Scientist I, Connectomics – Allen Institute for Brain Science

The mission of the Allen Institute is to understand the principles that govern life and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.

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. Built on the foundational knowledge of brain cell types, the mission of the Allen Institute for Brain Science is to conduct a series of large-scale projects designed to create “CAP” (Complete, Accurate, Permanent) datasets and experimental tools; gain fundamental knowledge in the development, evolution, connectivity and function of brain cell types; move towards a better understanding of mammalian brain function in healthy and diseased conditions; and disseminate the data, knowledge and tools broadly with the community, to accelerate research across the neuroscience field.

We are seeking an exceptional individual to develop innovative sectioning techniques for a large scale Electron Microscopy pipeline. The scientist will join a team responsible for scaling and automating the cutting of whole mouse brain samples prepared for Electron Microscopy. This will involve developing and optimizing robotic components to carefully control a nanometer scale mechanical process over centimeter scale ultrathin sections across thousands of iterations. The goal of the research is to create technologies that allow the complete mapping of synaptic connectivity of individual neurons across the entire mouse brain, something that has never been done before. The scientist will be an essential member of the Connectomics department studying cell types and will also have opportunities for data analysis in later phases of the project.

The team already includes several Electron Microscopy experts and therefore welcomes applicants that are new to electron microscopy but have a strong interest in automation and in the overall goals of the project.

Examples of our previous work related to this position can be found on:

1. https://www.nature.com/collections/bdigiaicbd
2. https://www.nature.com/articles/s41467-020-18659-3
3. https://elifesciences.org/articles/76534
4. https://www.cell.com/cell/pdf/S0092-8674(22)00134-9.pdf
5. https://www.pnas.org/doi/10.1073/pnas.2202580119

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 cutting whole mouse brain samples for electron microscopy
• Automate ultramicrotome cutting serial sections for volumetric Electron Microscopy
• Robotic manipulation for section delivery with high precision and minimal section loss
• 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, Engineering, or equivalent combination of degree and experience
• Strong background in automation or robotics
• Strong programming skills (please share GitHub repository as part of job application)
• Experience with software engineering best practices (e.g. version control and code reviews)

Preferred Education and Experience

• Experience in Connectomics
• Strong publication record
• Ability to work independently and within a collaborative, multi-disciplinary environment to meet aggressive timelines
• Exceptional oral and written communication and organizational skills
• Ability to guide teams and coordinate activities within and across institutions, including coaching/mentoring junior members

Work Environment

• Laboratory environment – often entering labs where experiments take place
• Laboratory environment - possible chemical, biological, or other hazardous substances exposure
• This may include wearing personnel protective equipment (PPE)
• Working at a desk with computer analyzing data

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 required to work onsite. 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.

Travel

• Occasional travel to collaborator sites
• Occasional attendance and participation in national and international conferences may be required

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer 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 Institutes 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