The Allen Institute for Neural Dynamics explores the brain’s activity, at the level of individual neurons and the whole brain, to reveal how we interpret our environments to make decisions. We aim to discover how neural signaling – and changes in that signaling – allow the brain to perform complex but fundamental computations and drive flexible behaviors. Our experiments and openly shared resources will shed light on behavior, memory, how we handle uncertainty and risk, how humans and other animals chase rewards – and how some or all of these complicated cognitive functions go awry in neuropsychiatric disorders such as depression, ADHD or addiction.

Available positions

Molecular Anatomy

Scientist - Machine Learning in Circuit Tracing
This Scientist will work with other quantitative and experimental scientists on high-priority problems in neuronal reconstruction and analysis that include (i) topology-preserving approaches to neuronal segmentation, (ii) deep learning-based analysis of morpho-molecular datasets, and (iii) high performance computing.

Scientist – Multi-regional neural circuits, Thalamus anatomy
This Scientist will lead a project to uncover the organizational logic of signal routing from subcortical areas to the frontal cortex via the thalamus at the level of defined cell types. This individual will leverage state-of-the-art imaging methods, molecular and transgenic resources to generate foundational anatomy data needed to study contributions of identified cell types within thalamic circuits during flexible behaviors.

Software Engineer II - Analysis of Large-scale (brain-wide) Microscopy Data
This software engineer will join a program to understand how neuron types from different brain regions are connected and whose activity underlies complex behavior and decision-making. The development and deployment of these workflows will be instrumental for the success of multiple projects at the Allen Institute and elsewhere, which will provide ample opportunity for growth and career development.

Research Associate
This Research Associate will support ongoing research projects investigating large-scale circuitry of the brain. Experimental approaches include tissue-sectioning, tissue clearing, immunohistochemistry, and microscopy.

Discovery Science

Principal Scientist and Senior Scientist; Systems Neuroscience and Behavior
These Scientists will lead a program in behavioral and system neuroscience. They will establish robust and flexible behavioral paradigms using the mouse as a model system. This platform will be used in conjunction with in vivo electrophysiology, optical physiology, and molecular anatomy to probe the mechanisms underlying learning and decision-making.

Scientist - Theory
This Scientist will model neural computation at the level of neural circuits and dynamics. This individual will analyze multi-dimensional neurophysiological and behavioral data to extract principles underlying neural computation.

Scientific Computing

Data Infrastructure Engineer III
This skilled data engineer will design and operate a modern, cloud-first data platform that enables multiple scientific teams collecting peta-scale biological datasets to manage metadata, orchestrate automated computational workflows, and share data with the neuroscience community adhering to FAIR standards.

Software Engineer II - Image Registration
This machine vision software engineer will join a program to understand the long-range connectivity patterns of neurons whose activity underlies complex behavior and decision-making. In this role, the candidate will build robust, scalable image processing and analysis pipelines. A key component of these pipelines is multimodal image registration between individuals and standardized coordinate systems.

Software Engineer II - Computer vision
This software engineer to help understand the brain-wide connectivity of neurons whose activity underlies complex behaviors. They will employ existing and novel computer vision algorithms to label and extract objects, such as neurons and their connections, from tera- and petabyte-scale microscopy images.

Scientist - Applied Statistics and Machine Learning
This computational scientist will model peta-scale, multimodal neuroscientific data collected on cutting-edge data generation platforms. Potential projects include: 1) building detailed maps of brain structures based on single-cell transcriptomic profiles; 2) refining these maps based on high-throughput measurements of morphology and connectivity; 3) linking these maps with cell type-specific measurements of neural activity during behavior.

Software Engineer I – Neurophysiology Software
This software engineer will collaborate closely with computational scientists to accelerate the collection, processing and analysis of large-scale neurophysiology data. They will bring engineering best practices to scientific software development to ensure our data pipelines are sustainable and reproducible. You’ll work with an exciting, dynamic team to build open source software analysis and visualization software that will be used not just in our institute but also by the broader neuroscience community.


Embedded Systems Engineer
This engineer will address challenges related to data acquisition, behavioral control, and automation in our experiments. He or she will interface closely with scientists and other engineers to design, implement, and maintain the hardware, software, and firmware comprising these systems.

Scientific Operations

Associate Scientific Project and Alliance Manager
This individual will provide the operational structure necessary for a large multi-disciplinary team to drive discoveries related to the functional connection of neuron types across the brain. As a leader and collaborator, the Scientific Project and Alliance Manager will drive momentum, effectively communicate, build consensus, and be the interface of multi-site and multi-disciplinary teams.