benjamin-sylvanus / gmcells

Getting Started

Overview

The goal of this repository is to provide an out of the box solution for dMRI Simulations on neuron skeletons. The provided tools fall under three categories, data preprocessing, simulation, and analysis.

Prerequisites

Before you begin using the tools, please ensure that you have the following prerequisites in place:

1. Python Environment: Make sure you have Python (version X.X or higher) installed on your system.
2. Neuron Skeleton Data: Obtain the neuron skeleton data you wish to prepare for dMRI simulations. Ensure that the data is in a compatible format (e.g., SWC, JSON) and stored in a location accessible to the tools.

Installation

To set up the CLI tools and get started, follow these steps:

1. Clone the Repository: Begin by cloning this repository to your local machine using the following command:

   git clone https://github.com/your/repository.git

2. Install Dependencies: Navigate to the repository directory and install the required dependencies by running the following command:

   pip install -r requirements.txt

3. Configuration: Modify the configuration file (config.json) to suit your specific needs. Adjust the parameters as necessary to align with your dataset and desired preprocessing options.