PvsNP

Python vs. Neuro-Physiological (PvsNP) serves as a toolbox for:

• Statistical analysis of neurophysiological data, including but not limited to cell selectivity, place cell analysis, and etc.
• Graph Theoretical Analysis of networks of neurons.
• Data Visualization tool - see the "full picture" of the data garnered from experiments with integration of calcium imaging movies, behavioral videos, and data processing results.
• Deconvolution of calcium imaging data. (Deprecated)

For any feature requests, feel free to create an issue.

_{^{image source}}

Getting Started

Docker

1. Download and install Anaconda (Python 3.X)

2. Download and install Docker

3. Clone the repository:

git clone https://github.com/smu160/PvsNP.git

3. Navigate into your local repository and build the Docker image:

cd PvsNP
docker build . -t jupyter

4. Use the image to run a container:

docker run -it -p 8888:8888 jupyter

If you need to mount data to the container, then use the following command:

docker run -it -p 8888:8888 -v source_directory:target_directory jupyter

5. You should see something along the lines of:

...
    Or copy and paste one of these URLs:
        http://(2958ngdf42t or 127.0.0.1):8888/?token=XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Now open your browser window and go to the URL that was created for you.

Installation on Mac or Linux (Python 3.x)

1. Download and install Anaconda (Python 3.X)

2. Clone the repository:

git clone https://github.com/smu160/PvsNP.git

3. Navigate into your local repository and create your environment:

cd PvsNP
bash create_env.sh

Troubleshooting

Create an issue

Dependencies

A list of dependencies can be found in the environment file