Optics / Microscopy Principal Scientist

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

Job summary

Vertex Pharmaceuticals is seeking a Principal Scientist in San Diego to lead optical instrument design and advanced imaging development for drug discovery. You will work with a multidisciplinary team to translate biology into engineering solutions, delivering innovative platforms and automated systems.

The role requires a PhD with 8+ years, strong project leadership, and hands-on experience with imaging modalities and data-driven instrument control.

Qualifications

• PhD with 8+ years of relevant optical design experience in biology or medicine.
• Hands-on experience developing imaging platforms and optical instruments.
• Proficiency in programming for data analysis and instrument control.

Responsibilities

• Collaborate with cross-disciplinary teams to identify opportunities for custom instrumentation.
• Design and build prototype optical instruments and production-ready systems.
• Lead proof-of-concept experiments, optimize assays with biologists and chemists.
• Work with engineers to deploy robust instruments for automated drug discovery.
• Communicate findings through reports and presentations.

Skills

Optical design

Ray tracing

ABCD matrices

Gaussian beams

Optical aberrations

Automation

High-throughput screening

Biology integration

Communication skills

Mentoring

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.

#LI-KM1 #LI-ONSITE

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

Designation 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.

Company Information

Vertex is a global biotechnology company that invests in scientific innovation. Vertex is committed to equal employment opportunity and non‑discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry, ethnicity, disability, veteran status, genetic information, sexual orientation, marital status, or any characteristic protected under applicable law. Vertex is an E‑Verify Employer in the United States. Vertex will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law. Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should make a request to the recruiter or hiring manager, or contact Talent Acquisition at [e-mail]

Help Us Achieve Our Mission: Vertex is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious diseases. The company has approved medicines that treat the underlying causes of multiple chronic, life‑shortening genetic diseases — cystic fibrosis, sickle cell disease and transfusion‑dependent beta thalassemia — and continues to advance clinical and research programs in these diseases. Vertex also has a robust clinical pipeline of investigational therapies across a range of modalities in other serious diseases where it has deep insight into causal human biology, including APOL1‑mediated kidney disease, acute and neuropathic pain, type 1 diabetes, myotonic dystrophy type 1 and alpha‑1 antitrypsin deficiency. Founded in 1989 in Cambridge, Mass., Vertex’s global headquarters is now located in Boston’s Innovation District and its international headquarters is in London. Additionally, the company has research and development sites and commercial offices in North America, Europe, Australia, Latin America and the Middle East. Vertex is consistently recognized as one of the industry's top places to work, including 14 consecutive years on Science magazine’s Top Employers list and one of Fortune’s 100 Best Companies to Work For. For company updates and to learn more about Vertex's history of innovation, visit www.vrtx.com or follow us on Facebook, Twitter/X, LinkedIn, YouTube and Instagram. The diversity and authenticity of our people is part of what makes Vertex unique, and we recognize that each employee brings diverse perspectives and strengths. By embracing those strengths and celebrating differences, we are fostering an inclusive culture where each of us can bring our authentic selves to work, inspire innovation together, and change people’s lives. Our vision is clear: to be the place where an authentic, diverse mix of talent want to come, to stay, and do their best work.