Scientist I - Neural Coding

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.

• 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.

• 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)

• 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

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

• 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

• 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

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

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

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

• $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.