Electrophysiology Crash Course
An introduction to basic concepts required to perform and evaluate whole-cell patch clamp experiments
- Getting Started - How to use this guide
- Introduction - Thinking about neurons as electrically excitable membranes
- Passive Properties - Electrical features of a cell membrane that do not require channels to actively open or close
- Ohm’s Law - How Membrane Properties Influence Synaptic Currents
- Action Potentials - Electrophysiology of neuron firing
- VC and IC Modes - Voltage-clamp and current-clamp whole-cell recording configurations
- Synaptic Currents - Electrical changes in a cell resulting from neurotransmitter released by another cell
- How to Patch Clamp Neurons - Steps for establishing whole-cell patch-clamp configuration with neurons in brain slices
Pages
Individual pages for a variety of topics
- Common Experiments - A summary of the most common whole-cell patch-clamp experiment types
- Common Pharmacological Agents - Pharmacological agents commonly used in whole-cell patch-clamp experiments
- Electrically Evoke Synapses - Using an electrical stimulator to evoke synaptic currents
- Liquid Junction Potential - What Liquid Junction Potential (LJP) is and how it can be corrected for in patch-clamp experiments
- Optogenetics - Using light-activated ion channels to optically excite specific cell populations
- Patch Clamp Internal Solutions - Common internal solutions used for whole-cell patch-clamp electrophysiology
- Patch Configurations - A summary of the most common techniques used to measure the electrical properties of cell membranes
- Reversal Potential - An introduction to reversal potentials, the Nernst equation, and their effect on synaptic currents
- Shunting - Synaptic inputs can be attenuated in a process known as current shunting
- The Membrane Test - A voltage-clamp step can reveal much about a neuron's passive membrane properties
Analysis and Tooling
Resources for analyzing electrophysiological and optical data
- Ratiometric Linescan Analysis with ImageJ and Excel - How to calculate ΔF/F from ratiometric linescans using ImageJ and Excel
- Fluorescence Analysis with ImageJ and Excel - How to calculate ΔF/F₀ from a series of fluorescence images
- AP Phase Plots - Visualizing fast action potential dynamics by plotting voltage against its rate of change
- Image Stabilization with ImageJ - How to correct for motion in time-series 2D and 3D images
- ImageJ Resources - Links, Notes, and Scripts related to Fiji/ImageJ
- Microscope Scale Calibration with ImageJ - How to add scale bars to microscope images using a ruler slide
- Remove ApoTome Artifacts with ImageJ - How to use ImageJ to remove ApoTome artifacts using FFT/iFFT
- Spectral Noise Reduction - How to remove periodic noise from electrophysiology traces
- Tonic/Phasic Analysis - How to separate slow (tonic) changes in holding current from fast (phasic) synaptic currents in voltage-clamp recordings
Laboratory Gear
Personal notes about hardware and software which may be laboratory-specific
- 2P Operation Notes - Notes about two-photon startup, shutdown, acquisition, and maintenance
- 2P Stage Control - Python scripts to automate two-photon stage positioning, image acquisition, and montage assembly using ImageJ and TrackEM
- Aligning the Mira Laser - Notes related to power and alignment of a Coherent Mira Optima 900-F
- Confocal Microscope - How to use the Nikon C2 confocal microscope to image slide-mounted fluorescent samples
- DIC Alignment Cheat-Sheet - How to align DIC optics for a fixed-stage Olympus BX-51WI microscope
- NT-RTSI Setup - National Instruments Real-Time System Integration System Setup
- Pipette Puller - How to make whole-cell patch-clamp pipettes using the P97 Flaming/Brown pipette puller
- Preamp Blade Setup - How to configure and switch between different preamplifier blades
- Two-Photon Laser Uncaging - How to setup, calibrate, and run mixed ephys/imaging/uncaging experiments
- Two-Photon Linescans - How to acquire fast imaging data using two-photon linescans