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

TitleA Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy.
Publication TypeJournal Article
Year of Publication2021
AuthorsSanchez-Arias, JC, Carrier, M, Frederiksen, SD, Shevtsova, O, McKee, C, van der Slagt, E, de Andrade, EGonçalves, Nguyen, HLam, Young, PA, Tremblay, M-È, Swayne, LAnne
JournalFront Neuroanat
Volume15
Pagination722443
Date Published2021
ISSN1662-5129
Abstract

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.

DOI10.3389/fnana.2021.722443
Alternate JournalFront Neuroanat
PubMed ID34949993
PubMed Central IDPMC8691181