matlab_analysis

MATLAB Behavioural Analysis

This directory contains MATLAB scripts for behavioral data analysis using the .txt file outputs from the automated behavioural task found here: https://github.com/clee162/whisker_tasks

For readability, its best to open this readme with markdown preview

Overview

MATLAB analysis of lick behavior during Pavlovian task. Designed for PavlovianTexture.ino

Directory Structure

• lick_analysis/ - Scripts for analyzing lick behavior data - textfile_lickanalysis.m - Main script for running lick analysis - lick_rate_plot.m - Average lick rate plotting utilities - number_licks_histogram.m - Histogram analysis for number of anticipatory licks - lick_rate_plot_mouse_all_days.m - Lick rate plotting for mice across all days - lickrasterplot.m - Raster plot generation for lick data - import_text_file.m - Text file import utilities - shadedErrorBar_cl.m - Shaded error bar plotting (customized colours) - shadedErrorBar.m - Shaded error bar plotting utilities
• read_aux_triggers.m - Auxiliary trigger reading script

Scripts

Main Script for running analysis

• textfile_lickanalysis.m - Primary script for analyzing lick data from text files

Functions for analysis/visualization

• lick_rate_plot.m - Plots average lick rate across mice
• number_licks_histogram.m - Creates histograms for number of licks analysis pooled across mice
• lick_rate_plot_mouse_all_days.m - Plots lick rates for individual mice across all experimental days
• lickrasterplot.m - Generates raster plots for lick timing data

Utility scripts

• import_text_file.m - Utility for importing text files containing lick data
• shadedErrorBar_cl.m - Adjusted the colours of shaded error bar plotting
• shadedErrorBar.m - Standard shaded error bar plotting utilities

Read auxillary inputs from tiff files

• read_aux_triggers.m - Reads and processes auxiliary trigger data

Usage

Data structure

1. Data must be structured as follows. Day indices and whisker trims are detected by counting the # of .txt. files in the directory with the specified naming convention

It is also critical to maintain the textfile formating as outputted from PavlovianTexture.ino

└── /path/to/your/textfile_data/ 
    └── animalname/
         └── animalname_20240101.txt 
         └── animalname_20240102.txt
         └── .....
         └── animalname_20240110.txt
         └── animalname_20240101_whiskertrim.txt (optional)

1. All functions are run from textfile_lickanalysis.m. User must set: - SAVE_FIGURES = true or false - BASE_SAVE_PATH - where you want to save figures - outerpath - this is your textfile_data parent folder. Inside this folder, should be animal folders - mousenames - a cell array where user specifies which mice they want to include in the analysis. example mousenames = {'CL019', 'CL020', 'CL021', 'CL022', 'CL023'};
2. Comment/uncomment the functions at the bottom to run specific analyses

Python version

• python_analysis/behavioral_analysis/analyze_textpav_textfiles.py contains implementations of similar functionality plus some plots that I never implemented in matlab - reads textfiles and automatically finds day indices and whisker trims - Lick rate plots for individual mice - Lick probability - lick index

read_aux_triggers.m

• This provides base text for how to read auxillary triggers using matlab
• it produces a basic subplot showing all auxillary triggers
  • I typically use this for short plots when setting up for experiments. This will be slow on full experiments
• The python implementation is much better developed. See the python_analysis/README

Citations

• shadedErrorBar.m - Rob Campbell (2025). raacampbell/shadedErrorBar (https://github.com/raacampbell/shadedErrorBar), GitHub. Retrieved October 20, 2025.