  Thread-like structures are pervasive across scales, from polymeric proteins
to root systems to galaxy filaments, and their characteristics can be readily
investigated in the network formalism. Yet, network links usually represent
only parts of filaments, which, when neglected, may lead to erroneous
conclusions from network-based analyses. The existing alternatives to detect
filaments in network representations require tuning of parameters over a large
range of values and treat all filaments equally, thus, precluding automated
analysis of diverse filamentous systems. Here, we propose a fully automated and
robust optimisation-based approach to detect filaments of consistent
intensities and angles in a given network. We test and demonstrate the accuracy
of our solution with contrived, biological, and cosmic filamentous structures.
In particular, we show that the proposed approach provides powerful automated
means to study properties of individual actin filaments in their network
context. Our solution is made publicly available as an open-source tool,
DeFiNe, facilitating decomposition of any given network into individual
filaments.
