Senior Software Engineer - Instrument Software

What if the work you did every day could impact the lives of people you know? Or all of humanity?At Illumina, we are expanding access to genomic technology to realize health equity for billions of people around the world. Our efforts enable life-changing discoveries that are transforming human health through the early detection and diagnosis of diseases and new treatment options for patients.Working at Illumina means being part of something bigger than yourself. Every person, in every role, has the opportunity to make a difference. Surrounded by extraordinary people, inspiring leaders, and world changing projects, you will do more and become more than you ever thought possible.

We are seeking a Senior Software Engineer for our Imaging platform team. This role is central to our instrument sequencing platforms, developing the software that enables precise optical alignment and focus control for DNA sequencing. You will design and implement complex features to enable image acquisition that directly impact sequencing quality and throughput. This will involve working on core imaging algorithms as well as coordinating hardware systems for imaging workflows.

Key Responsibilities

Software Design & Development

• Own small to medium imaging subsystems and feature implementations
• Design and implement complex imaging features, including contributions to core imaging algorithms
• Develop software that coordinates optical hardware subsystems including motors, optics, and focus tracking systems
• Create design proposals at the subsystem level and provide inputs to product-level architecture

Integration & Collaboration

• Work closely with firmware, primary analysis, and hardware control abstraction layer teams to define interfaces and integration strategies
• Design and implement imaging and sequencing workflows
• Develop imaging routines that coordinate stage movement, focus control, and image capture sequences
• Optimize system performance for real-time imaging requirements

Testing & Quality

• Create comprehensive testing strategies including unit tests, automation, and hardware simulation
• Develop and maintain simulators for imaging subsystem testing
• Assist with automation testing as needed

Problem Solving

• Lead investigation and resolution of technical problems within the imaging domain
• Debug complex issues involving timing, concurrency, and hardware interactions
• Perform root cause analysis on imaging quality issues and implement systemic improvements
• Contribute to risk identification and mitigation strategies

Mentorship & Communication

• Mentor supporting engineers on technical skills in imaging software development
• Communicate technical findings and progress in cross-project settings
• Contribute to product-level technical discussions and roadmap planning

Qualifications

• Strong proficiency in an object-oriented language such as C++, Java, or C#
• Strong algorithm design, optimization, and implementation skills
• Experience with Linux environments
• Solid understanding of object-oriented analysis and design, service-oriented architecture, and event-driven patterns
• Multi-threading, synchronization, and concurrent programming

Nice to Have

• Strong proficiency in C# and .NET Core
• Experience developing software that interfaces with hardware systems
• Experience with image processing or computer vision algorithms
• REST API design
• Background in imaging-related projects or optical systems
• Experience working on complex hardware systems involving optics, motors, or precision motion control
• Performance profiling and optimization
• CI/CD pipeline design and implementation
• Proficiency with Atlassian tools (Jira) and requirements management tools

Education & Experience

• Bachelor's degree in Computer Science, Software Engineering, Electrical Engineering, or related field
• 5+ years of professional software development experience

#LI-HYBRID

The estimated base salary range for the Senior Software Engineer - Instrument Software role based in the United States of America is: $129,400 - $194,000. Should the level or location of the role change during the hiring process, the applicable base pay range may be updated accordingly. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Additionally, all employees are eligible for one of our variable cash programs (bonus or commission) and eligible roles may receive equity as part of the compensation package. We offer a wide range of benefits as innovative as our work, including access to genomics sequencing, family planning, health/dental/vision, retirement benefits, and paid time off.
We are a company deeply rooted in belonging, promoting an inclusive environment where employees feel valued and empowered to contribute to our mission. Built on a strong foundation, Illumina has always prioritized openness, collaboration, and seeking alternative perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and offer opportunities to engage in social responsibility. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. Illumina conducts background checks on applicants for whom a conditional offer of employment has been made. Qualified applicants with arrest or conviction records will be considered for employment in accordance with applicable local, state, and federal laws. Background check results may potentially result in the withdrawal of a conditional offer of employment. The background check process and any decisions made as a result shall be made in accordance with all applicable local, state, and federal laws. Illumina prohibits the use of generative artificial intelligence (AI) in the application and interview process. If you require accommodation to complete the application or interview process, please contact To learn more, visit: . The position will be posted until a final candidate is selected or the requisition has a sufficient number of qualified applicants. This role is not eligible for visa sponsorship.