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A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting

Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient...

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Autores principales: Kleven, Heidi, Reiten, Ingrid, Blixhavn, Camilla H., Schlegel, Ulrike, Øvsthus, Martin, Papp, Eszter A., Puchades, Maja A., Bjaalie, Jan G., Leergaard, Trygve B., Bjerke, Ingvild E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10033636/
https://www.ncbi.nlm.nih.gov/pubmed/36970659
http://dx.doi.org/10.3389/fninf.2023.1154080
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author Kleven, Heidi
Reiten, Ingrid
Blixhavn, Camilla H.
Schlegel, Ulrike
Øvsthus, Martin
Papp, Eszter A.
Puchades, Maja A.
Bjaalie, Jan G.
Leergaard, Trygve B.
Bjerke, Ingvild E.
author_facet Kleven, Heidi
Reiten, Ingrid
Blixhavn, Camilla H.
Schlegel, Ulrike
Øvsthus, Martin
Papp, Eszter A.
Puchades, Maja A.
Bjaalie, Jan G.
Leergaard, Trygve B.
Bjerke, Ingvild E.
author_sort Kleven, Heidi
collection PubMed
description Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient atlas-based data analyses. Comparing findings reported using different atlases is also not trivial, and represents a barrier to reproducible science. With this perspective article, we provide a guide to how mouse and rat brain atlases can be used for analyzing and reporting data in accordance with the FAIR principles that advocate for data to be findable, accessible, interoperable, and re-usable. We first introduce how atlases can be interpreted and used for navigating to brain locations, before discussing how they can be used for different analytic purposes, including spatial registration and data visualization. We provide guidance on how neuroscientists can compare data mapped to different atlases and ensure transparent reporting of findings. Finally, we summarize key considerations when choosing an atlas and give an outlook on the relevance of increased uptake of atlas-based tools and workflows for FAIR data sharing.
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spelling pubmed-100336362023-03-24 A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting Kleven, Heidi Reiten, Ingrid Blixhavn, Camilla H. Schlegel, Ulrike Øvsthus, Martin Papp, Eszter A. Puchades, Maja A. Bjaalie, Jan G. Leergaard, Trygve B. Bjerke, Ingvild E. Front Neuroinform Neuroscience Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient atlas-based data analyses. Comparing findings reported using different atlases is also not trivial, and represents a barrier to reproducible science. With this perspective article, we provide a guide to how mouse and rat brain atlases can be used for analyzing and reporting data in accordance with the FAIR principles that advocate for data to be findable, accessible, interoperable, and re-usable. We first introduce how atlases can be interpreted and used for navigating to brain locations, before discussing how they can be used for different analytic purposes, including spatial registration and data visualization. We provide guidance on how neuroscientists can compare data mapped to different atlases and ensure transparent reporting of findings. Finally, we summarize key considerations when choosing an atlas and give an outlook on the relevance of increased uptake of atlas-based tools and workflows for FAIR data sharing. Frontiers Media S.A. 2023-03-09 /pmc/articles/PMC10033636/ /pubmed/36970659 http://dx.doi.org/10.3389/fninf.2023.1154080 Text en Copyright © 2023 Kleven, Reiten, Blixhavn, Schlegel, Øvsthus, Papp, Puchades, Bjaalie, Leergaard and Bjerke. 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 Neuroscience
Kleven, Heidi
Reiten, Ingrid
Blixhavn, Camilla H.
Schlegel, Ulrike
Øvsthus, Martin
Papp, Eszter A.
Puchades, Maja A.
Bjaalie, Jan G.
Leergaard, Trygve B.
Bjerke, Ingvild E.
A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
title A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
title_full A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
title_fullStr A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
title_full_unstemmed A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
title_short A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
title_sort neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting
topic Neuroscience
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10033636/
https://www.ncbi.nlm.nih.gov/pubmed/36970659
http://dx.doi.org/10.3389/fninf.2023.1154080
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