MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses
Open Access
- 25 May 2022
- journal article
- research article
- Published by Springer Nature in Scientific Data
- Vol. 9 (1) , 1-18
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).Keywords
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Funding Information
- Gouvernement du Canada | Canadian Institutes of Health Research (159920, 159920, 159920, 159920, 159920, 159920, 159920, 159920)
- U.S. Department of Health & Human Services | National Institutes of Health (2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638, U01DE028729, U01DE028729, 2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638, 2R01DE019638)
- UCalgary | Alberta Children's Hospital Research Institute
- Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (238992-17, 238992-17, 238992-17, 238992-17, 238992-17, 238992-17, 238992-17, 238992-17)
- U.S. Department of Health & Human Services | National Institutes of Health
- Alberta Innovates | Alberta Innovates - Health Solutions
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
- U.S. Department of Health & Human Services | National Institutes of Health
This publication has 96 references indexed in Scilit:
- ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenicsNucleic Acids Research, 2012
- Evolution of pleiotropy: epistatic interaction pattern supports a mechanistic model underlying variation in genotype–phenotype mapJournal of Experimental Zoology Part B: Molecular and Developmental Evolution, 2011
- A reproducible evaluation of ANTs similarity metric performance in brain image registrationNeuroImage, 2011
- False positives in neuroimaging genetics using voxel-based morphometry dataNeuroImage, 2011
- Unbiased average age-appropriate atlases for pediatric studiesNeuroImage, 2011
- Quantitative analyses link modulation of sonic hedgehog signaling to continuous variation in facial growth and shapeDevelopment, 2010
- A microarray analysis of sexual dimorphism of adipose tissues in high-fat-diet-induced obese miceInternational Journal of Obesity, 2010
- Deciphering the Palimpsest: Studying the Relationship Between Morphological Integration and Phenotypic CovariationEvolutionary Biology, 2009
- Spatial packing, cranial base angulation, and craniofacial shape variation in the mammalian skull: testing a new model using miceJournal of Anatomy, 2008
- BeetleBase: the model organism database for Tribolium castaneumNucleic Acids Research, 2006