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Installation

On github, download this repository. Alternative clone the repository on terminal: git clone https://github.com/pylattice/mitoTNT.git

Software requirements

  • Jupyter Notebook or get it from Anaconda

  • MitoGraph for mitochondria segmentation.
    Note that MitoGraph is currently only available on MacOS, but you can build it from source on Linux. Please contact ziw056@ucsd.edu if you need the Linux build.

  • ChimeraX for tracking visualization

Python dependencies

We will create a conda environment that automatically installs all the required dependencies.
1. Open anaconda prompt on Windows or just terminal on MacOS/Linux
2. Go to the root directory of MitoTNT repository
3. Create the enviroment using the provided .yml file: conda env create --name mitotnt --file=mitotnt_env.yml

To use MitoTNT, first activate the environmnet we created with conda activate mitotnt, and then open notebook with jupyter notebook.