MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses. Devine, J., Vidal-Garc\́ia, M., Liu, W., Neves, A., Vercio, L. D. L., Green, R. M., Richbourg, H. A., Marchini, M., Unger, C. M., Nickle, A. C., Radford, B., Young, N. M., Gonzalez, P. N., Schuler, R. E., Bugacov, A., Rolian, C., Percival, C. J., Williams, T., Niswander, L., Calof, A. L., Lander, A. D., Visel, A., Jirik, F. R., Cheverud, J. M., Klein, O., Birnbaum, R. Y., Merrill, A. E., Ackermann, R. R., Graf, D., Hemberger, M., Dean, W., Forkert, N. D., Murray, S. A., Westerberg, H., Marcucio, R. S., & Hallgr\́imsson, B. bioRxiv, Cold Spring Harbor Laboratory, 2021.
MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses [link]Paper  doi  abstract   bibtex   
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, doi.org/10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph).Competing Interest StatementThe authors have declared no competing interest.
@article{Devine2021a,
	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, doi.org/10.25550/3-HXMC) and GitHub (https://github.com/jaydevine/MusMorph).Competing Interest StatementThe authors have declared no competing interest.},
	author = {Devine, Jay and Vidal-Garc{\'\i}a, Marta and Liu, Wei and Neves, Amanda and Vercio, Lucas D. Lo and Green, Rebecca M. and Richbourg, Heather A. and Marchini, Marta and Unger, Colton M. and Nickle, Audrey C. and Radford, Bethany and Young, Nathan M. and Gonzalez, Paula N. and Schuler, Robert E. and Bugacov, Alejandro and Rolian, Campbell and Percival, Christopher J. and Williams, Trevor and Niswander, Lee and Calof, Anne L. and Lander, Arthur D. and Visel, Axel and Jirik, Frank R. and Cheverud, James M. and Klein, Ophir and Birnbaum, Ramon Y. and Merrill, Amy E. and Ackermann, Rebecca R. and Graf, Daniel and Hemberger, Myriam and Dean, Wendy and Forkert, Nils D. and Murray, Stephen A. and Westerberg, Henrik and Marcucio, Ralph S. and Hallgr{\'\i}msson, Benedikt},
	date-added = {2022-01-25 13:58:03 -0800},
	date-modified = {2022-01-25 13:58:03 -0800},
	doi = {10.1101/2021.11.11.468142},
	elocation-id = {2021.11.11.468142},
	eprint = {https://www.biorxiv.org/content/early/2021/11/12/2021.11.11.468142.full.pdf},
	journal = {bioRxiv},
	keywords = {preprint; dataset},
	publisher = {Cold Spring Harbor Laboratory},
	title = {MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses},
	url = {https://www.biorxiv.org/content/early/2021/11/12/2021.11.11.468142},
	year = {2021},
	bdsk-url-1 = {https://www.biorxiv.org/content/early/2021/11/12/2021.11.11.468142},
	bdsk-url-2 = {https://doi.org/10.1101/2021.11.11.468142}}

Downloads: 0