CryoVIA: An image analysis toolkit for the quantification of membrane structures from cryo-EM micrographs

Imaging of lipid structures and associated protein complexes using cryoelectron microscopy (cryo-EM) is a common visualization and structure determination technique. The quantitative analysis of the membrane structures, however, is not routine and time consuming in particular when large amounts of data are involved. Here, we introduce the automated image-processing software cryo-vesicle image analyzer (CryoVIA) that parametrizes lipid structures of large datasets from cryo-EM images. This toolkit combines segmentation, structure identification with methods to automatically perform a large-scale data analysis of local and global membrane properties such as bilayer thickness, size, and curvature including membrane shape classifications. We included analyses of exemplary datasets of different lipid compositions and protein-induced lipid changes through an endosomal sorting complexes required for transport III (ESCRT-III) membrane remodeling protein. The toolkit opens new possibilities to systematically study structural properties of membrane structures and their modifications from cryo-EM images.