Senior Instrumentation Engineer

Level: Senior / Staff    Type: Full-time, Boston (on-site, with limited travel)

About HyperSpectral

HyperSpectral builds Physical AI for the molecular world. We pair advanced spectral sensors with AI that reads the molecular fingerprints encoded in light, identifying pathogens, chemical contaminants, drug formulations, and material properties from the spectra they produce. Sepsis identification in 30 minutes instead of 4 days. Pharmaceutical quality control in real time instead of offline. Food contamination detection in minutes instead of 3 to 5 days.

Our SpecAI platform and CortX runtime serve customers across clinical diagnostics, biopharma manufacturing, food safety, and defense. The platform is designed for FDA-regulated medical and food applications and operates on SOC 2 controls. We are headquartered in the Cambridge / Boston area.

We are a lean, distributed team that scales through tooling and coordination, not headcount. Every hire is expected to operate comfortably in a controlled regulated environment, work AI-first as the primary method of producing output, and partner across functions and time zones without waiting for scheduled syncs.

Why This Role Matters

Our platform depends on working integrated instrumentation. The Senior Instrumentation Engineer is the single hire who takes that integrated reference device from build documentation to a calibrated, validated bench unit, owns its daily operation, and drives the engineering decisions that move it toward an operational product. The role is hands-on across mechanical, microfluidic, optical, and electrical domains. The right person is deep enough in each layer to debug across them.

About the Role

Lead the hands-on build, integration, and operation of advanced analytical instruments that combine sample preparation with spectroscopic detection. This role is responsible for taking an instrument from build documentation to a working, calibrated, validated bench unit, and then for owning its day-to-day operation, its long-term performance, and the engineering decisions that move it toward an operational product.

The work spans mechanical, microfluidic, optical, and electrical domains. It is not a manager role and it is not a research scientist role. It is the senior engineer who actually builds, integrates, and operates the system and is deep enough in each layer to debug across them.

Key Responsibilities

Instrument Build and Integration

• Build, calibrate, and validate integrated analytical instruments that combine microfluidic sample preparation with optical detection


• Source, qualify, and integrate microfluidic components from external microfabrication vendors; transition from hand-assembled prototypes to repeatable supply


• Integrate microfluidic front ends with optical readout, including sample handoff geometry, alignment, focus control, and acquisition triggering

Optical and Electrical Systems

• Characterize and tune the optical path


• Own electrical subsystem design and maintenance for the integrated instrument


• Diagnose cross-domain failures (a fluidic anomaly that surfaces as a spectral artifact, an electrical noise source that degrades capture efficiency) by reasoning across all four engineering layers

Validation and Regulated Operation

• Author andmaintainbuild SOPs, calibration procedures, performance qualification scripts, and acceptance criteria suitable for a regulated medical device context


• Operate the instrument daily for internal studies; produce the data that feeds regulatory submissions and the analytics pipeline

Cross-Functional and AI-First Practice

• Partner with the AI / ML function on data quality, instrument-side automation, and the path toward more autonomous workflows


• Use AI-assisted development tools (Claude Code, Cursor, Copilot, and equivalent) as a primary work method for instrument control software, scripting, and documentation


• Coordinate continuously with external technical partners, vendors, and cross-functional internal teams

Required Qualifications

• 7 years of professional engineering experience building andoperatingintegrated scientific instruments or analytical devices. Academic instrument work and scientific instrument industry experience both qualify


• Demonstrated cross-disciplinary depth across at least three of: mechanical engineering, microfluidics, optical engineering, electrical engineering. Depth, not survey familiarity, in each claimed area


• Hands-on experience with microfluidic device assembly, fluid handling at micro-liter-per-minute scale, and electrokinetic or analogous separation techniques


• Direct experience with confocal optical instrumentation. Confocal Raman is preferred; equivalent confocal optical experience (such as fluorescence confocal or hyperspectral imaging) is acceptable when paired with Raman exposure


• Working competence with electrical subsystem design and debug for scientific instruments: drive electronics, sensors, motion control, safety interlocks


• Experience reading vendor or academic build documentation and converting it into a working device, includingidentifyingand resolving gaps the documentation did not anticipate


• Demonstrated current use of AI-assisted development tools as a primary work method for code, scripting, and documentation


• Comfortoperatingin a regulated context with documented procedures, audit trails, and validation expectations. Formal FDA experience is notrequired, but the working style must fit


• Willingness and ability to travel periodically (domestic and international)

Preferred Qualifications

• Direct microfluidic chip design or microfabrication experience (PDMS, glass, or polymer chip processes; photolithography; electrode patterning)


• Prior work with biological sample preparation or sample handling across complex matrices


• Production Raman instrument experience or equivalent platforms


• LabVIEW, Python, or C / C instrument control development; integration of disparate vendor SDKs into a unified acquisition pipeline


• Familiarity with FDA SaMD, 21 CFR Part 11, or IVD development frameworks


• Graduate degree in mechanical, optical, electrical, or biomedical engineering, or applied physics. A strong industrytrack recordcan substitute

Work Environment and Schedule

• On-site at our Cambridge, MA laboratory


• Full-time, exempt


• Periodic domestic and international travel

• Small, collaborative engineering team within a lean company

Compensation

Competitive base salary commensurate with experience and seniority level. Equity participation as part of standard offer. Comprehensive benefits package including health, dental, and vision. Full-time exempt position.

How to Apply

Send a resume and a short note describing one integrated instrument you have personally built or substantially rebuilt, including the cross-domain debugging story that you are proudest of. Portfolio links, GitHub, or publication references are welcome.