Senior Software Engineer, Imaging

The Opportunity

insitro is an ML-driven biotech company tackling the grand challenge of drug discovery. We are transforming the pace and success of drug discovery by uniting biology, highly automated laboratory science, and machine learning.

Our teams are responsible for generating rich, large-scale datasets—from high-content cellular microscopy and functional assays to single-cell genomics—and translating them into actionable, machine-learned insights for target identification and drug development. We are a collaborative group of platform engineers and scientists committed to building reliable, state-of-the-art systems to enable discovery at unprecedented scale.

 We are seeking an experienced Senior Software Engineer to join our Imaging Software Team. This role is a unique opportunity to define and expand our Computer Vision and ML infrastructure across the full imaging data lineage, from on-microscope acquisition to high-throughput ML pipelines.

You will be responsible for building platform features that make novel imaging modalities and ML-derived phenotypes integral to our discovery workflows. Your work directly bridges experimental science and modern machine learning, transforming cutting-edge research prototypes into validated screening workflows that operate robustly at laboratory automation scale.

This position offers a clear path to shaping the future of drug discovery by setting the technical direction for how imaging, automation, and machine learning converge. This role will report to the Senior Manager, Imaging Software and will be hybrid with the expectation of being onsite 3 days a week.

Responsibilities

• Platform Enablement: Partner with lab and ML scientists to design, develop, and scale platform capabilities required to design, run, and interpret ML-powered high-content screens.

• Production Hardening: Scale and harden complex image processing and ML workflows, taking them from research prototype to reliable, routine use.

• User Tooling: Build and evolve robust tools and interactive interfaces for data exploration, quality assessment, and visualization to help scientists iterate quickly on experimental data.

• Collaboration: Collaborate closely with lab scientists, ML scientists, and microscopy teams to translate complex experimental needs into clear, actionable technical plans and high-quality, shipped software.

• Data Integrity: Set and uphold best-in-class practices for data integrity, lineage, reproducibility, and observability across the entire imaging data lifecycle.

About You

We are looking for a highly motivated and collaborative engineer who is passionate about enabling scientific breakthroughs through robust platform development.

• Senior Experience: You bring 6+ years of professional experience building and operating production-grade software and high-throughput data pipelines, primarily using Python.

• Architectural Leadership: You have a proven ability to own complex, end-to-end projects, making thoughtful architectural trade-offs, and delivering solutions incrementally with a focus on long-term maintainability.

• Cross-Functional Partnership: You thrive in cross-functional settings and excel at translating abstract research and experimental needs into practical, scalable software systems.

• Mentorship & Documentation: You enjoy sharing knowledge, mentoring others, and are capable of writing clear, exemplary technical specifications and documentation.

• ML Platform Focus (Highly Valued): Direct experience designing, building, and deploying machine learning pipelines, visualizations, and QC processes for large-scale imaging or similar high-dimensional datasets.

• Biotech Context (A Plus): Prior experience working with large biological datasets and/or high-content imaging is beneficial.

• Relevant Technologies: Familiarity with our core Python-first ML stack, distributed compute technologies (e.g., PyTorch/Lightning, Ray, Kubernetes), and workflow orchestration tools (e.g., Argo, Airflow, or redun).

Compensation & Benefits at insitro

Our target starting salary for successful US-based applicants for this role is $185,000 - $210,000. 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 also provides our employees:

• 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 cafe with daily lunch and breakfast for employees who are either onsite or hybrid

• Access to free onsite fitness center for employees who are either onsite or hybrid

• Access to a free commuter bus and ferry 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.

Please be aware of recruitment scams: we never request payments, all recruitment communications are from @insitro.com, and if in doubt, contact us at [email protected].

About insitro

insitro is a drug discovery and development company using machine learning (ML) and data at scale to decode biology for transformative medicines. At the core of insitro’s approach is the convergence of in-house generated multi-modal cellular data and high-content phenotypic human cohort data. We rely on these data to develop ML-driven, predictive disease models that uncover underlying biologic state and elucidate critical drivers of disease. These powerful models rely on extensive biological and computational infrastructure and allow insitro to advance novel targets and patient biomarkers, design therapeutics and inform clinical strategy. insitro is advancing a wholly owned and partnered pipeline of insights and therapeutics in neuroscience and metabolism. Since launching in 2018, insitro has raised over $700 million from top tech, biotech and crossover investors, and from collaborations with pharmaceutical partners. For more information on insitro, please visit www.insitro.com.