Installation

To use this plugin you need to be familiar with napari, an interactive viewer for images in Python, which is also becoming a popular standalone application for bioimage analysis. napari has a rich ecosystem of plugins such as napari-morphodynamics, which are extensions for specific image analysis tasks. To get started you need a running napari installation first. You will find more information on the napari website.

Commonly you will create a conda environment in which to first install napari:

mamba create -n naparimorpho python=3.9 napari pyqt

Then you activate the environment and install the plugin from pip:

mamba activate naparimorpho
pip install napari-morphodynamics

After restarting, the plugin will appear in the plugin menu.

Options

If you want to use cellpose for the segmentation step of the workflow, you can either install it in the usual way or directly with the plugin by using:

pip install "napari-morphodynamics[cellpose]"