Software Engineer II – Computer Vision for Biology

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

We are seeking a Machine Vision Software Engineer to join the Scientific Computing group at the Allen Institute for Neural Dynamics (AIND). The mission of AIND is to advance understanding of how neural circuits represent and process the external world to generate fundamental behaviors. A central component of this effort is the acquisition and analysis of large-scale animal video data to enable quantitative behavioral characterization. Video analysis is therefore a core methodological requirement across multiple research platforms at AIND. In this role, the engineer will develop, maintain, and optimize robust and scalable video processing and analysis pipelines in close collaboration with neuroscientists, experimentalists, and computational researchers.

The successful candidate will be motivated by supporting scientific discovery through high-quality software, demonstrate strong technical rigor, and work effectively in interdisciplinary research environments. This position is well suited for individuals who value reproducibility, scalability, and long-term maintainability in research software systems.

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

• Collaborate with scientists and engineers to design and build computer vision algorithms for large scale video data
• Pilot and implement methods for video analysis: pose tracking, object detection, activity segmentation, action recognition
• Work with a software team to integrate algorithms and results into a broader analytics platform
• Follow team software best practices - write unit and integration tests, participate in code
• reviews, track issues, version code, manage stage/production environments, write documentation
• Share your methods with the community via white papers, conference talks, and journal articles

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 or related field; or equivalent combination of degree and experience
• 1 year of relevant experience in a software development team
• Experience applying computer vision and image processing algorithms to imaging data, including segmentation and linear/nonlinear image registration
• Experience applying machine vision and CV libraries (e.g. OpenCV, scikit-image, ANTs, ITK)
• Experience with Python
• Familiarity with modern software development best practices (e.g., git, GitHub)

Preferred Education and Experience

• 3 - 5 years of experience in a software development team
• Excellent written and verbal communication skills
• Experience with machine learning/AI
• Experience with scaling software from local to cluster/cloud-based use
• Experience working in a shared code repository
• Experience with cloud-based computing (e.g. Amazon S3, Lambda, EMR)

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

Position Type/Expected Hours of Work

• 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.

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer work visa sponsorship**

Annual Salary Range

• $119,650 - $149,550 *

* 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 Institute's 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.