napari-morphodynamics

napari-morphodynamics is a plugin that allows to study the correlated dynamics of cell shape and molecular events in 2D+time fluorescence microscopy. It offers and interface to the MorphoDynamics package in napari.

Head to the Getting Started section to learn how to install the plugin and use its basics functionalities.

Head to the Examples section to discover how to use the plugin on a few examples.

Alternative: napari-roidynamics

As some of the processes in this plugin are computationally heavy, we have developed a spin-off plugin called napari-roidynamics, which allows to generate fixed geometries instead of precise segmentation and analyses intensity fluctuations in these regions of interest. Please refer to napari-roidynamics if you wish to apply intensity dynamics measurements in fixed geometries.

Authors

The Morphodynamics package on which this plugin relies was inspired by the Windowing-Protrusion Matlab package developed by the Danuser Lab. It was developed by Guillaume Witz and Cédric Vonesch at the Data Science Lab (DSL), University of Bern and Jakobus van Unen, Lucien Hinderling and Olivier Pertz from the Pertz Lab, Institute of Cell Biology, University of Bern. This plugin was developed thanks to a Chan Zuckerberg Initiative grant, by Guillaume Witz and Ana Stojiljkovic at DSL, again in collaboration with the Pertz lab.