Senior Software Engineer II, Instrument Software & Metrology

Madrona Venture Labs; San Carlos (CA); On-site; USD 150,000 - 210,000; Full time

Job summary

Nautilus in San Carlos, CA is seeking a Senior Software Engineer II to join our team and help advance a single‑molecule proteomics platform. You will design software to orchestrate instrument hardware, monitor data quality, and verify optical and fluidic system performance, enabling reliable biological insights.

You will collaborate with hardware engineers, bioinformaticians, and biology teams to translate customer needs into data quality standards, drive architecture decisions, mentor peers,

Qualifications

• 6+ years of professional software engineering experience.
• Expertise with Python and experience with C++.
• Experience interfacing software with hardware.
• Experience with CI/CD and automated testing pipelines.
• Skills in data analysis to inform technical decisions.
• Excellent communication and cross‑functional collaboration skills.
• Care about full lifecycle: design, testing, observability, maintainability.

Responsibilities

• Own and deliver important capabilities within the Instrument Software stack, including orchestration of hardware and telemetry warehousing.
• Collaborate with hardware engineers and scientists to measure and validate instrument performance during bring‑up and after delivery.
• Drive cross‑functional decisions using multivariate sensor telemetry and quality control data.
• Develop tools for rapid diagnosis and resolution of instrument support issues with Operations and Technical Support.
• Engage with bioinformaticians and product teams to understand customer data goals and instrument behavior.

Skills

Python

C++

Hardware interfacing

CI/CD

Data analysis

Communication

Ownership

Education

Bachelor's degree or equivalent

Tools

CI/CD pipelines

Job description

At Nautilus, we have a big and important mission: improve the health of millions by unleashing the potential of the proteome to accelerate drug development and enable a new world of precision and personalized medicine. We are developing a single-molecule protein analysis platform of unprecedented sensitivity, scale, and ease of use that we believe will democratize access to the proteome – one of the most dynamic and valuable sources of biological insight. To accomplish this, we are pursuing hard scientific problems with an entrepreneurial mindset and creating a world-class team of builders, innovators, and dreamers across a wide range of disciplines.

We are hiring a Senior Software Engineer II to join our growing team. This multifaceted role is central to the reliability of the instrument our customers depend on. You will design and deliver essential software to orchestrate instrument hardware devices, efficiently monitor quality control data, and verify the performance of onboard optics, fluidics, and other mechanical systems. You will partner closely with peers across engineering, bioinformatics, and biology teams to understand how instrument performance impacts biological insights and will guide cross‑disciplinary efforts to translate customer needs into data quality standards. Your strong communication, leadership, and technical skills, as well as an eagerness to learn new domains, will have a meaningful impact on our team and the company on our path to the future.

This position will report to the Senior Manager, Image Processing and is located in San Carlos, CA.

Here’s what you’ll be doing:

• You will own and deliver important capabilities within our Instrument Software stack. This will include orchestration of hardware components, measurement of instrument performance, warehousing of telemetry, and integration with systems that turn data into biological insights.

• You will collaborate with hardware engineers and integration scientists to develop tools for measuring and validating instrument performance during bring‑up, and for ensuring product quality stays high once delivered to a customer.

• You will drive cross‑functional decisions about our platform’s development using custom analysis of multivariate sensor telemetry and quality control data.

• You will develop tools to enable rapid diagnosis and resolution of instrument support issues alongside partners in Operations and Technical Support.

• You will bring genuine curiosity to the science behind the data, working alongside bioinformaticians, biologists, and product teams to deeply understand what our customers are trying to learn from their data and how our instrument’s behavior impacts their goals.

• You will lead with ownership. You will drive technical design, contribute to architecture decisions, and hold a high bar for software quality. You will also help develop the engineers around you through thoughtful code review, mentorship, and honest technical dialogue.

• You will join a tight‑knit team of friendly people solving meaningful problems together.

We need to see:

• 6+ years of professional experience in a high‑performing software engineering organization, plus a relevant 4‑year degree or equivalent experience.

• Expertise with Python and experience with C++.

• Experience building software that reliably interfaces with hardware.

• Experience with CI/CD. You've built or maintained pipelines for automated testing, builds, and artifact management, and you know how to get code from commit to production reliably.

• Skills in data analysis. You can develop useful metrics and make data‑driven technical decisions.

• Excellent communication and cross‑functional collaboration skills. You’re comfortable explaining software concepts to non‑software audiences and building alignment from ambiguity.

• You care about the full lifecycle of what you build—design, testing, observability, and long‑term maintainability—and have demonstrated it by shipping a product customers love.

• You’re excited to learn from others and develop skills outside of your typical area of expertise.

It’s a plus if:

• You are experienced with optical systems, especially TDI cameras and hardware‑controlled autofocus.

• You have experience in classical Image Processing / Computer Vision algorithms.

• You have built hardware test software or contributed software to a manufacturing line.

• You have worked in biotechnology and/or startups before.

Nautilus Team Culture

• We are curious go‑getters: this is a team of life‑long learners who aren’t afraid to tackle the big challenges while continuously pushing ourselves forward.

• We are detail oriented: we do great science by working smart and with diligence, and by learning from our mistakes.

• We are easy to work with: we want our workplace to be one where everyone can share their perspective and be treated with respect and kindness.