An FPGA-based platform for accelerated offline spike sorting

• Published in: Journal of neuroscience methods Vol. 215; no. 1; pp. 1 - 11
• Main Authors: Gibson, Sarah, Judy, Jack W., Marković, Dejan
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.04.2013
• Subjects: Algorithms; Cluster Analysis; Computer Systems; Computers; Electrophysiology - instrumentation; Electrophysiology - methods; Equipment Design; Extracellular Space - physiology; FPGA; Hardware acceleration; Neurology - instrumentation; Neurology - methods; Online Systems; Software; Spike sorting; User-Computer Interface; Spike sorting; FPGA; Hardware acceleration
• ISSN: 0165-0270; 1872-678X
• DOI: 10.1016/j.jneumeth.2013.01.026

► A hardware tool for accelerated offline spike sorting of extracellular data is presented. ► This tool is 135× faster than software running on a single-core personal computer. ► Flexibility was incorporated by including multiple sorting algorithms. ► The tool was benchmarked against similar software tools using published datasets. ► The fully functional tool is available for public use. There is a push in electrophysiology experiments to record simultaneously from many channels (upwards of 64) over long time periods (many hours). Given the relatively high sampling rates (10–40kHz) and resolutions (12–24bits per sample), these experiments accumulate exorbitantly large amounts of data (e.g. 100GB per experiment), which can be very time-consuming to process. Here, we present an FPGA-based spike-sorting platform that can increase the speed of offline spike sorting by at least 25 times, effectively reducing the time required to sort data from long experiments from several hours to just a few minutes. We attempted to preserve the flexibility of software by implementing several different algorithms in the design, and by providing user control over parameters such as spike detection thresholds. The results of sorting a published benchmark dataset using this hardware tool are shown to be comparable to those using similar software tools.