Software Engineer II - Computer Vision Biology

Software Engineer II - Computer Vision for Biology

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 is the analysis of large-scale microscopy and video data to enable the mapping of brain-wide neural circuits and characterization of behavior, respectively.

In this role, the engineer will develop, maintain, and optimize robust and scalable image processing and analysis pipelines in close collaboration with neuroscientists and computational researchers.

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

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 imaging data
• Pilot and implement methods for image analysis: segmentation, registration, pose tracking, object detection, action recognition
• Work with a software team to integrate algorithms and software into a broader analytics platform
• Follow 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)
• Deep experience with Python
• Familiarity with modern software development best practices (e.g., git, Git Hub)

Preferred Education and Experience

• PhD in neuroscience, with substantial experience in software engineering
• 3 - 5 years of experience in a software development team
• Advanced degree in CS, EE, or a discipline
• 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…