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Automated Tracking of Whiskers in Videos of Head Fixed Rodents

Author

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

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.

Suggested Citation

  • Nathan G Clack & Daniel H O'Connor & Daniel Huber & Leopoldo Petreanu & Andrew Hires & Simon Peron & Karel Svoboda & Eugene W Myers, 2012. "Automated Tracking of Whiskers in Videos of Head Fixed Rodents," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-8, July.
    • Handle: RePEc:plo:pcbi00:1002591
    DOI: 10.1371/journal.pcbi.1002591
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    References listed on IDEAS

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    1. D. Huber & D. A. Gutnisky & S. Peron & D. H. O’Connor & J. S. Wiegert & L. Tian & T. G. Oertner & L. L. Looger & K. Svoboda, 2012. "Multiple dynamic representations in the motor cortex during sensorimotor learning," Nature, Nature, vol. 484(7395), pages 473-478, April.
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    Cited by:

    1. Bettina Voelcker & Ravi Pancholi & Simon Peron, 2022. "Transformation of primary sensory cortical representations from layer 4 to layer 2," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Suma Chinta & Scott R. Pluta, 2023. "Neural mechanisms for the localization of unexpected external motion," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Mitchell Clough & Ichun Anderson Chen & Seong-Wook Park & Allison M. Ahrens & Jeffrey N. Stirman & Spencer L. Smith & Jerry L. Chen, 2021. "Flexible simultaneous mesoscale two-photon imaging of neural activity at high speeds," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    4. Anthony Renard & Evan R. Harrell & Brice Bathellier, 2022. "Olfactory modulation of barrel cortex activity during active whisking and passive whisker stimulation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Ravi Pancholi & Lauren Ryan & Simon Peron, 2023. "Learning in a sensory cortical microstimulation task is associated with elevated representational stability," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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