Quick Start

Pipeline Usage (Napari viewer)

PlantSeg app can also be started using napari as a viewer. First, activate the newly created conda environment with:

conda activate plant-seg

then, start the plantseg in napari

$ plantseg --napari

A more in depth guide can be found in our wiki.

Pipeline Usage (GUI)

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:

conda activate plant-seg

then, run the GUI by simply typing:

$ plantseg --gui

A more in depth guide can be found in our wiki.

Pipeline Usage (command line)

Our pipeline is completely configuration file based and does not require any coding.

First, activate the newly created conda environment with:

conda activate plant-seg

then, one can just 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 wiki for a detailed description of the parameters.