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Installation

This is the installation guide for the latest PlantSeg. Please check the installation guide for PlantSeg v1 at PlantSeg Legacy Installation.

Download

Download the installer from heibox and choose according to your platform.

Download

Installation

The installer comes complete with its own python installation. During the installation further dependencies need to be downloaded.

First Start

The first start can be quite slow, as the machine learning models need to be downloaded.

Download the Installer, make the installer script executable, then run it. 

chmod +x PlantSeg*.sh

Download the installer and execute it. As the installer is not signed you might need to confirm the download and that you want to run the installer.

Choose a installation path without spaces in it, as those can cause issues with conda packages.

If you want to install PlantSeg without the installer, you need to have conda and git installed. (We recommend Microforge to get conda, see installing mamba)

conda create --name plant-seg plant-seg
conda activate plant-seg
plantseg --napari

To get the latest pre-release features, install PlantSeg from git. You need to have conda and git installed. (We recommend Microforge to get conda, see installing mamba)

git clone https://github.com/kreshuklab/plant-seg.git
cd plant-seg
conda env create environment.yaml
conda activate plant-seg
plantseg --napari

Optional dependencies

Certain compressed TIFF files (e.g., Zlib, ZSTD, LZMA formats) require additional codecs to be processed correctly by PlantSeg. To handle such files, install the imagecodecs package:

conda activate plant-seg
pip install imagecodecs

If you plan to use SimpleITK-based watershed segmentation, you will need to install SimpleITK as an additional dependency:

conda activate plant-seg
pip install SimpleITK

Installing PlantSeg v1

Please check the installation guide for PlantSeg v1 at PlantSeg Legacy Installation.