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Emmett James Thompson

sequences_behaviour

scripts for running and post-hoc analysis of the 8 poke sequence behavioural task

Analysis of behavioural data for the Seqeuence task

See our publication for more details: Replay of Procedural Experience is Independent of the Hippocampus.

Task Schematic

Overview

This repository includes:

  • A version of the task in BPOD file format (matlab/Sequence_Automated)
  • Tidied* python notebook scripts for processing BPOD output
  • Some example notebook scripts for analysis of tracking and histology data

(*)These scripts are from the early years of my phd so are a little rough. I havent refactored them but I have been though and tidied them - so they should be useful and readable but are not fully polished...

Getting Started

Ensure you have the following software installed:

  • Git
  • Python (Version used: 3.12.3)
  • Jupyter notebook
  • Necessary Python libraries: this pipeline worked with the environment I have listed in requirements.txt (though some of these packages may be redundant)

Main data pipeline

1_process_bpod_output Notebook script which takes the matlab output from running the behaviour and produces python readable processed data

2_analyse_individual_sessions Takes output files from process_bpod_output and returns analysis plots for each behavioural session

3_analyse_across_sessions same as step 2 but produces summary data across the sessions for each animal

AcrossAnimal_analysis takes the outputs from the first 3 steps and creates plots which compare the task abilities of multiple animals