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A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy

The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to b...

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Autores principales: Sanchez-Arias, Juan C., Carrier, Micaël, Frederiksen, Simona D., Shevtsova, Olga, McKee, Chloe, van der Slagt, Emma, Gonçalves de Andrade, Elisa, Nguyen, Hai Lam, Young, Penelope A., Tremblay, Marie-Ève, Swayne, Leigh Anne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8691181/
https://www.ncbi.nlm.nih.gov/pubmed/34949993
http://dx.doi.org/10.3389/fnana.2021.722443
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author Sanchez-Arias, Juan C.
Carrier, Micaël
Frederiksen, Simona D.
Shevtsova, Olga
McKee, Chloe
van der Slagt, Emma
Gonçalves de Andrade, Elisa
Nguyen, Hai Lam
Young, Penelope A.
Tremblay, Marie-Ève
Swayne, Leigh Anne
author_facet Sanchez-Arias, Juan C.
Carrier, Micaël
Frederiksen, Simona D.
Shevtsova, Olga
McKee, Chloe
van der Slagt, Emma
Gonçalves de Andrade, Elisa
Nguyen, Hai Lam
Young, Penelope A.
Tremblay, Marie-Ève
Swayne, Leigh Anne
author_sort Sanchez-Arias, Juan C.
collection PubMed
description The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.
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spelling pubmed-86911812021-12-22 A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy Sanchez-Arias, Juan C. Carrier, Micaël Frederiksen, Simona D. Shevtsova, Olga McKee, Chloe van der Slagt, Emma Gonçalves de Andrade, Elisa Nguyen, Hai Lam Young, Penelope A. Tremblay, Marie-Ève Swayne, Leigh Anne Front Neuroanat Neuroanatomy The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research. Frontiers Media S.A. 2021-12-06 /pmc/articles/PMC8691181/ /pubmed/34949993 http://dx.doi.org/10.3389/fnana.2021.722443 Text en Copyright © 2021 Sanchez-Arias, Carrier, Frederiksen, Shevtsova, McKee, van der Slagt, Gonçalves de Andrade, Nguyen, Young, Tremblay and Swayne. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Neuroanatomy
Sanchez-Arias, Juan C.
Carrier, Micaël
Frederiksen, Simona D.
Shevtsova, Olga
McKee, Chloe
van der Slagt, Emma
Gonçalves de Andrade, Elisa
Nguyen, Hai Lam
Young, Penelope A.
Tremblay, Marie-Ève
Swayne, Leigh Anne
A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy
title A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy
title_full A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy
title_fullStr A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy
title_full_unstemmed A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy
title_short A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy
title_sort systematic, open-science framework for quantification of cell-types in mouse brain sections using fluorescence microscopy
topic Neuroanatomy
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8691181/
https://www.ncbi.nlm.nih.gov/pubmed/34949993
http://dx.doi.org/10.3389/fnana.2021.722443
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