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Senior Software Engineer, Instrument Control

San Diego, CA

We are looking for an experienced and ambitious instrument control software engineer to join our instrument software team. We are developing advanced life science research instruments that combine precision hardware control, imaging, and automation. Our software is at the intersection of control systems, hardware communication interfaces, distributed services, and Linux applications. This complex system requires experienced software engineers to maintain and improve existing code, as well as enable us to continue scaling the capabilities and throughput of our instrument platform as we develop future generations of instruments. 

This is an opportunity to work across the full technology stack—from low-level hardware integration and instrument automation to distributed services and user-facing applications—while helping shape the architecture of next-generation scientific instruments. 

As part of our team, your core responsibilities will be:  

  • Design, develop, and maintain software for the instrument, ensuring high performance and reliability. 
  • Develop and integrate data acquisition, motion control, signal processing, data analysis, automated workflows, and user interfaces for a complex scientific instrument. 
  • Collaborate with systems integration and engineering teams to define and implement new instrument functionality. 
  • Refactor and improve existing software architecture to enhance maintainability and reduce technical debt. 
  • Document software designs, code, and processes to ensure clarity and maintainability. 
  • Troubleshoot and debug software issues, providing timely resolutions. 

 

Qualifications 

Baseline skills/experiences/attributes: 

  • Bachelor’s degree in Computer Science, Electrical Engineering or related discipline (or equivalent practical experience) 
  • 5+ years of professional experience in software development, with a strong focus on C# 
  • Experience with .NET 6+ for developing and maintaining cross-platform applications 
  • Familiarity with Linux operating systems (Ubuntu preferred) 
  • Proficiency with Git and collaborative development workflows, including code review and Agile/Scrum practices 
  • Experience with automated testing (unit and integration) and CI/CD pipelines 
  • Experience with multi-threaded programming and real-time data acquisition 
  • Experience with RPC frameworks (e.g., gRPC) for inter-process and inter-service communication 
  • Proven track record in software architecture improvement, refactoring, and managing technical debt 
  • Strong documentation skills to ensure maintainability and clarity of the codebase 
  • Experience debugging, profiling, and optimizing software for performance, memory usage, and real-time constraints 

Ideally, you also have these skills/experiences/attributes (but it’s ok if you don’t!): 

  • Interfacing with communication protocols (Serial, USB, I2C, CAN) 
  • Knowledge of control systems, including PID control loops, motion control, and trajectory planning 
  • Proficiency in developing GUIs using Avalonia 
  • Experience with Python scripting for automation and control logic 
  • Experience with Linux system-level scripting and configuration (e.g., bash, systemd, udev) 

 

The estimated base salary range for this position in the United States is $155,000 - $175,000. In addition to base salary, full-time employees are eligible to participate in Quantum-Si's discretionary annual bonus program and may receive equity awards as part of the total compensation package. Actual compensation will be determined based on a variety of factors, including, but not limited to, the position level, relevant skills, knowledge, experience, qualifications, geographic location, internal equity, and market data.

Quantum-Si also offers a competitive benefits package designed to support employees' health, well-being, work-life balance, and family needs. Benefits include:

· Comprehensive medical, dental, and vision insurance coverage

· Health Savings Account (HSA) and Flexible Spending Account (FSA) options, where applicable

· Company-paid life and accidental death & dismemberment (AD&D) insurance

· Short-term and long-term disability coverage

· Employee Assistance Program (EAP) resources to support personal and professional well-being

· Discretionary paid time off and company-paid holidays

· Parental leave to support employees welcoming and caring for a new child

· 401(k) retirement savings plan with both pre-tax and Roth contribution options

Additional Information

Candidates must be authorized to work in the United States. Quantum-Si does not provide employment-based immigration sponsorship of any kind for this position, including support for applicants currently pursuing permanent residency (Green Card sponsorship).

 

Quantum-Si does not accept unsolicited agency resumes.

 

Quantum-Si is an E-Verify and equal opportunity employer regardless of race, color, ancestry, religion, gender, national origin, sexual orientation, age, citizenship, marital status, disability or Veteran status. All your information will be kept confidential according to EEO guidelines.

 

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