Scientific Data (May 2022)
MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
- Jay Devine,
- Marta Vidal-García,
- Wei Liu,
- Amanda Neves,
- Lucas D. Lo Vercio,
- Rebecca M. Green,
- Heather A. Richbourg,
- Marta Marchini,
- Colton M. Unger,
- Audrey C. Nickle,
- Bethany Radford,
- Nathan M. Young,
- Paula N. Gonzalez,
- Robert E. Schuler,
- Alejandro Bugacov,
- Campbell Rolian,
- Christopher J. Percival,
- Trevor Williams,
- Lee Niswander,
- Anne L. Calof,
- Arthur D. Lander,
- Axel Visel,
- Frank R. Jirik,
- James M. Cheverud,
- Ophir D. Klein,
- Ramon Y. Birnbaum,
- Amy E. Merrill,
- Rebecca R. Ackermann,
- Daniel Graf,
- Myriam Hemberger,
- Wendy Dean,
- Nils D. Forkert,
- Stephen A. Murray,
- Henrik Westerberg,
- Ralph S. Marcucio,
- Benedikt Hallgrímsson
Affiliations
- Jay Devine
- Alberta Children’s Hospital Research Institute, University of Calgary
- Marta Vidal-García
- Alberta Children’s Hospital Research Institute, University of Calgary
- Wei Liu
- Alberta Children’s Hospital Research Institute, University of Calgary
- Amanda Neves
- Department of Biology, McMaster University
- Lucas D. Lo Vercio
- Alberta Children’s Hospital Research Institute, University of Calgary
- Rebecca M. Green
- School of Dental Medicine, University of Pittsburgh
- Heather A. Richbourg
- Orthopaedic Trauma Institute, ZSFG, UCSF
- Marta Marchini
- Alberta Children’s Hospital Research Institute, University of Calgary
- Colton M. Unger
- The McCaig Institute for Bone and Joint Health, University of Calgary
- Audrey C. Nickle
- Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles
- Bethany Radford
- Alberta Children’s Hospital Research Institute, University of Calgary
- Nathan M. Young
- Orthopaedic Trauma Institute, ZSFG, UCSF
- Paula N. Gonzalez
- Institute for Studies in Neuroscience and Complex Systems (ENyS) CONICET
- Robert E. Schuler
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California
- Alejandro Bugacov
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California
- Campbell Rolian
- The McCaig Institute for Bone and Joint Health, University of Calgary
- Christopher J. Percival
- Department of Anthropology, Stony Brook University
- Trevor Williams
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus
- Lee Niswander
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder
- Anne L. Calof
- Department of Anatomy and Neurobiology, University of California, Irvine
- Arthur D. Lander
- Center for Complex Biological Systems, University of California, Irvine
- Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
- Frank R. Jirik
- Alberta Children’s Hospital Research Institute, University of Calgary
- James M. Cheverud
- Department of Biology, Loyola University Chicago
- Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco
- Ramon Y. Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev
- Amy E. Merrill
- Center for Craniofacial Molecular Biology, Department of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles
- Rebecca R. Ackermann
- Department of Archaeology, University of Cape Town, Rondebosch
- Daniel Graf
- School of Dentistry, Faculty of Medicine and Dentistry, University of Alberta
- Myriam Hemberger
- Alberta Children’s Hospital Research Institute, University of Calgary
- Wendy Dean
- Alberta Children’s Hospital Research Institute, University of Calgary
- Nils D. Forkert
- Alberta Children’s Hospital Research Institute, University of Calgary
- Stephen A. Murray
- The Jackson Laboratory
- Henrik Westerberg
- Department of Bioimaging Informatics, MRC Harwell Institute
- Ralph S. Marcucio
- Orthopaedic Trauma Institute, ZSFG, UCSF
- Benedikt Hallgrímsson
- Alberta Children’s Hospital Research Institute, University of Calgary
- DOI
- https://doi.org/10.1038/s41597-022-01338-x
- Journal volume & issue
-
Vol. 9,
no. 1
pp. 1 – 18
Abstract
Abstract 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 , https://doi.org/10.25550/3-HXMC ) and GitHub ( https://github.com/jaydevine/MusMorph ).
