This model provides a computational framework to support longstanding observations of concurrent autonomous and driven rhythmic motor actions and how the interaction of the Central whisking oscillator Breathing oscillator dynamics can be studied using conductance- and rate-based modeling. The github site includes computer programs and scripts for generating figures from the article:

David Golomb, Jeffrey D. Moore, Arash Fassihi, Jun Takatoh, Vincent Prevosto, Fan Wang and David Kleinfeld, Theory of hierarchically-organized neuronal oscillator dynamics that mediate rodent rhythmic whisking. Neuron, (2022) 110:3833-3851.
Software needed: julia compiler, XMGrace LaTeX

DOI: 10.1016/j.neuron.2022.08.020

Data

Simulation Programs

Software

This study identifies the neural circuit responsible for rhythmic whisker movements in rodents, pinpointing parvalbumin-expressing inhibitory neurons in the brainstem's vIRt region. These neurons form a recurrent inhibitory network that generates rhythmic activity through network dynamics rather than intrinsic properties. Disrupting this network abolishes regular whisking, highlighting the central role of synaptic inhibition in rhythm generation.

Jun Takatoh, Vincent Prevosto, P. M. Thompson, Jinghao Lu, Leeyup Chung, Andrew Harrahill, Shun Li, Shengli Zhao, Zhigang He, David Golomb, David Kleinfeld and Fan Wang , The whisking oscillator circuit. Nature, (2022) 609:560–568.


DOI: 10.1038/s41586-022-05144-8

Software

Samuel Andrew Hires, Lorenz Pammer, Karel Svoboda, and David Golomb, Tapered whiskers are required for active tactile sensation. Elife 2:e01350, 2013.

This is an ode script for XPPAUT that computes whisker bending in response to contact with object. The calculation is based on the quasi-static approximation, and conic whisker profile is considered.

Software

General software for control of Basler camera to record animal behavior

Coded by C. Foo. Matlab-based routines to acquire video (1280x1024 frames) at high frame rates (>200Hz) for hardware-dependent periods; we currently achieve continuous acquisition of 720x720 frames at ~350 Hz.

Software

Trigger module and software to control computer vision cameras

Kyle Severson and Vincent Prevosto

Software

Coded by Prof. Johnatan Aljadeff and Dr. Benjamin J. Lansdell. Matlab-based routines for capturing relationships between spiking activities and the external stimuli. The algorithm extracts features from the input stimulus and predicts the spike rate using different models (e.g. GLM). The predicted spike rate is then used to generate the spike train by a stochastic process (e.g. Poisson process). Three example datasets are included:

1. (Salamander) Multi-electrode array recording from retinal ganglion cells in response to white noise visual stimulus (Chichilnisky, 2001; Touryan et al., 2002; Rust et al., 2005; Pillow et al., 2008).
2. (Rat) Single unit recordings of thalamic neurons, with simultaneous vibrissa motion (Moore et al., 2015).
3. (Monkey) Single unit recordings of motor cortex with simultaneous recording of hand position and grip strength during joystick manipulation (Engelhard et al., 2013).

Please contact Prof. Johnatan Aljadeff for questions on the operation of this software. If you use this software in your research, please reference Aljadeff et al. (Neuron 2016) - ()

Further: (1) commercial software from MathWorks is required, including MATLAB, the Image Processing Toolbox, the Optimization Toolbox, the Signal Processing Toolbox, the Statistics Toolbox, and the Symbolic Math Toolbox. (2) download Daniel Hill’s code (code and datasets) for the Hilbert transform (code); (3) download Partha Mitra’s Chronux Toolbox (http://www.chronux.org); (4) download Jonathan Pillow’s Generalized Linear Model (GLM) implementation for spike trains (http://pillowlab.princeton.edu/code_GLM.html); (5) download Mark Schmidt’s L1-norm function L1GeneralGroup_Auxiliary.m (https://www.cs.ubc.ca/~schmidtm/Software/thesis.html); and (6) download multidimensional histogram function histcn.m download at http://www.mathworks.com/matlabcentral/fileexchange/23897-ndimensional-histogram/content/histcn.m. If you use this software in your research, please reference Aljadeff et al. (Neuron 2016)

Software and Data

Software

Manual

Coded by D. N Hill and S. B. Mehta following an initial version coded by M. S. Fee. Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. Please contact Dr. Daniel N. Hill for questions on the operation and maintenance of this software after consulting the manual. If you use this software in your research, please reference Hill et al. (J Neurosci 2012) - () and Fee et al. (J Neurosci Meth 1997) - () & ()

Software

Coded by D. N. Hill, this makes use of Matlab-based routines for the extraction of amplitude, midpoint, and phase from a rhythmic signal using Black's technique. Please contact Dr. Daniel N. Hill for questions on the operation of this software. If you use this software in your research, please reference Hill et al. (Neuron 2011) - ()

Algorithm and Demo Code

Coded by I. Valmianski and J. D. Driscoll. Matlab-based routines for the automatic identification of fluorescently labeled brain cells in two-photon scanning microscopy image stacks and the subsequent calculation of an optimized scan path through these cells. This program makes concurrent use of JBoost. Please contact Mr. Ilya Valmiansky for questions on the operation of this software. If you use this software in your research, please reference Valmianski et al. (J Neurophysiol 2010) - ()

Visualization and annotation tool for brains. Anatomists can view high-resolution tissue stacks and use the drawing tools to annotate and map the 3D topography of brain regions and the localization of injections via labelled cells. A groundbreaking automated system, employing cell shape parametric features and boosted decision trees, and featuring a simplified annotation process, is designed for premotor neuron detection.

brainsharer.org

Mac Key Shortcut Reference

Front End Code (Neuroglancer fork)

Back End Code (API)

ML (feature detection)

Deepfacetracking is a cross-platform package for automated tracking of a single head, eye, pupil, and rows of whiskers in the high-speed video. The package includes preprocessing and a graphical user interface for experimenters to modify and correct the automatic tracking outcomes.

Software (in progress)

The package contains codes to analyze and visualize the temporal and spectral coordination of orofacial (whisking, pad retraction, nose wiggling) and neck motor actions with respiration in the rat performing naturalistic behaviors (foraging and rearing) in an open arena.

A change in behavioral state switches the pattern of motor output that underlies rhythmic head and orofacial movements. S.-M. Liao and D. Kleinfeld, Current Biology (2023).

()

Software

NWB Data

Chemoreceptors in the nasal epithelium can trigger an apneic reaction and a grimace in response to airborne irritants. Callado Perez et al. find that the underlying circuit does not involve olfaction. Rather, activation of neurons in the muralis subnucleus of the spinal trigeminal complex will inhibit the Pre-Bötzinger inhalation oscillator.

Data

Software

The cognitive processes supporting complex animal behavior are closely associated with ubiquitous movements responsible for our posture, facial expressions, ability to actively sample our sensory environments, and other critical processes. These movements are strongly related to neural activity across much of the brain and are often highly correlated with ongoing cognitive processes, making it challenging to dissociate the neural dynamics that support cognitive processes from those supporting related movements. This study presents a novel method to disentangle neural dynamics associated with cognitive and motor processes in behaving animals. The accompanying codebase provides tools for subspace decomposition of single trial population activity into movement-potent and movement-null components using a binary metric of when animals or moving or stationary.

Current Data (raw)

Data (NWB) *in progress

Software