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 GUI documentation.
Run batch workflows¶
PlanSeg can perform batch jobs by running yaml workflow files.
You can easily generate them interactively through the napari GUI described above.
To edit a workflow file and set the correct paths use the editor:
plantseg --edit [workflow.yaml]
Then you can run the workflow:
plantseg --config workflow.yaml