Aims to analyze the dynamics of macromolecular assemblies with high spatial and temporal resolution. QFSM allows users to study spatial and temporal relations between the formation, turnover, and mechanical outputs of the filament network. It assists in identifying and tracking speckles and utilizes their location, appearance, and disappearance to derive network flows and assembly/disassembly maps.
Graphical User Interface for studying the growth of plant hypocotyl and root. KymoRod allows to select a collection of images following the growth of a plant organ. Several processing steps can be applied to segment hypocotyls on images, extract the contour, compute the Voronoi skeleton, measure curvilinear abscissa, identifies homologous positions on skeleton pairs, compute relative elongation rate, and finally display the result as a kymograph.
Assists in analysing cell shape and motion. 3D cell shape and migration allows users to study the correlation between these shape and motion parameters and subcellular fluorescence localization. It is based on a 3D Gaussian partial-derivative kernel surface filtering algorithm. This method is combined with a self-adjusting high intensity threshold.
Furnishes a method allowing extraction of biopolymer dynamics from kymographs. KymoButler is a program based on a fully convolutional deep neural networks (FCNs) that can serve for the analysis of kymographs from different dynamic processes such as retrograde actin flow in neuronal growth cones. It also includes features for quantifying actin speckle velocities in Aplysia growth cones.