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

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Frontiers in 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.


We would like to thank the University of Victoria Animal Care Committee and Animal Technician team, as well as Dr. Taimei Yang (Animal Research Technician for the Division of Medical Sciences the University of Victoria) for their support in taking care of the animals involved in this study. We acknowledge and respect the lək̓ʷəŋən peoples on whose traditional territory the university stands and the Songhees, Esquimalt and W̱SÁNEĆ peoples whose historical relationships with the land continue to this day.


open science, fluorescence microscopy, image analysis, mouse brain, reproducibility, experimental design, neuroscience


Sanchez-Arias, J. C., Carrier, M., Frederiksen, S. D., Shevtsova, O., McKee, C., van der Slagt, E., ... Swayne, L. A. (2021). A systematic, open-science framework for quantification of cell-types in mouse brain sections using fluorescence microscopy. Frontiers in Neuroanatomy, 15, 722443. https://doi.org/10.3389/fnana.2021.722443