minibrain

A Python module to analyze electrical signals and calcium fluorescence in brain organoids. For personal use only.

Requirements

The module has been extensively tested on Python >= 3.6. We recommend to have a package manager like Anaconda with:

1. Standard scientific modules for data handling (IPython and Jupyter , pandas),
2. Modules for scientific analysis (Scipy, NumPy and machine learning Scikit-learn)
3. The scientific library for data visualization (matplotlib).
4. Deep Learning platform (PyTorch)

You can create a conda environment with necessary packages with the following command

conda env create --name minibrain --file environment.yml

How to install it

If you prefer installing directly the minibrain package in one of your environments, just type this:

git clone https://github.com/JoseGuzman/minibrain.git
cd minibrain
pip install -r requirements.txt
pip install -e .

Examples of usage

• Calculate Bursts