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Installation

Prerequisites for Conda package

  • Linux, Windows, macOS (not all features are available on macOS)
  • (Optional) Nvidia GPU with official Nvidia drivers installed for GPU acceleration

Install Mamba

The easiest way to install PlantSeg is by using the conda (Anaconda) or mamba (Miniforge) package manager. We recommend using mamba because it is faster and usually more consistent than conda.

To download Miniforge open a terminal and type:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Then install by typing:

bash Miniforge3-$(uname)-$(uname -m).sh

and follow the installation instructions. Please refer to the Miniforge repo for more information, troubleshooting and uninstallation instructions. The miniforge installation file Miniforge3-*.sh can be deleted now.

The first step required to use the pipeline is installing mamba. The installation can be done by downloading the installer from the Miniforge repo. There you can find the download links for the latest version of Miniforge, troubleshooting and uninstallation instructions.

Install PlantSeg using Mamba

PlantSeg can be installed directly by executing in the terminal (or PowerShell on Windows). For conda users, the command is identical, just replace mamba with conda.

  • NVIDIA GPU version, CUDA=12.x

    mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=12.1 pyqt plant-seg --no-channel-priority

  • NVIDIA GPU version, CUDA=11.x

    mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch pytorch-cuda=11.8 pyqt plant-seg --no-channel-priority

  • CPU version

    mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly pyqt plant-seg --no-channel-priority

  • Apple silicon version

    mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch pyqt plant-seg --no-channel-priority

If you used older versions of PlantSeg, please delete the old config files in ~/.plantseg_models/configs/ after installing new PlantSeg.

The above command will create new conda environment plant-seg together with all required dependencies.

Please refer to the PyTorch website for more information on the available versions of PyTorch and the required CUDA version. The GPU version of Pytorch will also work on CPU only machines but has a much larger installation on disk.

Optional dependencies

If you want to use the headless mode of PlantSeg, you need to install dask[distributed]:

conda activate plant-seg
mamba install dask distributed

Some types of compressed tiff files require an additional package to be load correctly (e.g.: Zlib, ZSTD, LZMA, ...). To run PlantSeg on those stacks, you need to install imagecodecs. In the terminal:

conda activate plant-seg
pip install imagecodecs

Experimental support for SimpleITK watershed segmentation has been added to PlantSeg version 1.1.8. These features can be used only after installing the SimpleITK package:

conda activate plant-seg
pip install SimpleITK