JMG, Animals, Brain, Databases, Factual, Mice, X-Ray Microtomography
Sci Data 2022 May 25; 9(1):230
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 ).
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; and Hallgrímsson, Benedikt, "MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses." (2022). Faculty Research 2022. 75.