WhiskEras 2.0: Fast and Accurate Whisker Tracking in Rodents

Petros Arvanitis, Jan Harm L.F. Betting, Laurens W.J. Bosman, Zaid Al-Ars, Christos Strydis*

*Corresponding author for this work

Research output: Chapter in Book/Conference proceedings/Edited volumeConference contributionScientificpeer-review


Mice and rats can rapidly move their whiskers when exploring the environment. Accurate description of these movements is important for behavioral studies in neuroscience. Whisker tracking is, however, a notoriously difficult task due to the fast movements and frequent crossings and juxtapositionings among whiskers. We have recently developed WhiskEras, a computer-vision-based algorithm for whisker tracking in untrimmed, head-restrained mice. Although WhiskEras excels in tracking the movements of individual unmarked whiskers over time based on high-speed videos, the initial version of WhiskEras still had two issues preventing its widespread use: it involved tuning a great number of parameters manually to adjust for different experimental setups, and it was slow, processing less than 1 frame per second. To overcome these problems, we present here WhiskEras 2.0, in which the unwieldy stages of the initial algorithm were improved. The enhanced algorithm is more robust, not requiring intense parameter tuning. Furthermore, it was accelerated by first porting the code from MATLAB to C++ and then using advanced parallelization techniques with CUDA and OpenMP to achieve a speedup of at least 75x when processing a challenging whisker video. The improved WhiskEras 2.0 is made publicly available and is ready for processing high-speed videos, thus propelling behavioral research in neuroscience, in particular on sensorimotor integration.

Original languageEnglish
Title of host publicationEmbedded Computer Systems
Subtitle of host publicationArchitectures, Modeling, and Simulation - 21st International Conference, SAMOS 2021, Proceedings
EditorsAlex Orailoglu, Matthias Jung, Marc Reichenbach
Number of pages16
ISBN (Print)9783031045790
Publication statusPublished - 2022
Event21st International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2021 - Virtual, Online
Duration: 4 Jul 20218 Jul 2021

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume13227 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference21st International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation, SAMOS 2021
CityVirtual, Online

Bibliographical note

Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care
Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.


  • Acceleration
  • Algorithmic improvement
  • Whisker tracking


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