maxschelski / pyneurite

A computer vision package that traces and analyzes neurites in time-lapse videos fully automated.

pyNeurite

A computer vision package that traces and analyzes neurites fully automated. Optimized for time-lapse videos.

Used in Schelski and Bradke, 2022, Science Advances (https://www.science.org/doi/10.1126/sciadv.abo2336)

Installation

The package was developed and tested on Windows.

1. If you don't already have Anaconda installed: Download and install Anaconda from https://www.anaconda.com/.
2. If you don't already have git installed: Download and install git from https://git-scm.com/downloads
3. Open a terminal, navigate to the folder where you want to put pyneurite and clone the pyneurite repository:

git clone https://github.com/maxschelski/pyneurite.git

4. Navigate into the folder of the repository (pyneurite):

cd pyneurite

5. Create environment for pyneurite with Anaconda:

conda env create -f environment.yml

6. Activate environment in Anaconda:

conda activate pyneurite

6. Install pyneurite locally using pip:

pip install -e .

For any questions feel free to contact me via E-Mail to [e-mail].