Optics / Microscopy Principal Scientist

Vertex Pharmaceuticals; San Diego (CA); On-site; USD 144,000 - 217,000; Full time

Benefits offered by this job

Total Rewards benefits

Paid time off

Commuting subsidy

Equity awards

Job summary

Vertex Pharmaceuticals, located in San Diego, seeks a Principal Scientist to lead optical design and advanced imaging instrument development within the Engineering & Applied Physics group. You will work with physicists, biologists, chemists, and software specialists to create custom instruments that accelerate drug discovery.

The role requires a PhD with 8+ years of relevant experience in optics and imaging, including modalities like widefield, confocal, light sheet, super-resolution, or

Qualifications

• PhD in a relevant field with 8+ years of experience.
• Proven hands-on experience designing imaging platforms or technologies, e.g., optical table setups, in biological research.
• Proficiency in programming for data analysis and instrument control.

Responsibilities

• Collaborate with cross-disciplinary teams to understand project needs and identify opportunities for custom instrumentation.
• Align stakeholders and propose new projects to senior leaders.
• Design and build prototype optical instruments.
• Conduct proof-of-concept experiments and optimize assays with biologists and chemists.
• Work with engineers to specify, design, and build production-ready instruments for automated drug discovery.
• Communicate findings through reports, presentations, and discussions.

Skills

Optical design

Ray tracing

ABCD matrices

Gaussian beams

Optical aberrations

Automation & high-throughput

Biological imaging modalities

Mentoring & supervision

Communication

Education

PhD in Physics/Physical Chemistry/Bioengineering

Job description

Job Description

Vertex Pharmaceuticals is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious diseases. At our San Diego site, the Engineering & Applied Physics group is a dynamic, fast-paced team of 20 applied physicists and mechanical, electrical, and automation engineers. Together, we design and develop custom instruments that integrate cutting‑edge technology and full automation to accelerate Vertex's internal drug discovery pipeline. These instruments are tailored to specific project needs, enabling capabilities that are not commercially available.

We are seeking an experienced and innovative Principal Scientist with expertise in optical design, microscopy, and functional imaging to join our team. This role bridges the disciplines of science and engineering, requiring a deep understanding of disease biology and assays, as well as the ability to design and develop advanced optical instruments. While working directly in a multi-disciplinary team comprised of physicists, biologists, chemists, engineers and software specialists, the Principal Scientist will collaborate closely with drug discovery teams to ensure utility and integration of new approaches into therapeutic projects. This position offers exciting opportunities for career growth, with potential pathways to either a scientific leadership role driving cross-functional projects or a managerial role with increasing supervisory responsibilities within the group.

Key duties and responsibilities

• Collaborate with cross-disciplinary teams to understand project needs and identify opportunities where custom instrumentation can have a transformative impact.
• Align stakeholders and propose new projects to senior leaders.
• Design and build prototype optical instruments.
• Conduct proof‑of‑concept experiments and optimize assays in partnership with biologists and chemists.
• Work closely with engineers to specify, design, and build robust, production‑ready instruments for deployment in automated drug discovery applications.
• Communicate findings and progress effectively through written reports, presentations, and discussions.

Knowledge and Skills

• Knowledge of formal optical design principles, including ray tracing, ABCD matrices, Gaussian beams, and optical aberrations.
• Familiarity with formal engineering design processes, including developing quantitative instrument specifications.
• Familiarity with automation and high‑throughput screening technologies.
• Understanding of the pharmaceutical research and drug discovery process.
• Strong written and verbal communication skills.
• Experience supervising and mentoring junior researchers or staff.
• Demonstrated ability to deliver innovative solutions to complex scientific and technical challenges.

Education & Experience

• Ph.D. in Physics, Physical Chemistry, Bioengineering, or a related discipline and 8+ years of relevant experience.
• Proven hands‑on experience applying optical techniques in the design and development of novel imaging platforms or technologies (e.g., optical table setups), in biological research.
• Proficiency in programming for data analysis and instrument control.
• Experience with functional measurements in cells, such as voltage or calcium imaging.
• Expertise in multiple biological imaging modalities, such as widefield fluorescence, confocal, light sheet, super‑resolution, or two‑photon microscopy.

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Pay Range:

$144,400 - $216,600

Disclosure Statement:

The range provided is based on what we believe is a reasonable estimate for the base salary pay range for this job at the time of posting. This role is eligible for an annual bonus and annual equity awards. Some roles may also be eligible for overtime pay, in accordance with federal and state requirements. Actual base salary pay will be based on a number of factors, including skills, competencies, experience, and other job‑related factors permitted by law.

At Vertex, our Total Rewards offerings also include inclusive market‑leading benefits to meet our employees wherever they are in their career, financial, family and wellbeing journey while providing flexibility and resources to support their growth and aspirations. From medical, dental and vision benefits to generous paid time off (including a week‑long company shutdown in the Summer and the Winter), educational assistance programs including student loan repayment, a generous commuting subsidy, matching charitable donations, 401(k) and so much more.

Flex Designation:

On‑Site Designated

Flex Eligibility Status:

In this On‑Site designated role, you will work five days per week on‑site with ad hoc flexibility.

Note: The Flex status for this position is subject to Vertex's Policy on Flex @ Vertex Program and may be changed at any time.

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Company Information

Vertex is a global biotechnology company that invests in scientific innovation.

Vertex is committed to equal employment opportunity and non-discrimin