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Scientific Data Engineer II - Image Processing and Registration - Neural Circuits and Behavior

Department: Neural Circuits and Behavior
Location: Seattle

Data Scientist II (Scientific Data Engineer) – Imaging Processing and Registration - Neural Circuits and Behavior


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 MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing, and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

We are seeking a Scientific Data Engineer to be an integral member of a team investigating the role of neural circuits in learning and behavior. The primary role of this Engineer will be to develop and maintain tools for processing, registration and analysis of image based data acquired using 2-photon microscopy, epifluorescence microscopy, and light sheet fluorescence microscopy. This Engineer will collaborate with Scientists to develop robust, standardized workflows that will support large-scale data collection and analysis. This will involve building new tools as well as contributing to existing open source codebases for analysis of neural data (ex: and spatial transcriptomics (ex:

The ideal candidate will have strong software engineering skills, experience working with imaging data, and experience or interest in neuroscientific research. As part of a highly collaborative team environment, good communication and enthusiasm for working with, learning from, and teaching others is essential to this role.

The datasets and tools created as part of this project will be publicly released as an open resource for the community, in line with the Allen Institute’s core principles of big science, open science and team science.

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 neuroscientists and engineers to develop methods and workflows for image processing, registration and alignment
  • Build and support pipelines for analysis of imaging datasets across multiple modalities
  • Contribute to open source codebases in a collaborative manner
  • Produce well-documented, modular code that is useable and interpretable by research scientists
  • Participate in code review, scientific discussions, and project planning

Required Education and Experience

  • Bachelor’s in software engineering, computer science, bioengineering, computational neuroscience, bioinformatics or related field or equivalent combination of degree and experience
  • Minimum 1 year of relevant experience post bachelor's degree
  • Demonstrated excellent Python programming skills
  • Experience building, documenting and maintaining a modular system
  • Experience with microscopy, image processing or image registration
  • Excellent organizational and interpersonal skills
  • Ability to manage time and independently complete tasks to meet deadlines
  • Strong work ethic, reliable and enthusiastic team player

Preferred Education and Experience

  • Bachelors degree and 2 - 4 years of professional experience in software development, optical engineering, microscopy, bioengineering or related discipline
  • Experience working in a scientific research environment
  • Experience with R, Shiny apps, SQL, MongoDB
  • Experience with machine vision and/or machine learning
  • Experience contributing to open source codebases
  • Experience producing data visualizations and data dashboards

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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