Example-analyses

Example analyses making extensive use of nelpy and/or ghost.

Examples include:

• LinearTrackDemo.ipynb—using position and spike data (CA1) to estimate spatial tuning curves and identify putative place cells from a 15 minute linear track run session.
• WMazeDemo.ipynb—using position and spike data (CA1) to estimate 2D spatial tuning curves from two 15 minute w-maze sessions.
• DPGMMSpikeSort.ipynb—using a Dirichlet process Gaussian mixture model (DPGMM) to automatically spike sort some data from a single tetrode.

Spectral analyses with ghost:

• BackyardBrainsEEG.ipynb—analyze the spectral content from an EEG recorded from the human brain (see BackyardBrains/eeg)

Coming very soon!

• RippleDetection.ipynb—sharp wave ripple (SWR) detection from local field potential (LFP) recordings.
• PBEDetection.ipynb—population burst event (PBE) detection from hippocampal multiunit activity.
• WrappedEnvironments.ipynb—working with ring-like environments, such as running wheels, treadmills, or circular tracks.

Coming somewhat soon!

• BayesianDecoding.ipynb—simple 1D and 2D Bayesian decoding of position from hippocampal place cells.
• FilteringAndSpectralAnalyses.ipynb—basic spectral analyses and filtering to remove 60 Hz noise, or to identify sharp wave ripples.
• HiddenMarkovModels.ipynb—basic hidden Markov model analyses of neural data, including model training, evaluation, and decoding.
• KalmanSmoothing.ipynb—smoothing trajectory data using a Kalman smoother for better position and speed estimates.
• WrappedEnvironments.ipynb—working with ring-like environments, such as running wheels, treadmills, or circular tracks.
• BasicReplayAnalyses.ipynb—detecting simple hippocampal replay using Bayesian decoding. Need nice public data!!!.
• [Advanced] InertialMeasurementUnits.ipynb—working with inertial measurement units (IMUs) to obtain position, speed, and other behavioral variables.
• [Advanced] ProbabilityDistributions.ipynb—repurposing AnalogSignalArrays into probability distribution functions.
• more coming soon!
• [Advanced] WilsonPlot.ipynb—recreating a video in the style of "Hippocampal place cells recorded in the Wilson lab at MIT".