Scientist I - Neural Coding

• 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., * Occasional travel to partner sites for compliance oversight may be required

• Occasional attendance and participation in national and international conferences required

• 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

Pulled from the full job description

• 401(k)
• Health insurance
• Paid time off
• Vision insurance
• Dental insurance
• Life insurance
• Visa sponsorship, * 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.

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., 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.