Scientist I - Neural Coding 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:
- https://elifesciences.org/articles/76534
- https://elifesciences.org/articles/73783
- https://www.cell.com/cell/pdf/S0092-8674(22)00134-9.pdf
- 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.
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* 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.
