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Whisk specifications


Unique identifier OMICS_19745
Name Whisk
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.0.0e
Stability Stable
Source code URL https://codeload.github.com/nclack/whisk/tar.gz/v1.1.0e
Maintained Yes




No version available



  • person_outline Nathan Clack

Publication for Whisk

Whisk citations


Serial processing of kinematic signals by cerebellar circuitry during voluntary whisking

Nat Commun
PMCID: 5550418
PMID: 28794450
DOI: 10.1038/s41467-017-00312-1

[…] e was defined as the angle of the Hilbert transform on band-pass filtered (6–30 Hz) whisker angle. A phase of zero corresponds to maximal protraction and a phase of ±π denotes maximal retraction in a whisk cycle. […]


Mechanisms underlying a thalamocortical transformation during active tactile sensation

PLoS Comput Biol
PMCID: 5479597
PMID: 28591219
DOI: 10.1371/journal.pcbi.1005576

[…] ouch (; ; see Figs and for representative examples) []. VPM neurons were also highly sensitive to whisking () [, , ]. Spike rates increased after whisking onset (average, 3-fold; ). Given that mice whisk at approximately 15 Hz under these conditions [], the spike rates during whisking correspond to approximately one spike per whisking cycle, on average. The modulation depths with whisking amplit […]


Pixying Behavior: A Versatile Real Time and Post Hoc Automated Optical Tracking Method for Freely Moving and Head Fixed Animals

PMCID: 5318546
PMID: 28275712
DOI: 10.1523/ENEURO.0245-16.2017

[…] and one mouse had both forelimbs painted (see Materials and Methods). A high-speed Basler camera and a Pixy camera were positioned to track two whiskers (). In this paradigm, mice were conditioned to whisk to contact a piezo-film sensor after a sound go-cue turned on (). To ensure that the painted whiskers were used in the contact task, the large whiskers rostral to the painted ones were trimmed o […]


Decoupling kinematics and mechanics reveals coding properties of trigeminal ganglion neurons in the rat vibrissal system

PMCID: 4999311
PMID: 27348221
DOI: 10.7554/eLife.13969.019

[…] response of Vg neurons is strongly correlated with contact (; ), the mechanical variable will necessarily have a higher predictive value, especially at 100 ms time scales that match the duration of a whisk.The reason θhead is independent of contact is that this angle is measured with respect to the midline of the animal’s head. In contrast, change in curvature at the base (a proxy for bending mome […]


The cerebellum linearly encodes whisker position during voluntary movement

PMCID: 4737656
PMID: 26780828
DOI: 10.7554/eLife.10509.018

[…] was defined as the angle of the Hilbert transform on band-pass filtered (6–30 Hz) whisker angle. A phase of zero corresponds to maximal protraction and a phase of ± π denotes maximal retraction in a whisk cycle. […]


A direct translaminar inhibitory circuit tunes cortical output

Nat Neurosci
PMCID: 4624464
PMID: 26414615
DOI: 10.1038/nn.4123

[…] acquired with a framegrabber (Silicon Software) at 495fps with a 100us exposure and were synchronized with electrophysiology data via external triggers. Whisker tracking was performed offline using “Whisk” (Janelia Farms, HHMI) which returned whisker angles and positions for every frame. Tracking data was further processed and analyzed using custom MATLAB scripts written to extract whisker contac […]


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Whisk institution(s)
Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
Whisk funding source(s)
Supported by The Howard Hughes Medical Institute.

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