Leveraging Tools from Autonomous Navigation for Rapid, Robust Neuron Connectivity

Abstract

As biological imaging datasets continue to grow in size, extracting information from large image volumes presents a computationally intensive challenge. State-of-the-art algorithms are almost entirely dominated by the use of convolutional neural network approaches that may be difficult to run at scale given schedule, cost, and resource limitations. We demonstrate a novel solution for high-resolution electron microscopy brain image volumes that permits the identification of individual neurons and synapses. Instead of conventional approaches where voxels are labelled according to the neuron or neuron segment to which they belong, we instead focus on extracting the underlying brain graph represented by synaptic connections between individual neurons, while also identifying key features like skeleton similarity and path length. This graph represents a critical step and scaffold for understanding the structure of neuronal circuitry. Our approach, which we call Agents, recasts the segmentation problem to one of path finding between keypoints (i.e., connectivity) in an information sharing framework using virtual agents. We create a family of sensors which follow local decision-making rules that perform computationally cheap operations on potential fields to perform tasks such as avoiding cell membranes and finding synapses. These enable a swarm of virtual agents to efficiently and robustly traverse three-dimensional datasets, create a sparse segmentation of pathways, and capture connectivity information. We achieve results that meet or exceed state-of-the-art performance at a substantially lower computational cost. Agents offers a categorically different approach to connectome estimation that can augment how we extract connectivity information at scale. Our method is generalizable and may be extended to biomedical imaging problems such as tracing the bronchial trees in lungs or road networks in natural images.