Installation

Anipose can be installed with the steps described below, starting with installing Python 3. If you already have Python 3 installed through the Anaconda distribution, you can begin the installation process at Set up a virtual environment with Anipose.

Install Python 3 via Anaconda

1. We recommend installing Python 3 through the Anaconda distribution. You can download the installer for your machine here. The installation pages in the Anaconda documentation have screenshots that are helpful if you would like further guidence during the installation process.

2. After you have installed Anaconda, open the Anaconda Prompt (for Windows) or the terminal (for Linux and macOS) and enter

   conda list
   

   to make sure the installation was successful. If Anaconda is installed, this will output a list of installed packages and their versions. Enter python to launch a Python shell. The version information will be displayed, and it should include “Anaconda”. Exit the Python shell with quit().

Set up a virtual environment with Anipose

1. From the Anaconda Prompt (for Windows) or the terminal (for Linux and macOS), create a conda environment with Python 3.7 and Tensorflow. Activate the environment, then install DeepLabCut with pip. To do this, you can run the following commands:

   conda create -n yourenvname python=3.7 tensorflow=1.13.1
   conda activate yourenvname
   python -m pip install deeplabcut
   

2. Next, install wxPython with pip. For Windows and MacOS, run

   python -m pip install -U wxPython
   

   For Linux, you need the specific wheel. See the wxPython documentation for more details.

3. Install Anipose with pip with the following command:

   python -m pip install anipose
   

NOTE: You may need to remove opencv-python before running the above command, so that opencv-contrib-python is installed correctly:

python -m pip uninstall opencv-python

4. Install ffmpeg and mayavi in your conda environment with the commands shown below. Note that you will have to upgrade apptools after installing mayavi with conda.

   conda install mayavi ffmpeg
   pip install --upgrade apptools
   

Check if Anipose was installed

1. You can check if Anipose was installed by typing

   anipose
   

in the Anaconda Prompt or the terminal. If the installation was successful, you should see a list of commands that can be run with Anipose. The expected output is shown below.

Now you are all set to use Anipose!