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
.