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MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unf...

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Autores principales: Devine, Jay, Vidal-García, Marta, Liu, Wei, Neves, Amanda, Lo Vercio, Lucas D., Green, Rebecca M., Richbourg, Heather A., Marchini, Marta, Unger, Colton M., Nickle, Audrey C., Radford, Bethany, Young, Nathan M., Gonzalez, Paula N., Schuler, Robert E., Bugacov, Alejandro, Rolian, Campbell, Percival, Christopher J., Williams, Trevor, Niswander, Lee, Calof, Anne L., Lander, Arthur D., Visel, Axel, Jirik, Frank R., Cheverud, James M., Klein, Ophir D., Birnbaum, Ramon Y., Merrill, Amy E., Ackermann, Rebecca R., Graf, Daniel, Hemberger, Myriam, Dean, Wendy, Forkert, Nils D., Murray, Stephen A., Westerberg, Henrik, Marcucio, Ralph S., Hallgrímsson, Benedikt
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9133120/
https://www.ncbi.nlm.nih.gov/pubmed/35614082
http://dx.doi.org/10.1038/s41597-022-01338-x
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author Devine, Jay
Vidal-García, Marta
Liu, Wei
Neves, Amanda
Lo Vercio, Lucas D.
Green, Rebecca M.
Richbourg, Heather A.
Marchini, Marta
Unger, Colton M.
Nickle, Audrey C.
Radford, Bethany
Young, Nathan M.
Gonzalez, Paula N.
Schuler, Robert E.
Bugacov, Alejandro
Rolian, Campbell
Percival, Christopher J.
Williams, Trevor
Niswander, Lee
Calof, Anne L.
Lander, Arthur D.
Visel, Axel
Jirik, Frank R.
Cheverud, James M.
Klein, Ophir D.
Birnbaum, Ramon Y.
Merrill, Amy E.
Ackermann, Rebecca R.
Graf, Daniel
Hemberger, Myriam
Dean, Wendy
Forkert, Nils D.
Murray, Stephen A.
Westerberg, Henrik
Marcucio, Ralph S.
Hallgrímsson, Benedikt
author_facet Devine, Jay
Vidal-García, Marta
Liu, Wei
Neves, Amanda
Lo Vercio, Lucas D.
Green, Rebecca M.
Richbourg, Heather A.
Marchini, Marta
Unger, Colton M.
Nickle, Audrey C.
Radford, Bethany
Young, Nathan M.
Gonzalez, Paula N.
Schuler, Robert E.
Bugacov, Alejandro
Rolian, Campbell
Percival, Christopher J.
Williams, Trevor
Niswander, Lee
Calof, Anne L.
Lander, Arthur D.
Visel, Axel
Jirik, Frank R.
Cheverud, James M.
Klein, Ophir D.
Birnbaum, Ramon Y.
Merrill, Amy E.
Ackermann, Rebecca R.
Graf, Daniel
Hemberger, Myriam
Dean, Wendy
Forkert, Nils D.
Murray, Stephen A.
Westerberg, Henrik
Marcucio, Ralph S.
Hallgrímsson, Benedikt
author_sort Devine, Jay
collection PubMed
description Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase (www.facebase.org, 10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph).
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spelling pubmed-91331202022-05-27 MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses Devine, Jay Vidal-García, Marta Liu, Wei Neves, Amanda Lo Vercio, Lucas D. Green, Rebecca M. Richbourg, Heather A. Marchini, Marta Unger, Colton M. Nickle, Audrey C. Radford, Bethany Young, Nathan M. Gonzalez, Paula N. Schuler, Robert E. Bugacov, Alejandro Rolian, Campbell Percival, Christopher J. Williams, Trevor Niswander, Lee Calof, Anne L. Lander, Arthur D. Visel, Axel Jirik, Frank R. Cheverud, James M. Klein, Ophir D. Birnbaum, Ramon Y. Merrill, Amy E. Ackermann, Rebecca R. Graf, Daniel Hemberger, Myriam Dean, Wendy Forkert, Nils D. Murray, Stephen A. Westerberg, Henrik Marcucio, Ralph S. Hallgrímsson, Benedikt Sci Data Data Descriptor Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection. The MusMorph data and scripts are available on FaceBase (www.facebase.org, 10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph). Nature Publishing Group UK 2022-05-25 /pmc/articles/PMC9133120/ /pubmed/35614082 http://dx.doi.org/10.1038/s41597-022-01338-x Text en © The Author(s) 2022, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Data Descriptor
Devine, Jay
Vidal-García, Marta
Liu, Wei
Neves, Amanda
Lo Vercio, Lucas D.
Green, Rebecca M.
Richbourg, Heather A.
Marchini, Marta
Unger, Colton M.
Nickle, Audrey C.
Radford, Bethany
Young, Nathan M.
Gonzalez, Paula N.
Schuler, Robert E.
Bugacov, Alejandro
Rolian, Campbell
Percival, Christopher J.
Williams, Trevor
Niswander, Lee
Calof, Anne L.
Lander, Arthur D.
Visel, Axel
Jirik, Frank R.
Cheverud, James M.
Klein, Ophir D.
Birnbaum, Ramon Y.
Merrill, Amy E.
Ackermann, Rebecca R.
Graf, Daniel
Hemberger, Myriam
Dean, Wendy
Forkert, Nils D.
Murray, Stephen A.
Westerberg, Henrik
Marcucio, Ralph S.
Hallgrímsson, Benedikt
MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
title MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
title_full MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
title_fullStr MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
title_full_unstemmed MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
title_short MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
title_sort musmorph, a database of standardized mouse morphology data for morphometric meta-analyses
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9133120/
https://www.ncbi.nlm.nih.gov/pubmed/35614082
http://dx.doi.org/10.1038/s41597-022-01338-x
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