DeepLabCut

How To Install DeepLabCut2.0:

First, Technical Considerations:

INSTALLATION:

There are several modes of installation, and the user should decide to either use a system-wide (see note below), Anaconda environment based installation (recommended), or the supplied Docker container (recommended for Ubuntu advanced users). One can of course also use other Python distributions than Anaconda, but this is the easiest route.

All the following commands will be run in the app terminal in Ubuntu/MacOS, and called cmd in Windows. Please first open the terminal (search terminal or cmd).

Anaconda:

Anaconda is perhaps the easiest way to install Python and additional packages across various operating systems. First create an Anaconda environment. With Anaconda you create all the dependencies in an environment on your machine in the following way. More details can be found in the conda environment readme.

MacOS (Mojave+/CPU only):

Windows:

LINUX (Ubuntu 16.04):

conda create -n <nameyourenvironment> python=3.6
activate <nameyourenvironment>

Once the environment was activated, the user can install DeepLabCut. In the terminal type:

pip install deeplabcut

Then,

Windows: pip install -U wxPython

Linux: pip install https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-16.04/wxPython-4.0.3-cp36-cp36m-linux_x86_64.whl

Install TensorFlow - with GPU support or CPU support:

As users can use a GPU or CPU, TensorFlow is not installed with the command pip install deeplabcut. Here is more information on how to best install TensorFlow with pip: https://www.tensorflow.org/install/pip

CPU ONLY:

pip install --ignore-installed tensorflow==1.10

GPU:

Install TensorFlow. In the Nature Neuroscience paper we used TensorFlow 1.0 with CUDA (Cuda 8.0). Some other versions of TensorFlow have been tested, but use at your own risk (i.e. these versions have been tested 1.2, 1.4, 1.8 or 1.10-1.13, but might require different CUDA versions)! Please check your driver/cuDNN/CUDA/TensorFlow versions on this Stackoverflow post.

If you have a GPU, you should then install the NVIDIA CUDA package and an appropriate driver for your specific GPU. Please follow the instructions found here: https://www.tensorflow.org/install/gpu, and more tips below. The order of operations matters.

Some tips for installing TensorFlow 1.8 will follow here:

FIRST, install a driver for your GPU (we recommend the 384.xx) Find DRIVER HERE: https://www.nvidia.com/download/index.aspx

SECOND, install CUDA (9.0 here): https://developer.nvidia.com/cuda-90-download-archive

THIRD, install TensorFlow:

Package for pip install:

pip install tensorflow-gpu==1.8 —with GPU support (Ubuntu and Windows)

Note, the version is specified by using: ==1.8

FOURTH, Please check your CUDA and TensorFlow installation with the lines below:

Start a python session: ipython

import tensorflow as tf

sess = tf.Session(config=tf.ConfigProto(log_device_placement=True))

You can test that your GPU is being properly engaged with these additional tips.

Troubleshooting:

TensorFlow: Here are some additional resources users have found helpful (posted without endorsement):

FFMEG:

DEEPLABCUT:

System-wide considerations:

If you perform the system wide installation, and the computer has other Python packages or TensorFlow versions installed that conflict, this will overwrite them. If you have a dedicated machine for DeepLabCut, this is fine. If there are other applications that require different versions of libraries, then one would potentially break those applications. The solution to this problem is to create a virtual environment, a self-contained directory that contains a Python installation for a particular version of Python, plus additional packages. One way to manage virtual environments is to use conda environments (for which you need Anaconda installed).

You’re ready to Run DeepLabCut!

Now you can use Jupyter Notebooks, Spyder, and to train just use the terminal, to run all the code!

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