical microscopes optimized for imaging expanded brain tissue, take our current prototype through to a production‑ready instrument, and lead its replication into a small fleet for large‑scale acquisition.

This is a hands‑on role for someone who has personally built high‑throughput microscopes end to end — optics, optomechanics, illumination, detection, and control — and who is comfortable moving between instrument design, day‑to‑day acquisition, and the practical problem‑solving that scaling a novel imaging system demands.

Responsibilities

• Design and build custom, cost‑effective, high‑throughput optical microscopes (e.g., spinning-disk confocal) optimized for expanded tissue.
• Take a working prototype to a production‑ready instrument: motorized staging, optimized acquisition, and validated performance.
• Operate microscopes to acquire high‑resolution 3D image volumes of expanded neural tissue, sustaining high throughput and high instrument uptime.
• Produce complete build documentation — bills of materials, budgets, timelines, and assembly SOPs a technician can follow — and lead replication toward a small fleet.
• Troubleshoot imaging issues and perform routine maintenance on microscopy equipment.

Skills And Qualifications

• 5+ years designing and building optical microscopy instruments such as spinning‑disk confocal or lightsheet systems, with at least one high‑throughput microscope built end to end.
• Strong optical design and alignment skills, and hands‑on optomechanical build experience (CAD and rapid prototyping a plus).
• Practical command of illumination sources, objective/optics selection, and cameras/detectors.
• Ability to code for instrument control, automation, and image processing and analysis.
• Ability to work collaboratively in a dynamic, fast‑paced research environment.

Nice to have

• High‑speed image‑sensor integration, FPGA or custom data‑acquisition electronics e
• Experience with the storage and data pipelines required for large‑scale imaging.

Representative projects

• Bringing a prototype microscope to production and validating its performance on expanded tissue.
• Scaling from a single validated instrument to a small fleet for large‑scale acquisition.
• Developing robust mounting and handling for large expanded samples.

Salary and Benefits

$140,000–$200,000 base salary depending on experience, plus equity and benefits.

• plus equity and benefits.

Opportunity to work in a cutting‑edge field that impacts neuroscience and AI safety.