Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images
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ORIGINAL ARTICLE
Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images Pankaj Singh1 · Pooran Negi1 · Fernanda Laezza2 · Manos Papadakis1 · Demetrio Labate1
© Springer Science+Business Media New York 2016
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. Pankaj Singh and Pooran Negi contributed equally to this work. Demetrio Labate
[email protected] 1
Department of Mathematics, University of Houston, 4800 Calhoun Rd, Houston, TX 77004, USA
2
Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA
Numerical codes were implemented in Python and released open source and freely available to the scientific community. Keywords Axon guidance · Fluorescence microscopy · Image processing · Multiscale analysis · Neurite orientation · Neurite tracing
Introduction Estimating neurite orientation and quantifying their spatial organization are highly relevant in many areas of neuroscience research associated with neuronal development, such as neurogenesis and neuroregeneration. In the context of enhancing nerve regeneration following nervous system injuries, the guidance of regenerating axons into and across a lesion site is especially important for long-distance axon regeneration. As directional axonal growth was shown to significantly improve the chances of axons to cross a lesion site and to reconnect with distal neuronal targets (Walsh et al. 2005; Mahoney et al. 2005), the accurate quantification of axonal growth direction and alignment is essential to assess the efficacy of neuroregenerative therapies at the cellular scale. In the study of the development of the nervo
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