2P Imaging Analysis

Getting my hands dirty with the CaImAn analysis tools on 2-photon Imaging Data.

Setup

1. Create and activate anaconda environment with Python 3.8 and install relevant libraries

# Create anaconda environment.
conda create -n 2P_env python=3.8

# Install caiman and numpy.
conda install numpy caiman -c conda-forge

# Install jupyter.
conda install jupyter

# Pip install other libraries.
pip install imageio pathlib matplotlib opencv-python tqdm bokeh

# Activate anaconda environment.
conda activate 2P_env

2. Clone this repository and change into this directory

# Clone repository.
git clone https://github.com/chehanw/2P_Image_Analysis.git

# Change into this directory.
cd 2P_Image_Analysis

3. Download and unzip data into current directory
4. Launch jupyter notebook in current directory

jupyter notebook