Notebooks for Behrens lab GridMaze tutorial on 14/4/25

@peterdoohan @charlesburns

Note: you'll need to have access to ceph (SWC cluster) for these notebooks to run

Before the tutorial

• SSH into the SWC cluster

• Copy this folder to your working directory or navigate to:

  cd /ceph/behrens/peter_doohan/tutorials
  

• Make a new conda envionment from the requirements.txt in this repo:

  conda env create -f environment.yml --name GridMaze_tutorial
  
  conda activate GridMaze_tutorial
  

• Get some cluster resources and spin up a jupyter server (optional)

  srun --nodes=1 --ntasks-per-node=1 --cpus-per-task=8  --time=4:00:00 --mem=32G --pty bash -i
  jupyter-notebook --no-browser --ip=0.0.0.0 --port 8888
  # link notebook to this server
  

Overview

We have 3 notebook tutorials that go with the in-person presentation

1. maze_representations.ipynb Details how mazes are represented in code (Dataset: goalNav_mFC)

2. accessing_maze_data.ipynb Explains how experiments are represented on disk and how you can load that data for your own analyses (Dataset: goalNav_mFC)

3. using_unitmatch.ipynb Quick demonstration on how to match cells (recorded with ephys) across days and session types (Dataset: goalNav_mEC)