Quick Start

PlantSeg can be used in three different ways: interactively (using the Napari viewer), as a command line, or with a GUI. The following sections will guide you through the installation and usage of PlantSeg in each of these modes.

Interactive PlantSeg with Napari Viewer

PlantSeg app can be started from the terminal. After installing PlantSeg using the installer, there should be a menu entry for to launch PlantSeg.

Alternatively, launch PlantSeg in the terminal. First activate your environment (by default this is the installation directory, change the command if needed) with:

conda activate ~/plantseg

then, start PlantSeg with the napari GUI:

plantseg --napari

A more in depth guide can be found in our documentation (GUI).

Command Line PlantSeg

PlantSeg can be configured using YAML config files.

First, activate the newly created conda environment (by default this is the installation directory, change the command if needed) with:

conda activate ~/plantseg

then, start the pipeline with:

plantseg --config CONFIG_PATH

where CONFIG_PATH is the path to the YAML configuration file. See config.yaml for a sample configuration file and our documentation (CLI) for a detailed description of the parameters.

PlantSeg with Legacy GUI

Deprecated

This interface is deprecated and has been removed from PlantSeg v2. Please use the Napari viewer or the command line interface instead, or install PlantSeg v1.

PlantSeg app can also be started in a GUI mode, where basic user interface allows to configure and run the pipeline. First, activate the newly created conda environment with:

mamba activate plant-seg

then, run the GUI by simply typing:

plantseg --gui

A more in depth guide can be found in our documentation (Classic GUI).