SLEAP requires many complex dependencies, so we strongly recommend using a package manager such as Miniconda to install SLEAP in its own isolated environment. See the Miniconda website for installation instructions. The Anaconda or Mamba package managers will also work well; however, take care not to install multiple different conda-based package managers - choose one and stick with it.
+SLEAP requires many complex dependencies, so we strongly recommend using a package manager such as Miniforge or Miniconda to install SLEAP in its own isolated environment.
Note
If you already have Anaconda on your computer (and it is an older installation), then make sure to set the solver to libmamba in the base environment.
conda commands in the docs will need to be replaced with mamba if you have Mamba installed instead of Anaconda or Miniconda.
If you don’t have a conda package manager installation, here are some quick install options:
Miniforge is a minimal installer for conda that includes the conda package manager and is maintained by the conda-forge community. The only difference between Miniforge and Miniconda is that Miniforge uses the conda-forge channel by default, which provides a much wider selection of community-maintained packages.
Open a new PowerShell terminal (does not need to be admin) and enter:
+Invoke-WebRequest -Uri "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Windows-x86_64.exe" -OutFile "$env:UserProfile/Downloads/Miniforge3-Windows-x86_64.exe"; Start-Process -FilePath "$env:UserProfile/Downloads/Miniforge3-Windows-x86_64.exe" -ArgumentList "/InstallationType=JustMe /RegisterPython=1 /S" -Wait; Remove-Item -Path "$env:UserProfile/Downloads/Miniforge3-Windows-x86_64.exe"
+Open a new terminal and enter:
+curl -fsSL --compressed https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh -o "~/Downloads/Miniforge3-Linux-x86_64.sh" && chmod +x "~/Downloads/Miniforge3-Linux-x86_64.sh" && "~/Downloads/Miniforge3-Linux-x86_64.sh" -b -p ~/miniforge3 && rm "~/Downloads/Miniforge3-Linux-x86_64.sh" && ~/miniforge3/bin/conda init "$(basename "${SHELL}")" && source "$HOME/.$(basename "${SHELL}")rc"
+Open a new terminal and enter:
+curl -fsSL --compressed https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-arm64.sh -o "~/Downloads/Miniforge3-MacOSX-arm64.sh" && chmod +x "~/Downloads/Miniforge3-MacOSX-arm64.sh" && "~/Downloads/Miniforge3-MacOSX-arm64.sh" -b -p ~/miniforge3 && rm "~/Downloads/Miniforge3-MacOSX-arm64.sh" && ~/miniforge3/bin/conda init "$(basename "${SHELL}")" && source "$HOME/.$(basename "${SHELL}")rc"
+Open a new terminal and enter:
+curl -fsSL --compressed https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh -o "~/Downloads/Miniforge3-MacOSX-x86_64.sh" && chmod +x "~/Downloads/Miniforge3-MacOSX-x86_64.sh" && "~/Downloads/Miniforge3-MacOSX-x86_64.sh" -b -p ~/miniforge3 && rm "~/Downloads/Miniforge3-MacOSX-x86_64.sh" && ~/miniforge3/bin/conda init "$(basename "${SHELL}")" && source "$HOME/.$(basename "${SHELL}")rc"
+This is a minimal installer for conda that includes the conda package manager and is maintained by the Anaconda company.
Open a new PowerShell terminal (does not need to be admin) and enter:
+curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Windows-x86_64.exe -o miniconda.exe; Start-Process -FilePath ".\miniconda.exe" -ArgumentList "/S" -Wait; del miniconda.exe
+Open a new terminal and enter:
+mkdir -p ~/miniconda3 && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda3/miniconda.sh && bash ~/miniconda3/miniconda.sh -b -u -p ~/miniconda3 && rm ~/miniconda3/miniconda.sh && ~/miniconda3/bin/conda init "$(basename "${SHELL}")" && source "$HOME/.$(basename "${SHELL}")rc"
+Open a new terminal and enter:
+curl -fsSL --compressed https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-arm64.sh -o "~/Downloads/Miniconda3-latest-MacOSX-arm64.sh" && chmod +x "~/Downloads/Miniconda3-latest-MacOSX-arm64.sh" && "~/Downloads/Miniconda3-latest-MacOSX-arm64.sh" -b -u -p ~/miniconda3 && rm "~/Downloads/Miniconda3-latest-MacOSX-arm64.sh" && ~/miniconda3/bin/conda init "$(basename "${SHELL}")" && source "$HOME/.$(basename "${SHELL}")rc"
+Open a new terminal and enter:
+curl -fsSL --compressed https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o "~/Downloads/Miniconda3-latest-MacOSX-x86_64.sh" && chmod +x "~/Downloads/Miniconda3-latest-MacOSX-x86_64.sh" && "~/Downloads/Miniconda3-latest-MacOSX-x86_64.sh" -b -u -p ~/miniconda3 && rm "~/Downloads/Miniconda3-latest-MacOSX-x86_64.sh" && ~/miniconda3/bin/conda init "$(basename "${SHELL}")" && source "$HOME/.$(basename "${SHELL}")rc"
+See the Miniconda website for up-to-date installation instructions if the above instructions don’t work for your system.
+SLEAP can be installed three different ways: via conda package, conda from source, or pip package. Select one of the methods below to install SLEAP. We recommend conda package.
This is the recommended installation method.
+This is the recommended installation method.
conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a2
+conda create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.4.1a2
-conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a2
+
conda create -y -n sleap -c conda-forge -c anaconda -c sleap sleap=1.4.1a2
-This is the recommended method for development.
+This is the recommended method for development.
First, ensure git is installed:
git --version
@@ -434,15 +489,15 @@ Package Manager
Finally, install SLEAP from the environment file:
-
-conda env create -f environment.yml -n sleap
+
+conda env create -f environment.yml -n sleap
-conda env create -f environment_no_cuda.yml -n sleap
+
conda env create -f environment_no_cuda.yml -n sleap
-conda env create -f environment_mac.yml -n sleap
+
conda env create -f environment_mac.yml -n sleap
@@ -455,14 +510,14 @@ Package ManagerChange the -n sleap in the command to create an environment with a different name (e.g., -n sleap_develop).
-This is the recommended method for Google Colab only.
+This is the recommended method for Google Colab only.
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!
-
+
Note
Requires Python 3.7
Package Manager
Otherwise, create a new conda environment where we will pip install sleap:
-conda create --name sleap pip python=3.7.12 cudatoolkit=11.3 cudnn=8.2
+conda create --name sleap pip python=3.7.12 cudatoolkit=11.3 cudnn=8.2
-conda create --name sleap pip python=3.7.12
+
conda create --name sleap pip python=3.7.12
@@ -507,7 +562,7 @@ Package Manager
-
Not supported.
+Not supported.
@@ -515,7 +570,7 @@ Package Manager
-Testing that things are working#
+Testing that things are working#
If you installed using conda, first activate the sleap environment by opening a terminal and typing:
conda activate sleap
@@ -528,7 +583,7 @@ Testing that things a
-GUI support#
+GUI support#
To check that the GUI is working, simply type:
sleap-label
@@ -536,7 +591,7 @@ GUI supportYou should see the SLEAP labeling interface pop up within a few moments.
-Importing#
+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()"
@@ -552,7 +607,7 @@ Importing
-GPU support#
+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()"
@@ -629,7 +684,7 @@ GPU support
-Upgrading and uninstalling#
+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
@@ -645,7 +700,7 @@ Upgrading and uninsta
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#
+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
@@ -707,7 +762,11 @@ Getting help