# Extracellular electrophysiology analysis

## Overview

This course aims to provide a comprehensive introduction to the analysis of in vivo extracellular electrophysiology. This 
includes spike sorting theory, manual curation and quality checks in Phy, theory of commonly used preprocessing steps, and pipeline development in Python (using [SpikeInterface](https://github.com/SpikeInterface/spikeinterface)).

On the first day, we will cover:
- Introduction to the analysis of extracellular electrophysiology data.
- Introduction and theory of spike sorting.
- Hands-on curation of spike sorting results in Phy.
- Understanding what makes a good unit and quality control methods.
- Dealing with spike sorting outputs (e.g. histogram generation from spike times) (time permitting) .

On the second and third day, we will cover:
- Introduction to data preprocessing steps 
- Hands-on generation of a full analysis pipeline (preprocessing, sorting, quality metrics) in Python [SpikeInterface](https://github.com/SpikeInterface/spikeinterface).

## Prerequisites
Students should bring their own laptop with Python installed. If you require any assistance, please contact
<a href="mailto:j.ziminski@ucl.ac.uk?subject=SWC/GCNU Software Skills">Joe Ziminski</a> in advance of the course.

## Materials
Tuesday 5th Nov

* [Slides](https://docs.google.com/presentation/d/1VTX5mogZXG-9ssQRjg3d0SCZ_jgR800KfvNfVZOhkUs/edit?usp=sharing)

* [Download Data](https://www.dropbox.com/sh/h782frjxyugifle/AABANGRWOGrtUmpWkJvHON9Ya?dl=0)
 
6th - 7th November

* [Slides](https://docs.google.com/presentation/d/1_GMxwcyVmpvXq4BpUYwgDgEKsr23Ifl1oc0mRyWB25s/edit?usp=sharing)

* [Repo](https://github.com/neuroinformatics-unit/course-extracellular-ephys-analysis)