Senior Machine Learning Scientist, Imaging

insitro; South San Francisco (CA); Hybrid; USD 215,000 - 235,000; Full time

Benefits offered by this job

401(k) plan with employer matching

Medical, dental, and vision coverage

Flexible vacation policy

Paid parental leave

Quarterly budget for self-development

Support for attending professional conferences

Home office setup stipend

Monthly stipend for cell phone & internet

Onsite baristas and daily lunch

Commuter bus network access

Job summary

insitro in South San Francisco is looking for an Imaging ML Scientist to develop ML-based pipelines for insights from microscopy data. The role involves collaboration with scientists to optimize imaging workflows and developing novel computer vision methods. Candidates should have a Ph.D. in related fields or equivalent experience, strong Python skills, and familiarity with deep learning frameworks. This hybrid position requires presence on-site at least three days a week, offering a competitive salary between $215,000 - $235,000, along with various benefits including medical coverage and a flexible vacation policy.

Qualifications

• Ph.D. in computer vision, machine learning, computer science or a related discipline.
• Strong programming skills in Python, including handling TB-scale datasets.
• Experience developing models for computer vision tasks including segmentation.

Responsibilities

• Partner with scientists to design high-throughput imaging experiments.
• Develop novel ML methods for microscopy image analysis.
• Build robust image analysis workflows for user accessibility.

Skills

Computer vision

Machine learning

Python programming

Deep learning frameworks (e.g., PyTorch, TensorFlow)

Microscopy data experience

Collaboration skills

Education

Ph.D. in computer vision, machine learning, or related discipline

Master's degree with 2+ years relevant experience

Tools

AWS

SQL

Job description

The Opportunity

Imaging based phenotyping of in‑vitro biology is at the heart of insitro's efforts to accelerate drug development. At insitro, we use machine learning to derive clinically relevant insights from rich datasets generated in‑house.

As an Imaging ML Scientist, you will develop ML‑empowered computer vision pipelines to extract insights about disease mechanisms from multiple microscopy modalities. You will be part of a cross‑functional team of life scientists, software engineers, computational biologists, and machine learning scientists that strive to identify therapeutic targets and develop drugs of high efficacy and low toxicity.

You will be joining a vibrant biotech startup that is in a high growth phase, with multiple pre‑clinical drug targets in areas such as ALS and metabolic disease. A lot can change in this exciting phase, providing many opportunities for significant impact. You will work closely with a very talented team, learn a broad range of skills, and help shape insitro's culture, strategic direction, and outcomes.

This role will be reporting to the Director of Imaging, Cellular Machine Learning. This is a hybrid position that requires you to be in our South San Francisco headquarters at least three days per week. Join us, and help make a difference to patients!

Responsibilities

• Partner with experimental and computational biologists to design, troubleshoot, and optimize high-throughput imaging‑based experiments and workflows
• Identify, understand, develop, and deploy novel computer vision and machine learning methods such as segmentation, feature extraction, and representation learning to extract features from microscopy image datasets
• Work closely with software engineers to build robust and well‑tested image analysis workflows, able to be used by experimental and computational biologists with minimal direct support
• Calibrate analysis tools and workflows, define performance metrics, and conduct benchmarking to select fit‑for‑purpose solutions
• Communicate findings to cross‑functional stakeholders through reports, visualizations, presentations, and publications
• Identify novel disease‑relevant phenotypes and propose new screening paradigms that translate to actionable program decisions

About You

• Ph.D. in computer vision, machine learning, computer science or a related discipline, or equivalent practical experience (e.g., a Master's degree and 2+ years of relevant industry experience)
• Ability to communicate effectively and collaborate with people of diverse backgrounds and job functions on a daily basis
• Demonstrated ability to identify, understand, and find novel applications of state-of-the-art ML/CV methods from literature or other sources
• Strong programming skills in Python, including working with TB‑scale image datasets and leveraging modern agentic software tools to accelerate development
• Experience developing models for diverse computer vision tasks (e.g. segmentation, recognition, classification, domain adaptation) including using modern deep learning frameworks (PyTorch, TensorFlow, Keras, etc)
• Extensive hands‑on experience working with microscopy data or similar biomedical or physical imaging modalities
• Passion for making a difference in the world

Nice to Have

• Demonstrated ability to write software in a team, industry experience or substantial involvement with open source projects.
• Experience modeling with video or imaging time‑series datasets
• Experience with microscopy hardware, and/or image data acquisition in other contexts
• Understanding of optical physics, resolution, numerical aperture, etc.
• Familiarity with cloud computing services (e.g., AWS or Azure)
• Experience with database languages (e.g., SQL)
• Publication record of meaningful contributions to high‑quality work in relevant computer vision, clinical ML, or biomedical venues

Compensation & Benefits At Insitro

Our target starting salary for successful US‑based applicants for this role is $215,000 - $235,000. To determine starting pay, we consider multiple job‑related factors including a candidate's skills, education and experience, market demand, business needs, and internal parity. We may also adjust this range in the future based on market data.

This role is eligible for participation in our Annual Performance Bonus Plan (based on company targets by role level and annual company performance) and our Equity Incentive Plan, subject to the terms of those plans and associated policies.

In addition, Insitro provides its employees with the following benefits:

• 401(k) plan with employer matching for contributions
• Excellent medical, dental, and vision coverage as well as mental health and well‑being support
• Open, flexible vacation policy
• Paid parental leave of at least 16 weeks to support parents who give birth, and 10 weeks for a new parent (inclusive of birth, adoption, fostering, etc)
• Quarterly budget for books and online courses for self‑development
• Support to attend professional conferences that are meaningful to your career growth and role's responsibilities
• New hire stipend for home office setup
• Monthly cell phone & internet stipend
• Access to free onsite baristas and daily lunch for employees who are either onsite or hybrid
• Access to a free commuter bus network that provides transport to and from our South San Francisco HQ from locations all around the Bay Area

insitro is an equal opportunity employer. All applicants will be considered for employment without attention to race, color, religion, sex, sexual orientation, gender identity, national origin, veteran or disability status.

We believe diversity, equity, and inclusion need to be at the foundation of our culture. We work hard to bring together diverse teams—grounded in a wide range of expertise and life experiences—and work even harder to ensure those teams thrive in inclusive, growth‑oriented environments supported by equitable company and team practices. All candidates can expect equitable treatment, respect, and fairness throughout the interview process.