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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-12-01
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| Series: | Frontiers in Neuroanatomy |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnana.2021.722443/full |
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| author | Juan C. Sanchez-Arias Micaël Carrier Micaël Carrier Simona D. Frederiksen Olga Shevtsova Chloe McKee Emma van der Slagt Elisa Gonçalves de Andrade Hai Lam Nguyen Penelope A. Young Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Leigh Anne Swayne Leigh Anne Swayne Leigh Anne Swayne Leigh Anne Swayne |
| author_facet | Juan C. Sanchez-Arias Micaël Carrier Micaël Carrier Simona D. Frederiksen Olga Shevtsova Chloe McKee Emma van der Slagt Elisa Gonçalves de Andrade Hai Lam Nguyen Penelope A. Young Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Leigh Anne Swayne Leigh Anne Swayne Leigh Anne Swayne Leigh Anne Swayne |
| author_sort | Juan C. Sanchez-Arias |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T07:20:18Z |
| format | Article |
| id | doaj.art-4b094bc79d59432e86e9ad5035daf280 |
| institution | Directory Open Access Journal |
| issn | 1662-5129 |
| language | English |
| last_indexed | 2024-12-19T07:20:18Z |
| publishDate | 2021-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroanatomy |
| spelling | doaj.art-4b094bc79d59432e86e9ad5035daf2802022-12-21T20:30:57ZengFrontiers Media S.A.Frontiers in Neuroanatomy1662-51292021-12-011510.3389/fnana.2021.722443722443A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence MicroscopyJuan C. Sanchez-Arias0Micaël Carrier1Micaël Carrier2Simona D. Frederiksen3Olga Shevtsova4Chloe McKee5Emma van der Slagt6Elisa Gonçalves de Andrade7Hai Lam Nguyen8Penelope A. Young9Marie-Ève Tremblay10Marie-Ève Tremblay11Marie-Ève Tremblay12Marie-Ève Tremblay13Marie-Ève Tremblay14Marie-Ève Tremblay15Leigh Anne Swayne16Leigh Anne Swayne17Leigh Anne Swayne18Leigh Anne Swayne19Division of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaAxe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaAxe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, CanadaDepartment of Neurology and Neurosurgery, McGill University, Montréal, QC, CanadaDepartment of Molecular Medicine, Université de Laval, Québec City, QC, CanadaDepartment of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, CanadaDjavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, CanadaDivision of Medical Sciences, University of Victoria, Victoria, BC, CanadaDjavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, CanadaDepartment of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, CanadaDepartment of Neurology and Neurosurgery, Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, CanadaThe 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.https://www.frontiersin.org/articles/10.3389/fnana.2021.722443/fullopen sciencefluorescence microscopyimage analysismouse brainreproducibilityexperimental design |
| spellingShingle | Juan C. Sanchez-Arias Micaël Carrier Micaël Carrier Simona D. Frederiksen Olga Shevtsova Chloe McKee Emma van der Slagt Elisa Gonçalves de Andrade Hai Lam Nguyen Penelope A. Young Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Marie-Ève Tremblay Leigh Anne Swayne Leigh Anne Swayne Leigh Anne Swayne Leigh Anne Swayne A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy Frontiers in Neuroanatomy open science fluorescence microscopy image analysis mouse brain reproducibility experimental design |
| 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 | open science fluorescence microscopy image analysis mouse brain reproducibility experimental design |
| url | https://www.frontiersin.org/articles/10.3389/fnana.2021.722443/full |
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