Animal Electrophysiology

This repository contains the code of the Neuronal Spike Shapes (NSS), a simple approach for analyzing the electrophysiological profiles of cells based on their Action Potential (AP) waveforms. The NSS method explores the heterogeneity of cell types and states by summarizing the AP waveform into a triangular representation complemented by a set of derived electrophysiological (EP) features.

This protocol collection explains how to build a low-cost, lightweight system to implant 1 Neuropixels 1.0 probe or 2 Neuropixels 2.0 probes into mice, record during freely moving behavior, then recover the probes for future use.

DataJoint Elements is a growing compilation of community-curated, open-source software modules for building automated data pipelines and analysis workflows for neuroscience experiments. DataJoint Elements enables: Secure tracking of animal subjects, equipment, and procedures Automatic data ingestion Customized research workflows Faster deployment Improved reproducibility Greater continuity across projects Secure tracking.

DataJoint Core is an open-source toolkit for defining and operating computational data pipelines (i.e., sequences of steps for data acquisition, processing, and transformation). Pipelines built in DataJoint Core offer: Efficient design with intuitive queries Automated, reproducible computation with full referential integrity Coordination of multiple human and computer workers Flexibility to adapt and change DataJoint Core includes libraries for Python and MATLAB, a REST API, and GUI tools for data entry and visualizations.

While accurate behavioral state classification is critical for many research applications, it is often done manually, which can be both tedious and inaccurate. Here we present a novel artificial neural network that uses electrophysiological features to automatically classify behavioral state in rats with high accuracy, sensitivity, and specificity.

CASCADE translates calcium imaging ΔF/F traces into spiking probabilities or discrete spikes. CASCADE is based on deep networks and runs on Python (Linux/Windows/Mac); it can be used either as a web application (Colaboratory notebook), or locally on a CPU or GPU.

ACQ4 is a python-based platform for experimental neurophysiology developed at the Allen Institute for Brain Science and the University of North Carolina, Chapel Hill. It includes support for patch-clamp electrophysiology, multiphoton imaging, scanning laser photostimulation, and many other experimental techniques.

The large diversity of cell-types of the brain, provides the means by which circuits perform complex operations. Understanding such diversity is one of the key challenges of modern neuroscience. Neurons have many unique electrophysiological and behavioral features from which parallel cell-type classification can be inferred.

World Wide Series Seminar Kilosort is a software package for identifying neurons and their spikes in extracellular electrophysiology, a process known as “spike sorting”. Kilosort has been primarily developed and tested on the Neuropixels 1.

Extracellular microelectrodes frequently record neural activity from more than one neuron in the vicinity of the electrode. The process of labeling each recorded spike waveform with the identity of its source neuron is called spike sorting and is often approached from an abstracted statistical perspective.