MED-PC Data Analysis

Overview

This project helps extract and process MED-PC (https://www.med-associates.com/med-pc-v/) recording data. The overall goal is to train mice to associate a tone with a reward(sugary liquid). MED-PC records the times that the tones are played, when the mice enter/exit the port where the reward is dispensed, and the relevant metadata. The experiment is usually run with one subject for a recording that takes about a hour for multiple days. The data processing will calculate various metrics that displays or averages all the trials(each tone going off in a session and it's associated port entry/exit) for each recording session for all the subjects.

./bin
- Directory that has the relevant documents and files for the Conda environments
./jupyter_notebooks
- Directory that has the Jupyter Notebooks to extract/process the MED-PC and the accompanying dataframes/plots that are created from it.
./results
- Directory that has a record of previous iterations of the Jupyter Notebooks
./src
- Directory that has the Python source code used in the Jupyter Notebooks. All the original functions used in the notebooks will be imported from this.

Check if you have the Git program on your computer. Do this on the Bash terminal(Linux), Powershell(Windows), and Terminal(Mac). In the terminal, type git then enter.
- If you don't have Git on your computer, install it following these instructions: https://git-scm.com/downloads
Once you have Git, download the repository in a folder that you want to save it in
- From the terminal: git clone https://github.com/padillacoreanolab/med_pc_repo
NOTE: Every time you use this repo after cloning it, check for updates with:
- cd {./path/to}/med_pc_repo
- git pull origin main

Check if you have Anaconda:
- Use the python command in your terminal. If you have Anaconda, then it will say "Anaconda" somewhere in the output.
- If you don't have Anaconda, follow the installation instructions on: https://www.anaconda.com/
Create the Conda environment by following the instructions in: ./bin/conda_environments/doc/README.md
This step only needs to be done once. Every subsquent time you want to run the analysis, you'll turn on the Conda environment with:
- conda deactivate
- conda activate {./path/to}/med_pc_repo/bin/conda_environments/env/med_pc_env

1 Use the command jupyter notebook --allow-root in your terminal
1.1 If a browser window doesn't pop up with Jupyter notebooks, open up a browser window. Then copy and paste the URL given in the command line. It will be followed by To access the notebook, open this file in a browser: and Or copy and paste one of these URLs:
- It should have a format similar to: http://localhost:8888/?token=gsOH0vx373NRzHUmDzwX9TFzBf5Wx6czWIr1irV7ERKBLmlK
2 Click on ./jupyter_notebooks in the Jupyter Notebooks GUI (Should be in the web browser)

Follow the instructions to run the Jupyter Notebooks at ./jupyter_notebooks/README.MD
The dataframes and the plots should be saved in subdirectories in: (./jupyter_notebooks/proc)[./jupyter_notebooks/proc]