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 (Napari viewer)

PlantSeg app can be started from the terminal. First, activate the newly created conda environment with:

mamba activate plant-seg

then, start the plantseg in napari

plantseg --napari

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

Pipeline Usage (command line)

PlantSeg can be configured using YAML config files.

First, activate the newly created conda environment with:

mamba 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 documentation (CLI) for a detailed description of the parameters.

PlantSeg (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:

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).

Using LiftedMulticut segmentation

As reported in our paper, if one has a nuclei signal imaged together with the boundary signal, we could leverage the fact that one cell contains only one nucleus and use the LiftedMultict segmentation strategy and obtain improved segmentation. This workflow is now available in all PlantSeg interfaces.