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.