ephysCode

Personal electrophysiology acquisition, preprocessing & analysis code

Usage

Code base with 3 major functions:

1. To perform system integration necessary to acquire electrophysiology neural and behaviour signals across a wide range of experiment types and equipment.
   • Contained in ExperimentCode and ExperimentTypes
2. To preprocess raw digital signals representing neural activity and behavioural variables of interest.
   • Contained in Analysis_code/preprocessCode and Analysis_code/General
3. To analyze these signals to understand the link between neural activity and behaviour.
   • Contained in Analysis_code
   • Unique to each cell type and experiment, a lot of test code & WIP, see WesteindeWilson2024 for examples.

Example signal preprocessing pipeline:

Raw signal acquisition

Communication between devices mediated by the Data Acquisition Toolbox with National Instruments support.

Behaviour preprocessing

Behaviour data is collected at 60Hz. Perform light filtering, unwrapping, unit conversion, and resampling as necessary to reduce noise but minimize signal distortion.

Electrophysiology preprocessing

Detect action potentials (spikes) Convert binary spikes to instantaneous firing rate, example shown uses a gaussian kernal. Electrophysiology data is collected at 5kHz, resampled to 1kHz for usability and lightly filtered to remove noise without distorting biological signals. Finally action potentials (spikes) are detected and converted to instantaneous firing rate.