Installation#

SLEAP can be installed as a Python package on Windows, Linux and Mac OS X. We currently provide experimental support for M1 Macs.

SLEAP requires many complex dependencies, so we strongly recommend using Miniconda to install it in its own isolated environment. See Installing Miniconda below for more instructions.

The newest version of SLEAP can always be found in the Releases page.

Installing Miniconda#

Anaconda is a Python environment manager that makes it easy to install SLEAP and its necessary dependencies without affecting other Python software on your computer.

Miniconda is a lightweight version of Anaconda that we recommend. To install it:

  1. Go to: https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links

  2. Download the latest version for your OS.

  3. Follow the installer instructions.

On Windows, just click through the installation steps. We recommend using the following settings:

  • Install for: All Users (requires admin privileges)

  • Destination folder: C:\Miniconda3

  • Advanced Options: Add Miniconda3 to the system PATH environment variable

  • Advanced Options: Register Miniconda3 as the system Python 3.X These will make sure that Anaconda is easily accessible from most places on your computer.

On Linux, it might be easier to do this straight from the terminal (Ctrl + Alt + T) with this one-liner:

wget -nc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && bash Miniconda3-latest-Linux-x86_64.sh -b && ~/miniconda3/bin/conda init bash

Restart the terminal after running this command.

On Macs, you can run the graphical installer using the pkg file, or this terminal command:

wget -nc https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh && bash Miniconda3-latest-MacOSX-x86_64.sh -b && ~/miniconda3/bin/conda init zsh

Installation methods#

Hint

Installation requires entering commands in a terminal. To open one:

Windows: Open the Start menu and search for the Anaconda Command Prompt (if using Miniconda) or the Command Prompt if not.

Note

On Windows, our personal preference is to use alternative terminal apps like Cmder or Windows Terminal.

Linux: Launch a new terminal by pressing Ctrl + Alt + T.

Mac: Launch a new terminal by pressing Cmd + Space and searching for Terminal.

conda package#

conda create -y -n sleap -c sleap -c nvidia -c conda-forge sleap=1.2.9

This is the recommended installation method. Works on Windows and Linux.

Note

  • This comes with CUDA to enable GPU support. All you need is to have an NVIDIA GPU and updated drivers.

  • If you already have CUDA installed on your system, this will not conflict with it.

  • This will also work in CPU mode if you don’t have a GPU on your machine.

conda from source#

  1. First, ensure git is installed:

    git --version

    If ‘git’ is not recognized, then install git.

  2. Then, clone the repository:

    git clone https://github.com/talmolab/sleap && cd sleap

  3. Finally, install from the environment file:

    conda env create -f environment.yml -n sleap

    If you do not have a NVIDIA GPU, then you should use the no CUDA environment file:

    conda env create -f environment_no_cuda.yml -n sleap

    This works on Windows, Linux and Mac OS X (pre-M1). This is the recommended method for development.

Note

  • This installs SLEAP in development mode, which means that edits to the source code will be applied the next time you run SLEAP.

  • Change the -n sleap in the command to create an environment with a different name (e.g., -n sleap_develop).

pip package#

pip install sleap==1.2.9

This works on any OS except M1 and on Google Colab.

Note

  • Requires Python 3.7 or 3.8.

  • To enable GPU support, make sure that you have CUDA Toolkit v11.3 and cuDNN v8.2 installed.

Warning

This will uninstall existing libraries and potentially install conflicting ones.

We strongly recommend that you only use this method if you know what you’re doing!

M1 Macs#

SLEAP can be installed on newer M1 Macs by following these instructions:

  1. In addition to being on an M1 Mac, make sure you’re on macOS Monterey, i.e., version 12+. We’ve tested this on a MacBook Pro (14-inch, 2021) running macOS version 12.0.1.

  2. If you don’t have it yet, install homebrew, a convenient package manager for Macs (skip this if you can run brew from the terminal):

    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

    This might take a little while since it’ll also install Xcode (which we’ll need later). Once it’s finished, run this to enable the brew command in your shell, then close and re-open the terminal for it to take effect:

    echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> ~/.zprofile && eval "$(/opt/homebrew/bin/brew shellenv)"

  3. Install wget, a CLI downloading utility (also makes sure your homebrew setup worked):

    brew install wget

  4. Install the M1 Mac version of Miniconda – this is important, so make sure you don’t have the regular Mac version! If you’re not sure, type which conda and delete the containing directory to uninstall your existing conda. To install the correct Miniconda, just run:

    wget -nc https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh && bash Miniconda3-latest-MacOSX-arm64.sh -b && rm Miniconda3-latest-MacOSX-arm64.sh && ~/miniconda3/bin/conda init zsh

    Then close and re-open the terminal again.

