GeoV: An Open‐Source Software Package for Quantitative Image Analysis of 3D Vesicle Morphologies

Abstract

Bottom‐up synthetic biology has reconstituted processes like adhesion, cortex formation, or division of giant lipid vesicles (GUVs), which all rely on changes in the vesicle morphology. However, oftentimes, GUV morphologies and shape transitions are described qualitatively, which makes it difficult to quantitatively compare results from different studies and to advance precision engineering. Herein, open‐source software package GeoV for the 3D reconstruction and analysis of GUV shapes from confocal microscopy z‐stacks is presented. The accuracy of the reconstruction by comparing the output for the Hausdorff distance of the surface, the curvature, and the bending energy to ground truth data for simulated shapes of different complexities is quantified. Next, GeoV on a variety of confocal microscopy datasets, including z‐stacks from spherical GUVs and GUVs deformed with DNA origami, adherent GUVs, DNA droplets, and cells, is tested. Additionally, the effect of membrane‐binding DNA origami on the vesicle shape, volume, and bending energy is quantified. It is found that osmotic deflation and attachment of DNA origami can increase the bending energy of GUVs by a factor of 10. All in all, GeoV as an open‐source software package for the quantitative analysis of confocal microscopy data for bottom‐up synthetic biology is provided.