Scientist I – Computational Image Analysis

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 Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through the integration of experiments, modeling, and theory.

The Imaging department within Brain Science is a team of ~25 research associates, analysists, and scientists who operate commercial and customized optical systems to collect and interpret data serving a wide variety of scientific work at the Institute. Characterizing transgenic animal lines, viral genetic tools, molecular and morphological cell types, histological labels, and disease markers are examples of work supported by imaging personnel within the Allen Institute for Brain Science.

We seek a Scientist to develop methods to reconstruct cell and circuit anatomy from mouse brain fluorescence datasets, furthering our understanding of fundamental anatomical properties such as neuronal cell types and connectivity within the brain. The ideal candidate will be team-oriented, have deep knowledge of computational image analysis, and have a strong interest in neuroscience. The successful applicant will develop/apply computational image processing and machine vision tools to extract scientific output from raw data. Examples include cell segmentation and signal extraction, image data quality assessment and quantification, mapping of experimental data to generalized anatomical coordinate systems, and the automation of these tasks for application to steadily accumulating data volumes.

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

• Develop and apply scalable computational tools to co-register image datasets, such as in vivo and ex vivo images of the same tissue
• Contribute to the characterization of lightsheet images of whole mouse brain
• Research, evaluate, and apply novel computational tools, likely statistical and machine learning tools, for spatial analysis with clear documentation and good source code management

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

• PhD degree in computer science, neuroscience, physics, mathematics, applied mathematics, engineering, or related field, or equivalent combination of degree and experience
• Experience in scientific computing

Preferred Education and Experience

• Experience with computational image processing, particularly related to volumetric fluorescence microscopy data
• An understanding of how optical systems collect data and how to characterize their performance
• Use of Python libraries/frameworks such as NumPy, SciPy, pandas, scikit-image, and Matplotlib
• Experience with distributed computing tools and data formats (e.g., dask and zarr)
• Experience with cloud infrastructure tools such as AWS S3
• Collaboration with non-engineering teams in development, deployment and testing of software products
• Experience working in a scientific environment
• Knowledge of neuroanatomy and cell atlases
• Strong problem-solving skills and the ability to work as part of a team
• Excellent communication and documentation skills

Work Environment

• May enter laboratory environment - possible chemical, biological, or other hazardous substances exposure

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 hybrid / onsite. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Additional Comments

• To be considered, applications should include a cover letter summarizing career goals, motivation for working at the Allen Institute, and suitability for the position

Annualized Salary Range

• *$77,250 - $103,000

*Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outline in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

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.