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Benchmarking of tools for axon length measurement in individually-labeled projection neurons
Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8824366/ https://www.ncbi.nlm.nih.gov/pubmed/34879058 http://dx.doi.org/10.1371/journal.pcbi.1009051 |
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author | Rubio-Teves, Mario Díez-Hermano, Sergio Porrero, César Sánchez-Jiménez, Abel Prensa, Lucía Clascá, Francisco García-Amado, María Villacorta-Atienza, José Antonio |
author_facet | Rubio-Teves, Mario Díez-Hermano, Sergio Porrero, César Sánchez-Jiménez, Abel Prensa, Lucía Clascá, Francisco García-Amado, María Villacorta-Atienza, José Antonio |
author_sort | Rubio-Teves, Mario |
collection | PubMed |
description | Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple brain regions. Axon length is a principal estimate of the functional impact of the neuron, as it directly correlates with the number of synapses formed by the axon in its target regions; however, its measurement by direct 3D axonal tracing is a slow and labor-intensive method. On the contrary, axon length estimations have been recently proposed as an effective and accessible alternative, allowing a fast approach to the functional significance of the single neuron. Here, we analyze the accuracy and efficiency of the most used length estimation tools—design-based stereology by virtual planes or spheres, and mathematical correction of the 2D projected-axon length—in contrast with direct measurement, to quantify individual axon length. To this end, we computationally simulated each tool, applied them over a dataset of 951 3D-reconstructed axons (from NeuroMorpho.org), and compared the generated length values with their 3D reconstruction counterparts. The evaluated reliability of each axon length estimation method was then balanced with the required human effort, experience and know-how, and economic affordability. Subsequently, computational results were contrasted with measurements performed on actual brain tissue sections. We show that the plane-based stereological method balances acceptable errors (~5%) with robustness to biases, whereas the projection-based method, despite its accuracy, is prone to inherent biases when implemented in the laboratory. This work, therefore, aims to provide a constructive benchmark to help guide the selection of the most efficient method for measuring specific axonal morphologies according to the particular circumstances of the conducted research. |
format | Online Article Text |
id | pubmed-8824366 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-88243662022-02-09 Benchmarking of tools for axon length measurement in individually-labeled projection neurons Rubio-Teves, Mario Díez-Hermano, Sergio Porrero, César Sánchez-Jiménez, Abel Prensa, Lucía Clascá, Francisco García-Amado, María Villacorta-Atienza, José Antonio PLoS Comput Biol Research Article Projection neurons are the commonest neuronal type in the mammalian forebrain and their individual characterization is a crucial step to understand how neural circuitry operates. These cells have an axon whose arborizations extend over long distances, branching in complex patterns and/or in multiple brain regions. Axon length is a principal estimate of the functional impact of the neuron, as it directly correlates with the number of synapses formed by the axon in its target regions; however, its measurement by direct 3D axonal tracing is a slow and labor-intensive method. On the contrary, axon length estimations have been recently proposed as an effective and accessible alternative, allowing a fast approach to the functional significance of the single neuron. Here, we analyze the accuracy and efficiency of the most used length estimation tools—design-based stereology by virtual planes or spheres, and mathematical correction of the 2D projected-axon length—in contrast with direct measurement, to quantify individual axon length. To this end, we computationally simulated each tool, applied them over a dataset of 951 3D-reconstructed axons (from NeuroMorpho.org), and compared the generated length values with their 3D reconstruction counterparts. The evaluated reliability of each axon length estimation method was then balanced with the required human effort, experience and know-how, and economic affordability. Subsequently, computational results were contrasted with measurements performed on actual brain tissue sections. We show that the plane-based stereological method balances acceptable errors (~5%) with robustness to biases, whereas the projection-based method, despite its accuracy, is prone to inherent biases when implemented in the laboratory. This work, therefore, aims to provide a constructive benchmark to help guide the selection of the most efficient method for measuring specific axonal morphologies according to the particular circumstances of the conducted research. Public Library of Science 2021-12-08 /pmc/articles/PMC8824366/ /pubmed/34879058 http://dx.doi.org/10.1371/journal.pcbi.1009051 Text en © 2021 Rubio-Teves et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Rubio-Teves, Mario Díez-Hermano, Sergio Porrero, César Sánchez-Jiménez, Abel Prensa, Lucía Clascá, Francisco García-Amado, María Villacorta-Atienza, José Antonio Benchmarking of tools for axon length measurement in individually-labeled projection neurons |
title | Benchmarking of tools for axon length measurement in individually-labeled projection neurons |
title_full | Benchmarking of tools for axon length measurement in individually-labeled projection neurons |
title_fullStr | Benchmarking of tools for axon length measurement in individually-labeled projection neurons |
title_full_unstemmed | Benchmarking of tools for axon length measurement in individually-labeled projection neurons |
title_short | Benchmarking of tools for axon length measurement in individually-labeled projection neurons |
title_sort | benchmarking of tools for axon length measurement in individually-labeled projection neurons |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8824366/ https://www.ncbi.nlm.nih.gov/pubmed/34879058 http://dx.doi.org/10.1371/journal.pcbi.1009051 |
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