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System Design Engineer, Principal
| Department: | ND - SIPE |
System Design Engineer, Principal
The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.
The Allen Institute for Neural Dynamics is seeking a Principal System Design Engineer to join the Scientific Instrumentation and Process Engineering (SIPE) team. In this critical role, the principal engineer will lead the design and integration of advanced scientific instruments, developing innovative and robust solutions that meet the complex demands of neuroscience research. Responsibilities include setting technical direction, mentoring senior engineers, and ensuring all design and execution processes meet the highest standards of excellence.
Candidates for this role should possess extensive experience in systems engineering, with a proven background in integrating both hardware and software components. The ability to lead multidisciplinary teams is essential, as collaboration is a key aspect of the SIPE team’s approach. Mastery of system design principles is required, along with demonstrated leadership in technical innovation.
At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.
We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.
We are an equal opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.
Essential Functions
- Spearhead the architecture, design, and integration of complex scientific instruments that combine robotics, imaging, automation, and control systems
- Serve as a pillar of technical leadership for SIPE initiatives, providing guidance to senior and mid-level engineers and overseeing collaborative development efforts that span both hardware and software domains
- Manage projects from concept through production, including feasibility studies, prototyping, and final rollout, while formulating comprehensive project plans to ensure timely delivery
- Collaborate with scientific stakeholders to capture system requirements, translate them into actionable team tasks, and remain engaged throughout prototyping and development
- Set and refine standards for engineering processes, including documentation, validation, source code management, issue tracking, deployment procedures, and observability
- Design, develop, evaluate, and implement equipment for control operations, data acquisition, and analysis workflows, ensuring reliable collection of large-scale datasets
- Leverage broad technical expertise and creativity to resolve complex challenges
- Champion organizational strategies that enhance innovation, open science, and operational efficiency
Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.
Required Education and Experience
- Bachelor's degree in mechanical, electrical, optical, or systems engineering, or related field; or equivalent combination of education and experience
- 7 years of progressive experience in system design engineering, including leadership of complex instrumentation projects
- Demonstrated success in delivering production-ready systems for scientific or medical instrumentation
Preferred Experience and Competencies
- Master’s degree or PhD in mechanical, electrical, optical, or systems engineering
- 15+ years of combined education and experience in multidisciplinary system design
- Multidisciplinary expertise: Demonstrated leadership-level or hands-on expertise in three or more of the following technical domains:
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Systems Integration: Proven ability to design and integrate complex systems across mechanical, electrical, optical, and software domains
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Optical Engineering: Deep knowledge of microscopy techniques (confocal, multiphoton, fluorescence) and application of lenses, mirrors, filters, and opto-mechanical components
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Electronics: Design of AC/DC circuits, electrical schematics, and PCB layouts for microcontrollers and embedded systems
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Software: Knowledge and familiarity of programming languages such as C/C++, C#, Matlab or Python, the software development lifecycle, and common software development tools, e.g. IDE’s, Git, CI/CD
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Imaging & Data Acquisition: Integration of imaging systems and analog/digital data acquisition tools into automated workflows
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Robotics & Automation: Development of robotic systems for surgical, tissue handling, and precision automation applications
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Fluidics: Application of fluidics concepts for gases and Newtonian fluids, including regulators, valves, flow control, gauges, and fittings
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AI and Machine Learning: Hands-on experience applying artificial intelligence and machine learning algorithms for image analysis, anomaly detection, and predictive maintenance within automated instrumentation and high-throughput workflows
Physical Demands
- Occasional lifting up to 30 pounds
- Fine motor movements in fingers/hands to operate computers and other office equipment
- Push/pull up to 50 lbs
- Stooping, bending, crouching
- Reaching or climbing ladders
Position Type/Expected Hours of Work
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This role is currently working onsite and is expected to work onsite for the majority of the working hours. We are a Washington State employer, and the primary work location for Allen Institute employees is 710 9th Ave N.; any remote work must be performed in Washington State
Additional Comments
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**Please note, this opportunity does not provide work visa sponsorship or relocation assistance**
Annualized Salary Range
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$167,850 - $209,750 *
* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable
Benefits
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Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.
It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.
