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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

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

cd pyneurite

  1. Create environment for pyneurite with Anaconda:

conda env create -f environment.yml

  1. Activate environment in Anaconda:

conda activate pyneurite

  1. Install pyneurite locally using pip:

pip install -e .

For any questions feel free to contact me via E-Mail to [email protected].