A systematic, open-science framework for quantification of cell-types in mouse brain sections using fluorescence microscopy

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dc.contributor.authorSanchez-Arias, Juan C.
dc.contributor.authorCarrier, Micaël
dc.contributor.authorFrederiksen, Simona D.
dc.contributor.authorShevtsova, Olga
dc.contributor.authorMcKee, Chloe
dc.contributor.authorvan der Slagt, Emma
dc.contributor.authorGonçalves de Andrade, Elisa
dc.contributor.authorNguyen, Hai Lam
dc.contributor.authorYoung, Penelope A.
dc.contributor.authorTremblay, Marie-Ève
dc.contributor.authorSwayne, Leigh Anne
dc.date.accessioned2024-03-20T16:00:05Z
dc.date.available2024-03-20T16:00:05Z
dc.date.issued2021
dc.descriptionWe 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.
dc.description.abstractThe 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.
dc.description.reviewstatusReviewed
dc.description.scholarlevelFaculty
dc.description.sponsorshipResearch in the Swayne lab has recently been supported by grants from the Canadian Institutes of Health Research (CIHR; MOP-142215; GA4-177766, and PJT-169064) and from the Natural Sciences and Engineering Research Council (NSERC; RGPIN-2017-03889) awarded to LAS. JCS-A is supported by a MSFHR Research Trainee Award (RT-2021-1735). EvdS is supported by a University of Victoria Fellowship Graduate Award. MC is supported by a doctoral training award from the Fond de Recherche du Québec, Santé (FRQS). CM is supported by a University of Victoria Faculty of Science Undergraduate Research Award (SURA) and a Jamie Cassels Undergraduate Research Award (JCURA). EGA is supported by a University of Victoria Graduate Entrance Award. PY was supported by the NSERC CGS-M. M-ÈT is supported by the Tier 2 Canada Research Chair in Neurobiology of Aging and Cognition. The Leica TCS SP8 microscope system was purchased using grants from the Canada Foundation for Innovation (29462) and the BC Knowledge Development Fund (804754) awarded to LAS.
dc.identifier.citationSanchez-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
dc.identifier.urihttps://doi.org/10.3389/fnana.2021.722443
dc.identifier.urihttps://hdl.handle.net/1828/16234
dc.language.isoen
dc.publisherFrontiers in Neuroanatomy
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectopen science
dc.subjectfluorescence microscopy
dc.subjectimage analysis
dc.subjectmouse brain
dc.subjectreproducibility
dc.subjectexperimental design
dc.subjectneuroscience
dc.subject.departmentDivision of Medical Sciences
dc.subject.departmentSchool of Medical Sciences
dc.titleA systematic, open-science framework for quantification of cell-types in mouse brain sections using fluorescence microscopy
dc.typeArticle

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We acknowledge and respect the Lək̓ʷəŋən (Songhees and Esquimalt) Peoples on whose territory the university stands, and the Lək̓ʷəŋən and W̱SÁNEĆ Peoples whose historical relationships with the land continue to this day.