  5. Download the SLEAP:

    cd ~ && git clone https://github.com/talmolab/sleap.git sleap && cd sleap

  6. Install SLEAP in a conda environment:

    conda env create -f environment_m1.yml

    Your Mac will then automatically sign a devil’s pact with Apple to install the correct versions of everything on your system. Once the blood sacrifice/installation process completes, SLEAP will be available in an environment called sleap.

    Note: This installs SLEAP in development mode, so changes to the source code are immediately applied in case you wanted to mess around with it. You can also just do a git pull to update it (no need to re-do any of the previous steps).

  7. Test it out by activating the environment and opening the GUI!

    conda activate sleap

    sleap-label

Testing that things are working#

If you installed using conda, first activate the sleap environment by opening a terminal and typing:

conda activate sleap

Hint

Not sure what conda environments you already installed? You can get a list of the environments on your system with:

conda env list

GUI support#

To check that the GUI is working, simply type:

sleap-label

You should see the SLEAP labeling interface pop up within a few moments.

Importing#

To check if SLEAP is installed correctly in non-interactive environments, such as remote servers, confirm that you can import it with:

python -c "import sleap; sleap.versions()"

Output:

(sleap_develop) λ python -c "import sleap; sleap.versions()"
SLEAP: 1.2.0
TensorFlow: 2.7.1
Numpy: 1.21.5
Python: 3.7.11
OS: Windows-10-10.0.19041-SP0

GPU support#

Assuming you installed using either of the conda-based methods on Windows or Linux, SLEAP should automatically have GPU support enabled.

To check, verify that SLEAP can detect the GPUs on your system:

python -c "import sleap; sleap.system_summary()"

Output:

(sleap_develop) λ python -c "import sleap; sleap.system_summary()"
GPUs: 2/2 available
  Device: /physical_device:GPU:0
         Available: True
        Initalized: False
     Memory growth: None
  Device: /physical_device:GPU:1
         Available: True
        Initalized: False
     Memory growth: None

SLEAP uses TensorFlow for GPU acceleration. To directly check if TensorFlow is detecting your GPUs:

python -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"

Output:

(sleap_develop) λ python -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"
[PhysicalDevice(name='/physical_device:GPU:0', device_type='GPU'), PhysicalDevice(name='/physical_device:GPU:1', device_type='GPU')]

Note

  • GPU support requires an NVIDIA GPU.

  • If you haven’t yet (or in a while), update to the latest NVIDIA drivers for your GPU.

  • We use the official conda packages for cudatoolkit and cudnn, so no external installations are required. If you already have those installed on your system, they should not interfere with the ones in the SLEAP environment.

  • TensorFlow 2.6-2.8 are compatible with CUDA Toolkit v11.3 and cuDNN v8.2.

Warning

TensorFlow 2.7+ is currently failing to detect CUDA Toolkit and CuDNN on some systems (see Issue thread).

If you run into issues, try downgrading the TensorFlow 2.6:

pip install tensorflow==2.6.3

Upgrading and uninstalling#

We strongly recommend installing SLEAP in a fresh environment when updating. This is because dependency versions might change, and depending on the state of your previous environment, directly updating might break compatibility with some of them.

To uninstall an existing environment named sleap:

conda env remove -n sleap

Hint

Not sure what conda environments you already installed? You can get a list of the environments on your system with:

conda env list

Once the environment has been removed, you are free to install SLEAP using any of the installation methods above into an environment of the same name.

Getting help#

If you run into any problems, check out the Github Discussions and GitHub Issues to see if others have had the same problem.

If you get any errors or the GUI fails to launch, try running the diagnostics to see what SLEAP is able to detect on your system:

sleap-diagnostic

If you were not able to get SLEAP installed, activate the conda environment it is in and generate a list of the package versions installed:

conda list

Then, open a new Issue providing the versions from either command above, as well as any errors you saw in the console during the installation. Or start a discussion to get help from the community.