Installation - kreshuklab/plant-seg GitHub Wiki

Prerequisites for Conda package

  • Linux or Windows

  • (Optional) Nvidia GPU with official Nvidia drivers installed

  • Native MacOS installation (not yet M1) coming soon.

Install on Linux

Install Anaconda python

The first step required to use the pipeline is installing anaconda python. You can go directly to the next item if you already have a working anaconda setup. Anaconda can be downloaded for all platforms from here anaconda. We suggest using Miniconda because it is lighter and install fewer unnecessary packages.

To download Anaconda Python open a terminal and type

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

Then install by typing:

bash ./Miniconda3-latest-Linux-x86_64.sh

Follow the instructions to complete the anaconda installation. The Miniconda3-latest-Linux-x86_64.sh file can be safely deleted.

Install PlantSeg using conda

PlantSeg can be installed directly by executing in the terminal:

conda create -n plant-seg -c pytorch -c conda-forge -c lcerrone -c awolny python=3.9 pytorch-3dunet=1.3.7 plantseg napari

The above command will create a new Conda environment, plant-seg, with all required dependencies.

Install on Windows

Install Anaconda python

The first step required to use the pipeline is installing anaconda python. You can go directly to the next item if you already have a working anaconda setup. Anaconda can be downloaded for all platforms from here anaconda. We suggest using Miniconda because it is lighter and install fewer unnecessary packages.

Miniconda can be downloaded from miniconda. Download the executable .exe for your Windows version and follow the installation instructions.

Install PlantSeg using conda

PlantSeg can be installed directly by executing in the terminal:

conda create -n plant-seg -c pytorch -c conda-forge -c lcerrone -c awolny python=3.9 pytorch-3dunet=1.3.7 plantseg napari

The above command will create a new Conda environment, plant-seg, with all required dependencies.

Optional dependencies (not fully tested on Windows)

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