Towards real-time whisker tracking in rodents for studying sensorimotor disorders

Yang Ma, Prajith Ramakrishnan Geethakumari, Georgios Smaragdos, Sander Lindeman, Vincenzo Romano, Mario Negrello, Ioannis Sourdis, Laurens W.J. Bosman, Chris I. De Zeeuw, Zaid Al-Ars, Christos Strydis

Research output: Chapter/Conference proceedingConference proceedingAcademicpeer-review

2 Citations (Scopus)

Abstract

The rodent whisker system is a prominent experimental subject for the study of sensorimotor integration and active sensing. As a result of improved video-recording technology and progressively better neurophysiological methods, there is now the prospect of precisely analyzing the intact vibrissal sensori-motor system. The vibrissae and snout analyzer (ViSA), a widely used algorithm based on computer vision and image processing, has been proven successful for tracking and quantifying rodent sensorimotor behavior, but at a great cost in processing time. In order to accelerate this offline algorithm and eventually employ it for online whisker tracking (less than 1 ms/frame latency), we have explored various optimizations and acceleration platforms, including OpenMP multithreading, NVidia GPUs and Maxeler Dataflow Engines. Our experimental results indicate that the optimal solution for an offline implementation of ViSA is currently the OpenMP-based CPU execution. By using 16 CPU threads, we achieve more than 4,500x speedup compared to the original Matlab serial version, resulting in an average processing latency of 1.2 ms/frame, which is a solid step towards real-time (and online) tracking. Analysis shows that running the algorithm on a 32-thread-enabled machine can reduce this number to 0.72 ms/frame, thereby enabling real-time performance. This will allow direct interaction with the whisker system during behavioral experiments. In conclusion, our approach shows that a combination of software optimizations and the careful selection of hardware platform yields the best performance increase.

Original languageEnglish
Title of host publicationProceedings - 2017 17th International Conference on Embedded Computer Systems
Subtitle of host publicationArchitectures, Modeling, and Simulation, SAMOS 2017
EditorsYale Patt, S. K. Nandy
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages137-145
Number of pages9
ISBN (Electronic)9781538634370
DOIs
Publication statusPublished - 20 Apr 2018
Event17th International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2017 - Samos, Greece
Duration: 16 Jul 201720 Jul 2017

Publication series

SeriesProceedings - 2017 17th International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2017
Volume2018-January

Conference

Conference17th International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2017
Country/TerritoryGreece
CitySamos
Period16/07/1720/07/17

Bibliographical note

Funding Information:
ACKNOWLEDGMENTS This work was supported by the Neuroscience department of the Erasmus MC. We are grateful to Dr. Sebastiaan Koekkoek for his help, to the NVidia Corporation for their donation of the Titan X GPU, and to Maxeler Technologies for their continuous support throughout this research effort.

Publisher Copyright: © 2017 IEEE.

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