Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

Pankaj Singh, Pooran Negi, Fernanda Laezza, Manos Papadakis, Demetrio Labate

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1-13
Number of pages13
JournalNeuroinformatics
DOIs
StateAccepted/In press - Jul 1 2016

Fingerprint

Neurites
Brain
Neurons
Dendrites
Axons
Boidae
Neurogenesis
Carisoprodol
Tissue
Synapses
Geometry
Noise

Keywords

  • Axon guidance
  • Fluorescence microscopy
  • Image processing
  • Multiscale analysis
  • Neurite orientation
  • Neurite tracing

ASJC Scopus subject areas

  • Neuroscience(all)
  • Information Systems
  • Software

Cite this

Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images. / Singh, Pankaj; Negi, Pooran; Laezza, Fernanda; Papadakis, Manos; Labate, Demetrio.

In: Neuroinformatics, 01.07.2016, p. 1-13.

Research output: Contribution to journalArticle

Singh, Pankaj ; Negi, Pooran ; Laezza, Fernanda ; Papadakis, Manos ; Labate, Demetrio. / Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images. In: Neuroinformatics. 2016 ; pp. 1-13.
@article{2c4d95d4e5324b46821194a9aadf6cf4,
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.",
keywords = "Axon guidance, Fluorescence microscopy, Image processing, Multiscale analysis, Neurite orientation, Neurite tracing",
author = "Pankaj Singh and Pooran Negi and Fernanda Laezza and Manos Papadakis and Demetrio Labate",
year = "2016",
month = "7",
day = "1",
doi = "10.1007/s12021-016-9306-9",
language = "English (US)",
pages = "1--13",
journal = "Neuroinformatics",
issn = "1539-2791",
publisher = "Humana Press",

}

TY - JOUR

T1 - Multiscale Analysis of Neurite Orientation and Spatial Organization in Neuronal Images

AU - Singh, Pankaj

AU - Negi, Pooran

AU - Laezza, Fernanda

AU - Papadakis, Manos

AU - Labate, Demetrio

PY - 2016/7/1

Y1 - 2016/7/1

N2 - 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.

AB - 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.

KW - Axon guidance

KW - Fluorescence microscopy

KW - Image processing

KW - Multiscale analysis

KW - Neurite orientation

KW - Neurite tracing

UR - http://www.scopus.com/inward/record.url?scp=84976519450&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84976519450&partnerID=8YFLogxK

U2 - 10.1007/s12021-016-9306-9

DO - 10.1007/s12021-016-9306-9

M3 - Article

SP - 1

EP - 13

JO - Neuroinformatics

JF - Neuroinformatics

SN - 1539-2791

ER -