Scientist – Image Registration & Multimodal Data Integration

at Allen Institute for Brain Science
Published January 31, 2023
Location Seattle, United States of America
Category Computer Vision  
Job Type Full-time  


Scientist – Image Registration & Multimodal Data Integration
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 integration of experiments, modeling and theory.
As part of the NIH BRAIN Initiative Cell Atlas Network, the Allen Institute is helping to lead a major new international consortium effort to create a comprehensive cell atlas of the human and closely related non-human primate brain. This project aims to make the most detailed map of the human brain ever produced, linking cellular and molecular phenotypes to brain imaging and functional architecture. To tackle this ambitious goal, we are seeking talented and highly motivated individuals to help create these atlases and help to make them transformative for neuroscience and biomedical research through open data sharing. The atlas will be based on a range of cutting edge high-throughput single cell molecular, spatial and cell phenotyping assays to map the structural and functional organization of the primate brain. We strive to build a catalytic brain cell reference and resource that will dramatically accelerate our understanding of brain structure, function and disease, and to create tools to help the community take advantage of these resources.
We seek to hire an exceptional scientist to create an integrated common coordinate framework ecosystem that brings together multimodal data spanning multiple species, modalities and developmental stages. The scientist will work with spatial transcriptomics, histological and functional imaging data, register them to species and time specific reference templates and perform analysis to create integrated maps as part of a brain knowledge base.
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

  • Register multiscale spatial transcriptomics, structural and functional imaging data to species and time specific reference brain templates through the selection and creation of registration methods and tools
  • Define and implement registration quality metrics
  • Create tools and workflow to enable manual input, visualization, quality assessment and manual correction of registration results
  • Participate in the co-analysis of registered images towards creation of multimodal common coordinate frameworks and atlases
  • Regularly communicate findings to collaborators, cross-functional teams, and the Institute regarding key insights, findings, and questions derived from data analysis
  • Interact with scientists from diverse backgrounds and perspectives to design analytical approaches and refine computational strategies
  • Develop code libraries, tutorials, and user guides to enable use and dissemination of the selected and/or developed registration and quality metric tools

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, engineering, applied mathematics, or related field, or equivalent combination of degree and experience

Preferred Education And Experience

  • 0-5 years experience in scientific computing and analysis using Python and Bash/LINUX environments
  • 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
  • Experience with modern software development best practices (e.g., git, GitHub)
  • Experience in applied statistics and machine learning and command of current literature
  • Knowledge of human neuroanatomy and neurodegenerative disease processes

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 both remotely and onsite in a hybrid work environment. 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.


  • Occasional travel to partner sites for collaborative development
  • Attendance and participation in national and international conferences required

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

Annualized Salary Range

  • $80,253 - $112,355 *
  • Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.


  • 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: .

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.