BIO-482 Miniproject 🧠 🐭 🧑‍💻

Repository for the data analysis miniproject of the course Neuroscience: cellular and circuit mechanisms (BIO-482), EPFL.

This repository contains a MATLAB and Python version of this project, as well as associated functions used for computations.

This project is based on the published dataset of single-cell recordings in awake mice previously collected at LSENS, which resulted in the publication Membrane potential dynamics of excitatory and inhibitory neurons in mouse barrel cortex during active whisker sensing.

Setting up

Download

• Clone git clone ... or download as zip file this repository (green button).
• Download Data_Bio482.mat dataset at the provided link.

The repository should contain the following folders:

• doc: documentation related to the project and to the data.
• matlab: code and helper functions to do the project with MATLAB.
• python: code and helper functions to do the project using Python.

Note: add the .mat file in a bio482_miniproject/data folder.

Installation and usage

1. If you're using MATLAB:

• Add the /matlab folder to your MATLAB path to run the code.
• Make sure you also have installed the following:
  • Signal Processing Toolbox
  • MATLAB Curve Fitting Toolbox
  • Statistics and Machine Learning Toolbox

2. If you're using Python:

• You need to have Anaconda installed for your system: install anaconda here.

• Once Anaconda is installed, open a terminal and install a "bio482" conda environment: conda create -n bio482 numpy scipy matplotlib seaborn h5py pandas jupyterlab statsmodels scikit-learn

• Close terminal to make the conda environment effective.

• Make sure the environment is installed. Open a terminal: conda env list. The "bio482" environment should be there.

  Then, to work on the project:

• Go to python and open a terminal

• Activate the environment: conda activate bio482.

• Then run: jupyter lab.

• Open notebooks to start working on the project.

• To run the dataviewer.py, edit the file by replacing the location of MiniProjectData.mat to where your current .mat file is (i.e. full path).

  Note about paths:

  • MATLAB: You must add folders to MATLAB's path: Right-click on folder -> Add to path...
  • Python: In jupyter notebooks, you must change paths based on where you cloned this repository.

fin