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Software Engineer II Image Registration Allen Institute for Neural Dynamics

Department: Neural Dynamics - Scientific Computing

Software Engineer II Image Registration 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 to answer fundamental questions about brain function. Specifically, how does our brain build our understanding of the complex world around us to guide the flexible behaviors that address our biological needs? The answers will be in terms of defined neuron types interacting across the whole brain and body, requiring us to develop next-generation neurotechnologies and employ a team-based approach for discovery neuroscience. Knowledge, data, 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 join a program to understand the long-range connectivity patterns of neurons whose activity underlies complex behavior and decision-making. In this role, the candidate will build robust, scalable image processing and analysis pipelines. A key component of these pipelines is multimodal image registration between individuals and standardized coordinate systems. The ideal candidate will be focused on scientific and technical excellence, highly motivated, agile and team-oriented.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. Progress in science benefits from multiple 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 large scale bioimaging data
  • Pilot and implement methods for multi-modal 2D and 3D registration, stitching, and fusing
  • Monitor algorithm performance tera- and peta-scale data sets 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 experience in a software development team, or equivalent combination of degree and experience
  • Experience applying computer vision and image processing algorithms to imaging data, including segmentation and linear/nonlinear image registration
  • Experience applying machine vision and image registration libraries (e.g. OpenCV, scikit-image, ANTs, ITK)
  • Experience with C/C++, Java, and/or 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 working with terabyte-scale datasets
  • Experience with machine learning: SVMs, neural networks
  • 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. 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 in a hybrid work environment.

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.

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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