Automated tracking of whiskers in videos of head fixed rodents

Nathan G. Clack, Daniel H. O'Connor, Daniel Huber, Leopoldo Petreanu, Andrew Hires, Simon Peron, Karel Svoboda, Eugene W. Myers

Research output: Contribution to journalArticle

Abstract

We have developed software for fully automated tracking of vibrissae (whiskers) in high-speed videos (>500 Hz) of head-fixed, behaving rodents trimmed to a single row of whiskers. Performance was assessed against a manually curated dataset consisting of 1.32 million video frames comprising 4.5 million whisker traces. The current implementation detects whiskers with a recall of 99.998% and identifies individual whiskers with 99.997% accuracy. The average processing rate for these images was 8 Mpx/s/cpu (2.6 GHz Intel Core2, 2 GB RAM). This translates to 35 processed frames per second for a 640 px×352 px video of 4 whiskers. The speed and accuracy achieved enables quantitative behavioral studies where the analysis of millions of video frames is required. We used the software to analyze the evolving whisking strategies as mice learned a whisker-based detection task over the course of 6 days (8148 trials, 25 million frames) and measure the forces at the sensory follicle that most underlie haptic perception.

Original languageEnglish (US)
Article numbere1002591
JournalPLoS Computational Biology
Volume8
Issue number7
DOIs
StatePublished - Jul 2012

Fingerprint

Vibrissae
rodent
Rodentia
rodents
Head
Random access storage
software
Software
Haptics
mice
Processing
Mouse
High Speed
Trace
video
speed

ASJC Scopus subject areas

  • Cellular and Molecular Neuroscience
  • Ecology
  • Molecular Biology
  • Genetics
  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

Cite this

Clack, N. G., O'Connor, D. H., Huber, D., Petreanu, L., Hires, A., Peron, S., ... Myers, E. W. (2012). Automated tracking of whiskers in videos of head fixed rodents. PLoS Computational Biology, 8(7), [e1002591]. https://doi.org/10.1371/journal.pcbi.1002591

Automated tracking of whiskers in videos of head fixed rodents. / Clack, Nathan G.; O'Connor, Daniel H.; Huber, Daniel; Petreanu, Leopoldo; Hires, Andrew; Peron, Simon; Svoboda, Karel; Myers, Eugene W.

In: PLoS Computational Biology, Vol. 8, No. 7, e1002591, 07.2012.

Research output: Contribution to journalArticle

Clack, NG, O'Connor, DH, Huber, D, Petreanu, L, Hires, A, Peron, S, Svoboda, K & Myers, EW 2012, 'Automated tracking of whiskers in videos of head fixed rodents', PLoS Computational Biology, vol. 8, no. 7, e1002591. https://doi.org/10.1371/journal.pcbi.1002591
Clack, Nathan G. ; O'Connor, Daniel H. ; Huber, Daniel ; Petreanu, Leopoldo ; Hires, Andrew ; Peron, Simon ; Svoboda, Karel ; Myers, Eugene W. / Automated tracking of whiskers in videos of head fixed rodents. In: PLoS Computational Biology. 2012 ; Vol. 8, No. 7.
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