title: Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images.
abstract: The spatial organization of neurites, the thin processes (i.e., dendrites and axons) that stem from a neuron's soma, conveys structural information required for proper brain function. The alignment, direction and overall geometry of neurites in the brain are subject to continuous remodeling in response to healthy and noxious stimuli. In the developing brain, during neurogenesis or in neuroregeneration, these structural changes are indicators of the ability of neurons to establish axon-to-dendrite connections that can ultimately develop into functional synapses. Enabling a proper quantification of this structural remodeling would facilitate the identification of new phenotypic criteria to classify developmental stages and further our understanding of brain function. However, adequate algorithms to accurately and reliably quantify neurite orientation and alignment are still lacking. To fill this gap, we introduce a novel algorithm that relies on multiscale directional filters designed to measure local neurites orientation over multiple scales. This innovative approach allows us to discriminate the physical orientation of neurites from finer scale phenomena associated with local irregularities and noise. Building on this multiscale framework, we also introduce a notion of alignment score that we apply to quantify the degree of spatial organization of neurites in tissue and cultured neurons. Numerical codes were implemented in Python and released open source and freely available to the scientific community.
authors.affiliation: Department of Mathematics, University of Houston, 4800 Calhoun Rd, Houston, TX, 77004, USA.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Singh
authors.affiliation: Department of Mathematics, University of Houston, 4800 Calhoun Rd, Houston, TX, 77004, USA.
authors.forename: Pooran
authors.initials: P
authors.lastname: Negi
authors.affiliation: Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555, USA.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Laezza
authors.affiliation: Department of Mathematics, University of Houston, 4800 Calhoun Rd, Houston, TX, 77004, USA.
authors.forename: Manos
authors.initials: M
authors.lastname: Papadakis
authors.affiliation: Department of Mathematics, University of Houston, 4800 Calhoun Rd, Houston, TX, 77004, USA. dlabate@math.uh.edu.
authors.forename: Demetrio
authors.initials: D
authors.lastname: Labate
mesh_terms: D000465:Algorithms; D000818:Animals; D006624:Hippocampus / Q000166:cytology*; D007091:Image Processing, Computer-Assisted; D008297:Male; D008810:Mice, Inbred C57BL; D016501:Neurites; D015203:Reproducibility of Results
keywords: Axon guidance; Fluorescence microscopy; Image processing; Multiscale analysis; Neurite orientation; Neurite tracing