Software Engineer II - Connectomics Services

Software Engineer II – Connectomics Services - Allen Institute for Brain Science

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

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 through integration of experiments, modeling, and theory.

We are seeking a Software Engineer to work on developing backend infrastructure services to support the mapping of cells between the light and electron microscopy dataset. The goal of the research is to create the technologies to allow the complete mapping of synaptic connectivity of individual neurons across the entire mouse brain, and then register this connectivity maps to other modalities (such as gene expression) to create a reference atlas of cell type connectivity and morphology that is integrated with transcriptomic taxonomies.

The Software Engineer will help build open-source services and libraries that facilitate large scale analysis of dynamic connectomics datasets that will be used by researchers around the world. The engineer will help us consider how to efficiently scale existing systems that manage dynamic connectivity graphs with hundreds of millions of edges to manage hundreds of billions of rows. The engineer will work closely with Institute scientists to design and build new services that enable efficient scientifically driven queries of the data.

We are a dynamic multi-disciplinary team with deep expertise in electron and light microscopy reconstructions and contribute to innovative research in the field! Our team has already generated the largest reconstructions of neurons from EM with tens of thousands of cells per dataset, making it an exciting time to join and achieve the next level of impact and scaling. We welcome enthusiastic applicants who are new to the field but have a strong interest in building technology that impacts scientific progress in neuroscience.

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

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

• Collaborate with others to develop software to further scale web-based services for managing large-scale connectomics and morphology datasets.
• Work closely with a team of anatomists, physiologists, theoreticians, and modelers to create APIs that facilitate their research.
• 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

• Bachelor’s degree or equivalent combination of degree and experience.
• Minimum 1 year of experience with programming services that manage large scale data.
• Experience with Python or with at least 2 other programming languages.

Preferred Education And Experience

• Masters or PhD in a scientific or technical field (such as Computer Science, Computer Engineering, Neuroscience, Physics).
• Excellent verbal and written communication skills.
• Experience with multi-tasking/prioritizing.

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment.

Position Type/Expected Hours of Work

• Occasional evening and weekend hours required.
• This role is currently able to work both remotely and onsite (at least 3 days per week) in a hybrid work environment. 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 partner sites for compliance oversight required.
• Opportunities for attendance and participation in national and international conferences.

Additional Comments

• Please note, this opportunity offers relocation assistance.
• Please note, this opportunity offers work visa sponsorship.

Annualized Salary Range

$108,350 - $151,650

Final salary depends on the required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable.

Benefits

Employees (and their families) are eligible to enroll in benefits per eligibility rules outline 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: .

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.