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Allen Institute

Software Engineer III – Scientific Instrumentation and Process Engineering

Seattle, WA, United States

$148,800 - $186,000*

Apply on alleninstitute.clearcompany.com About employer

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Job details

Pay: $148,800 - $186,000*
Posting language: English
Posted: Nov 5, 2026

Original job description

Software Engineer III – Scientific Instrumentation and Process Engineering

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

We are searching for a Software Engineer III to independently develop, integrate, and support software for complex automated scientific instruments and hardware-integrated systems. This engineer will own substantial software components and bounded subsystem-level work; translate scientific, operational, and system requirements into maintainable designs and implementation plans; and collaborate with senior engineers, scientists, hardware engineers, systems engineers, and end users. The role contributes to architecture and technical decisions while delivering reliable solutions across robotics, motion control, machine vision, data acquisition, infrastructure, telemetry, user interfaces, and electromechanical subsystems. Through iterative build-test-learn cycles, the engineer will use evidence from prototypes, simulations, experiments, and laboratory operation to reduce uncertainty and improve system performance.

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

Independently design, implement, test, and maintain substantial software components and bounded subsystems for automated scientific instruments, following established program architecture and technical direction
Translate scientific, operational, user, and system requirements into software designs, estimates, implementation plans, milestones, and delivered functionality
Integrate software with robotics, motion control, imaging, sensors, actuators, data-acquisition devices, and other electromechanical subsystems
Develop and maintain user interfaces, data collection and transfer workflows, infrastructure automation, and supporting services needed for dependable laboratory operation
Contribute to modular architecture, stable device interfaces, interprocess communication, data flows, hardware-abstraction layers, and event-driven or state-machine behaviors
Plan and execute iterative build-test-learn cycles using prototypes, simulation, experiments, telemetry, and operator feedback to reduce technical uncertainty and refine requirements
Write and maintain unit, integration, system, and automated tests; contribute to CI/CD, release, deployment, logging, monitoring, and observability practices
Lead integration and troubleshooting for assigned components or bounded subsystems from prototype through verification, validation, deployment, and laboratory operation; escalate cross-system risks and complex failures
Own software and process technical learning loops aligned with the candidate's interest and skills or team needs
Collaborate with scientists, hardware and systems engineers, software peers, and end users; participate in design and code reviews; document decisions and results; share technical knowledge; and propose practical improvements to engineering practices

*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 computer science, software engineering, computer engineering, robotics, or a related technical field, or an equivalent combination of education and experience
At least 5 years of professional software engineering experience developing, testing, integrating, and maintaining software applications, services, or hardware-integrated systems
3 years of experience with robotics, motion planning or control, machine vision, image processing, and precision automation
Familiarity with vision based quality assessment, image registration, software product instrumentation, and telemetry analysis including root cause analysis
Demonstrated ability to independently own substantial software components or bounded subsystem-level work within established architecture and technical direction
Professional experience developing software in Python, C++, C#, or comparable languages used for instrument control, automation, data systems, or user applications
Experience integrating software with hardware devices or external systems, including motion systems, cameras, sensors, actuators, data-acquisition devices, or related instrumentation
Experience with source control, code review, automated testing, continuous integration, release practices, troubleshooting, and technical documentation
Experience translating user and system requirements into software designs, estimates, implementation plans, milestones, and delivered functionality while communicating risks and tradeoffs

Preferred Education and Experience

Experience with robotics, motion planning or control, machine vision, image processing, precision automation, or other complex hardware-integrated systems
Experience with distributed systems, interprocess communication, hardware abstraction, device APIs, event-driven systems, or state-machine architectures
Experience developing user interfaces, data acquisition and management workflows, infrastructure automation, telemetry, logging, and system health monitoring
Experience using prototypes, simulation, experiments, telemetry, or user feedback in iterative learning cycles to evaluate alternatives, reduce uncertainty, and improve a system
Experience moving components or subsystems from prototype into reliable laboratory or production operation, including verification, validation, deployment, and sustainment
Experience with safety critical software systems and design for reliabillity, maintainability, and support of software products
Experience collaborating across scientific, software, electrical, mechanical, and systems engineering disciplines and sharing technical knowledge with peers
Experience using modern software and AI-assisted engineering tools responsibly to improve development, testing, documentation, or maintenance

Work Environment

Work is performed in office, software-development, engineering, and laboratory environments
Regular onsite work with automated scientific instruments, robotics, imaging systems, and electromechanical prototypes
Possible exposure to laboratory materials or chemical, biological, mechanical, electrical, or other hazards; use of required personal protective equipment and adherence to established safety procedures are expected

Physical Demands

Occasional lifting up to 30 pounds
Fine motor movements in fingers and hands to operate computers, instruments, and other office or laboratory equipment
Occasional pushing or pulling of laboratory carts or equipment up to 50 pounds
Occasional stooping, bending, crouching, and reaching while integrating or servicing equipment

Position Type/Expected Hours of Work

This is a full-time, exempt position with standard business hours
Occasional evening or weekend work may be required to support instrument integration, testing, deployment, or time-sensitive project milestones
Onsite: This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Travel

No travel is required

Additional Comments

**Please note, this opportunity does not offer relocation assistance, provide work visa sponsorship or work visas**

Annualized Salary Range

$148,800 - $186,000*
Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

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.

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More about this job

Skills

Process engineering
Robotics
Communication skills
CI/CD
Troubleshooting
Computer science
Computer engineering
Root cause analysis
Python
C++
C#
Test automation
Documentation
Software development
Personal protective equipment
Heavy lifting
Laboratory equipment

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Work requirements

Jobs in the United States