FiberApp: An Open-Source Software for Tracking and Analyzing Polymers, Filaments, Biomacromolecules, and Fibrous Objects

2015-12-17T07:35:24Z (GMT) by Ivan Usov Raffaele Mezzenga
Biological semiflexible polymers and filaments such as collagen, fibronectin, actin, microtubules, coiled-coil proteins, DNA, siRNA, amyloid fibrils, etc., are ubiquitous in nature. In biology, these systems have a direct relation to critical processes ranging from the movement of actin or assembly of viruses at cellular interfaces to the growth of amyloid plaques in neurodegenerative diseases. In technology and applied sciences, synthetic macromolecules or fibrous objects such as carbon nanotubes are involved in countless applications. Accessing their intrinsic properties at the single molecule level, such as their molecular conformations or intrinsic stiffness, is central to the understanding of these systems, their properties, and the design of related applications. In this Perspective we introduce FiberAppa new tracking and analysis software based on a cascade of algorithms describing structural and topological features of objects characterized by a very high length-to-width aspect ratio, generally described as “fiber-like objects”. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects by a semiautomated tracking procedure based on A* pathfinding algorithm followed by the application of active contour models and generating virtually any statistical, topological, and graphical output derivable from these coordinates. Demonstrative features of the software include statistical polymer physics analysis of fiber conformations, height, bond and pair correlation functions, mean-squared end-to-end distance and midpoint displacement, 2D order parameter, excess kurtosis, fractal exponent, height profile and its discrete Fourier transform, orientation, length, height, curvature, and kink angle distributions, providing an unprecedented structural description of filamentous synthetic and biological objects.