Mechatronics Engineer III

Mechatronics Engineer III - Scientific Instrumentation & Process Engineering (SIPE)

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 Mechatronics Engineer III is a hands-on engineering role within the Scientific Instrumentation and Process Engineering (SIPE) team. This position designs, builds, and integrates robotic and automated systems for SIPE's custom scientific instruments, bringing together mechanical design, sensors, motion control, and software to deliver reliable, high-performance automation for neuroscience research.

The Mechatronics Engineer III works with minimal supervision and exercises independent judgment, leading defined subsystems and projects from concept through deployment. On any given week, this might mean tuning a control loop and integrating a force or vision sensor into a robot's motion routine, programming and validating tool paths for dissection automation, and updating CAD models and drawings for an end effector used in robotic wafer handling. This role works closely with the Principal System Design Engineer (robotics focus) on tissue processing and dissection automation. A successful candidate takes ownership of complex technical problems, contributes to engineering standards and documentation, and mentors less experienced team members. This role reports to the Hardware Engineering Manager.

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

Robotics & Automation Integration

• Implement, integrate, and commission robotic systems, such as robotic wafer handling to load and unload samples from imaging instruments
• Partner with the Principal System Design Engineer to develop robotic subsystems for tissue processing and dissection automation
• Program robot motion and tool paths; define, test, and validate trajectories, teach points, and coordinate frames for precision handling tasks
• Integrate sensors (e.g., force/torque, vision, encoders, proximity, limit and presence sensors) into robotic control and feedback systems
• Design, tune, and validate control loops for motors, stages, and actuators to meet positioning, speed, and repeatability requirements
• Perform kinematic and dynamic analysis, size motors and actuators, and evaluate accuracy and repeatability of motion systems
• Develop and execute calibration procedures for robots, cameras, and work cells (e.g., tool, frame, and hand-eye calibration), and verify positioning accuracy
• Develop firmware and control code for microcontrollers and motion controllers; implement communication between sensors, drives, and controllers (e.g., digital I/O, serial, CAN, EtherCAT, Modbus)
• Implement interlocks, e-stops, error handling, and recovery routines to protect samples, instruments, and operators; support safety reviews and risk assessments led by senior engineers

Mechanical & Electrical Design and Build

• Create parts, assemblies, and drawings in CAD (OnShape preferred) for end effectors, fixtures, mounts, and mechanisms; perform tolerance analysis and basic FEA as needed
• Specify, evaluate, and select motors, drives, actuators, sensors, controllers, and mechanical components
• Design power and signal wiring, wiring harnesses, and control enclosures; select motor drives and power supplies; develop simple circuit boards for sensor interfaces as needed
• Create and maintain bills of material (BOMs), system diagrams, and wiring schematics for assemblies and subassemblies
• Build, assemble, and debug prototypes and production instruments using the SIPE workshop (3D printing, laser cutting, hand tools, and bench electronics)

Testing, Documentation & Collaboration

• Work with scientists and engineers to capture requirements and translate them into specifications and test plans
• Plan and execute verification and validation testing; write reports and document processes, procedures, and SOPs
• Use source control (e.g., Git) and issue tracking to manage code, configurations, and design changes
• Troubleshoot and resolve complex hardware/software issues on deployed automated instruments with minimal guidance
• Mentor and provide technical guidance to less experienced engineers and instrument specialists
• Identify opportunities for continuous improvement and contribute to SIPE engineering standards and best 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 mechanical, mechatronics, electrical, robotics, or systems engineering, or related field; or equivalent combination of education and experience
• 3 years of relevant experience designing, building, and integrating electromechanical, robotic, or automated systems
• Hands-on experience with motion control and sensor integration, including programming robots or multi-axis motion systems
• Proficiency with CAD and with a programming language (e.g., Python, C/C++, C#) for hardware control
• Experience with operational safety working with complex machinery and automation

Preferred Education and Experience

• Master’s degree in mechanical, mechatronics, electrical, robotics, or systems engineering
• 5 years of experience designing and developing electromechanical, robotic, or automated systems
• Experience automating precision handling of delicate or high-value parts, samples, or materials (e.g., laboratory automation, medical device, semiconductor, or manufacturing equipment)
• Electrical design for electromechanical systems: motor drive and power supply selection, wiring, schematics, and PCB design
• Kinematics, motor/actuator sizing, and precision mechanism design, including accuracy, repeatability, and error budget analysis
• Experience with robot programming environments (e.g., vendor robot languages, ROS/ROS 2), motion controllers, PLCs, microcontrollers, and industrial communication protocols (e.g., EtherCAT, CAN, Modbus)
• Experience with machine vision for robot guidance, inspection, or registration
• Familiarity with machine and robot safety practices and standards (e.g., ISO 10218, ISO/TS 15066)
• Familiarity with design for manufacturing, GD&T, and working with machine shops and vendors
• Experience with OnShape, PDM systems, and software tools such as Git and CI/CD
• Strong organizational skills and high attention to detail

Work Environment

• This role may include wearing personnel protective equipment (PPE)
• Laboratory environment, including potential exposure to lasers, biohazards, live animals
• Machine shop and assembly areas

Physical Demands

• Occasional lifting to 30 pounds
• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment
• Occasionally required to push/pull up to 50 lbs
• Frequent stooping, bending, crouching, reaching, or climbing ladders

Position Type/Expected Hours of Work

• Full time employment; 40-hour work week M-F during regular business hours
• Occasional evening and weekend hours required
• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with flexibility to work remotely on a limited basis.

Additional Comments

• Please note, this opportunity does not sponsor work visas
• Please note, this opportunity does not offer relocation assistance

Annualized Salary Range

• $121,450 - $151,800*

* Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with 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