nAdder: A scale-space approach for the 3D analysis of neuronal traces

Phan, Minh Son, Matho, Katherine, Beaurepaire, Emmanuel, Livet, Jean, Chessel, Anatole (July 2022) nAdder: A scale-space approach for the 3D analysis of neuronal traces. PLoS Computational Biology, 18 (7). e1010211. ISSN 1553-734X

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Abstract

Tridimensional microscopy and algorithms for automated segmentation and tracing are revolutionizing neuroscience through the generation of growing libraries of neuron reconstructions. Innovative computational methods are needed to analyze these neuronal traces. In particular, means to characterize the geometric properties of traced neurites along their trajectory have been lacking. Here, we propose a local tridimensional (3D) scale metric derived from differential geometry, measuring for each point of a curve the characteristic length where it is fully 3D as opposed to being embedded in a 2D plane or 1D line. The larger this metric is and the more complex the local 3D loops and turns of the curve are. Available through the GeNePy3D open-source Python quantitative geometry library (https://genepy3d.gitlab.io), this approach termed nAdder offers new means of describing and comparing axonal and dendritic arbors. We validate this metric on simulated and real traces. By reanalysing a published zebrafish larva whole brain dataset, we show its ability to characterize different population of commissural axons, distinguish afferent connections to a target region and differentiate portions of axons and dendrites according to their behavior, shedding new light on the stereotypical nature of neurites' local geometry.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > computational biology > algorithms organism description > animal organs, tissues, organelles, cell types and functions > tissues types and functions > axon organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions > cell types organs, tissues, organelles, cell types and functions > cell types and functions bioinformatics > computational biology organism description > animal > fish organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons > neuronal circuits organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions > cell types and functions > cell types > neurons organs, tissues, organelles, cell types and functions organs, tissues, organelles, cell types and functions > tissues types and functions organism description > animal > fish > zebrafish
CSHL Authors:	Matho, Katherine
Communities:	CSHL labs > Huang lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	5 July 2022
Date Deposited:	20 Jul 2022 03:43
Last Modified:	16 Jan 2024 21:15
PMCID:	PMC9286273
URI:	https://repository.cshl.edu/id/eprint/40677

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