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Software Engineer II Computer Vision Allen Institute for Neural Dynamics

Department: Neural Dynamics - Scientific Computing

Software Engineer II Computer Vision Allen Institute for Neural Dynamics

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.

The mission of the Allen Institute for Neural Dynamics is focused on fundamental discoveries in systems neuroscience. We are interested in how the brain builds our understanding of the complex world to guide the flexible behaviors that address our biological needs. The answers will be in terms of defined neuron types and circuits interacting across the whole brain and body. We will develop next-generation methods and theories and employ a team-based approach for discovery neuroscience. Knowledge, data, models and tools will be widely shared, in part to support the development of therapies for brain disorders.

We are seeking a machine vision software engineer to help understand the brain-wide connectivity of neurons whose activity underlies complex behaviors. The candidate will employ existing and novel computer vision algorithms to label and extract objects, such as neurons  and their connections, from tera- and petabyte-scale microscopy images.  The ideal candidate will be focused on scientific and technical excellence and adept at building and maintaining computer vision models in a production analytics environment.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role. 

Essential Functions

  • Collaborate with scientists and engineers to design and build computer vision algorithms for tera- and petabyte-scale microscopy data
  • Pilot, implement, and deploy algorithms for object detection and quantification in 3D image stacks
  • Monitor algorithm performance for regressions and iteratively improve results
  • 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

 Required Education and Experience

  • Bachelor's Degree in computer science or related field; or equivalent combination of degree and experience
  • 1 year of equivalent experience on a software development team
  • Experience applying computer vision and image processing algorithms to imaging data, including both deep learning architectures and traditional feature-based methods
  • Experience applying standard machine learning techniques (e.g. SVMs, CNNs, other neural networks)
  • Experience applying standard computer vision libraries (e.g. OpenCV, pytorch, tensorflow)
  • Experience with scientific computing in Python (e.g. pandas, scipy, scikit-image, scikit-learn)

Preferred Education and Experience

  • 3-5 years of experience in a software development team
  • Familiarity with modern software development best practices (e.g., git, GitHub)
  • Excellent written and verbal communication skills
  • Experience working with terabyte-scale datasets
  • Experience with scaling software from local to cluster/cloud-based use
  • Experience working in a shared code repository
  • Experience with cluster-based computing (e.g. Slurm, Spark)
  • 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

Position Type/Expected Hours of Work

  • This role is currently able to work remotely due to COVID-19 and our focus on employee safety. We are a Washington State employer, and remote work must be performed in Washington State. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role will return to work onsite.

Additional Comments:

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

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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