Scientist I - Image Processing and Scientific Computing

alleninstitute; Seattle (WA); On-site; USD 86,000 - 107,000; Full time

Benefits offered by this job

Medical insurance

401k plan

Paid time off

Job summary

The Allen Institute in Seattle seeks a Scientist I – Image Processing and Scientific Computing to lead image processing and analysis of large-scale Electron Microscopy datasets. You will oversee EM data processing and contribute to datasets studying brain cell types across modalities.

You will collaborate with neuroscientists, anatomists, and modelers, publish findings, and mentor junior team members while advancing scalable pipelines on cloud and on-prem infrastructure at a cutting-edge

Qualifications

• Ph.D. in Neuroscience, Computer Science, Applied Math, Engineering; or equivalent degree/experience.
• Strong background in image processing.
• Strong programming skills; experience with software engineering practices.

Responsibilities

• Collaborate to scale high-throughput EM image processing for whole-brain datasets.
• Oversee EM data 2D stitching and 3D alignment pipelines.
• Analyze EM data to relate structure to cell types and modalities.
• Publish and present findings in peer-reviewed venues.

Skills

Image processing

Programming skills

Python

Education

Ph.D. in Neuroscience, Computer Science, Applied Math, Engineering

Job description

Scientist I – Image Processing and Scientific Computing

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

The goal of the Brain Science accelerator is to produce three interlocking resources: cell type atlases that catalog every kind of brain cell across ages and species, connectomes that chart the brain's intricate wiring, and a knowledge platform that knits it all together with powerful analysis tools. Every dataset is freely shared, so discoveries made here fuel discoveries everywhere.

We are seeking a neuroscientist to lead the effort in image processing and analysis of large-scale Electron Microscopy (EM) datasets. The scientist will be responsible for overseeing EM image processing and will participate in the analysis of large-scale datasets. Examples of work related to this position can be found on:

1. https://elifesciences.org/articles/76534
2. https://elifesciences.org/articles/73783
3. https://www.cell.com/cell/pdf/S0092-8674(22)00134-9.pdf
4. https://www.nature.com/immersive/d42859-025-00001-w/index.html

The scientist will be an essential member of the Connectomics Department creating the datasets to study cell types across multiple modalities and their relationship with brain function.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.

We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Essential Functions

• Collaborate with others to further scale the image processing of a high throughput electron microscopy pipeline towards whole mouse brain datasets
• Oversee EM data 2D stitching and 3D alignment automated pipeline
• Work closely with a team of anatomists, physiologists, theoreticians, and modelers to analyze EM data in the context of cell types and interpret the relationship between structure and modalities of cells such as molecular and physiology properties
• Publish/present findings in peer-reviewed journals/scientific conferences

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

• Ph.D. in Neuroscience, Computer Science, Applied Math, Engineering; or equivalent combination of degree and experience
• Strong background in image processing
• Strong programming skills
• Experience with software engineering best practices (e.g. version control and code reviews)

Preferred Education and Experience

• Experience with Python
• Experience with cloud computing
• 3 - 5 years experience with relevant computer programing
• Experience in Connectomics
• Strong publication record
• Ability to work independently and within a collaborative, multi-disciplinary environment to meet aggressive timelines
• Ability to guide teams and coordinate activities within and across institutions, including coaching/mentoring junior members
• Machine learning experience
• Excellent verbal and written communication skills

Work Environment

• Laboratory environment, including potential exposure to lasers, biohazards
• This may include wearing personnel protective equipment (PPE)

Physical Demands

• Occasional lifting up to 30 pounds
• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment
• Stooping, bending, crouching
• Reaching, or climbing ladders

Position Type/Expected Hours of Work

• Occasional evening and weekend hours may be required
• This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with the flexibility to work remotely on a limited basis

Travel

• Occasional travel to partner sites for compliance oversight may be required
• Occasional attendance and participation in national and international conferences required

Additional Eligibility Qualifications

• Please share GitHub repository as part of job application
• Include cover letter with your job application

Additional Comments

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

Annualized Salary Range

• $86,150 - $106,650*

* 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 outlined 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 Institute’s 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.