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.

Note: the dataviewer.py script cannot be used currently.

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.

Note:

• 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