Filamentous biopolymer networks in cells and tissues are routinely imaged by confocal microscopy. Image analysis methods enable quantitative study of the properties of these curvilinear networks. However, software tools to quantify the geometry and topology of these often dense 3D networks and to localize network junctions are scarce. To fill this gap, we developed a new software tool called “SOAX”, which can accurately extract the centerlines of 3D biopolymer networks and identify network junctions using Stretching Open Active Contours (SOACs). It provides an open-source, user-friendly platform for network centerline extraction, 2D/3D visualization, manual editing and quantitative analysis. We propose a method to quantify the performance of SOAX, which helps determine the optimal extraction parameter values. We quantify several different types of biopolymer networks to demonstrate SOAX's potential to help answer key questions in cell biology and biophysics from a quantitative viewpoint.

Cardiolipin is a cone-shaped lipid predominantly localized in curved membrane sites of bacteria and in the mitochondrial cristae. This specific localization has been argued to be geometry-driven, since the CL’s conical shape relaxes curvature frustration. Although previous evidence suggests a coupling between CL concentration and membrane shape in vivo, no precise experimental data are available for curvature-based CL sorting in vitro. Here, we test this hypothesis in experiments that isolate the effects of membrane curvature in lipid-bilayer nanotubes. CL sorting is observed with increasing tube curvature, reaching a maximum at optimal CL concentrations, a fact compatible with self-associative clustering. Observations are compatible with a model of membrane elasticity including van der Waals entropy, from which a negative intrinsic curvature of −1.1 nm⁻¹ is predicted for CL. The results contribute to understanding the physicochemical interplay between membrane curvature and composition, providing key insights into mitochondrial and bacterial membrane organization and dynamics.

Significance: Animal cells continuously move, divide, and transmit forces by actively reorganizing their internal scaffold or cytoskeleton. Molecular motors pull actin filaments together and generate contraction of the cytoskeleton underneath the cell membrane. We address the detailed mechanism of contraction by using a minimal in vitro assay: a liposome membrane to which we attach actin filaments and molecular motors in a controlled manner. We reproduce contraction like in cells. We show that the scaffold needs to be tightly attached to the membrane for efficient contraction, but, under some conditions, efficient contraction can lead to liposome destruction. These results suggest that cells must precisely control their contractility to remain intact during cellular events.