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

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.