The Role of Experience in Prioritizing Hippocampal Replay by Huelin Gorriz et al 2023
Code repository for "The Role of Experience in Prioritizing Hippocampal Replay". If you use this code in your research, please cite this paper.
Prerequisites and installation
MATLAB 2017a or newer (working on MATLAB 2021a and MATLAB 2022b).
MATLAB Toolboxes: Parallel Computing Toolbox Signal Processing Toolbox Statistics and Machine Learning Toolbox
Add this repository into the path by using 'set path' -> 'Add with subfolders' (installation time less than 10 seconds)
klustakwik 2.0 (http://klustakwik.sourceforge.net/)
Ph-GUI (https://github.com/kwikteam/phy)
Preprocessing
Go to batch_analysis.m for most basic preprocessing pipelines including:
1 - spikes & video ;
2 - position & laps ;
3 - sleep processing ;
4 - CSC & PSD ;
5 - Place cells and Bayesian decoding ;
6 - Candidate replay event extraction and replay decoding ;
7 - replay scoring and significance
Main analysis
Place field analysis folder (main code: place_field_analysis_pipeline.m) for place cell quantification and decoding error quantification
Theta analysis folder (main code: theta_phase_pipeline.m) for theta cycles and theta sequence quantification
Replay analysis folder (main code: replay_analysis_pipeline.m) for:
Replay quantification
Quantifying the relationship between theta and awake replay and behavioral parameters vs sleep replay