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

PLoS Comput Biol. 2022 Jul 5;18(7):e1010211. doi: 10.1371/journal.pcbi.1010211. eCollection 2022 Jul.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Axons / physiology
  • Neurites
  • Neurons* / physiology
  • Zebrafish*

Grants and funding

EB received funding from Agence Nationale de la Recherche (https://anr.fr/) under contract ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging JL received funding from Fondation pour la Recherche Médicale (https://www.frm.org/) (DBI20141231328) and Agence Nationale de la Recherche (https://anr.fr/) under contracts LabEx LIFESENSES (ANR-10-LABX-65) and IHU FOReSIGHT (ANR-18-IAHU-01) EB and JL received funding from European Research Council (Horizon 2020 programme, grant No 951330 HOPE) The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.