A cloud-based brain connectivity analysis tool

With advances in high throughput brain imaging at the cellular and sub-cellular level, there is growing demand for platforms that can support high performance, large-scale brain data processing and analysis. In this paper, we present a novel pipeline that combines Accumulo, D4M, geohashing, and parallel programming to manage large-scale neuron connectivity graphs in a cloud environment. Our brain connectivity graph is represented using vertices (fiber start/end nodes), edges (fiber tracks), and the 3D coordinates of the fiber tracks. For optimal performance, we take the hybrid approach of storing vertices and edges in Accumulo and saving the fiber track 3D coordinates in flat files. Accumulo database operations offer low latency on sparse queries while flat files offer high throughput for storing, querying, and analyzing bulk data. We evaluated our pipeline by using 250 gigabytes of mouse neuron connectivity data. Benchmarking experiments on retrieving vertices and edges from Accumulo demonstrate that we can achieve 1–2 orders of magnitude speedup in retrieval time when compared to the same operation from traditional flat files. The implementation of graph analytics such as Breadth First Search using Accumulo and D4M offers consistent good performance regardless of data size and density, thus is scalable to very large dataset. Indexing of neuron subvolumes is simple and logical with geohashing-based binary tree encoding. This hybrid data management backend is used to drive an interactive web-based 3D graphical user interface, where users can examine the 3D connectivity map in a Google Map-like viewer. Our pipeline is scalable and extensible to other data modalities.

I. Introduction

Top on the list of the US Government's BRAIN Initiative is the ability to map the human brain at different scales with improved throughput and resolutions [1]. A complete picture of the brain structure will provide new insights into how the human brain functions and may facilitate new treatments and drug discovery for brain disorders. Recent advances in intact brain imaging, such as the CLARITY [2] and MAP (Magnified Analysis of the Proteome) [3] tissue clearing techniques, make it possible to collect large volumetric images of brain tissue at cellular and sub-cellular resolutions. The high throughput and high resolution brain imagery, however, poses a challenge for efficient processing and analysis.