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.
- 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.
- 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
- 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 ofMiniProjectData.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