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Software Engineer II - Analysis of Large-scale (brain-wide) Microscopy Data

Department: Neural Dynamics - Molecular Anatomy

Software Engineer II - Analysis of Large-scale (brain-wide) Microscopy Data, 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 Allen Institute has been a leader in the field of neuroscience for over 17 years; in 2021 we launched a new research division, the Allen Institute for Neural Dynamics, to understand how dynamic neuronal signals at the level of the entire brain implement fundamental computations and drive flexible behaviors.

We are seeking a software engineer to join a program to understand how neuron types from different brain regions are connected and whose activity underlies complex behavior and decision-making. The development and deployment of these workflows will be instrumental for the success of multiple projects at the Allen Institute and elsewhere, which will provide ample opportunity for growth and career development. 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 a team of scientists to build an analysis pipeline for large-scale light-sheet microscopy
  • Deploy large-scale data analysis pipelines on cluster and cloud-based architectures
  • Pilot new methods for aligning, stitching, fusing, and compressing multi-terabyte imaging datasets
  • Perform software development duties using best practices - follow industry standards, develop unit and integration tests, participate in code reviews, etc.and follow the Allen Institute's software management and deployment standards including source code management, issue tracking, staging and deployment standards, and documentation

Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managementís 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 and 1+ years of experience in a software development team, or equivalent combination of degree and experience
  • Experience with C/C++, Java, and Python
  • Experience with cluster-based computing (e.g. Spark)
  • Experience with cloud-based computing (e.g. Amazon S3, Lambda, EMR)
  • Familiarity with modern software development best practices (e.g., git, GitHub)

Preferred Education and Experience

  • 2-4 years of experience in a software development team preferred
  • 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

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 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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