SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology

Rolfe, Sara; Pieper, Steve; Porto, Arthur; Diamond, Kelly; Winchester, Julie; Shan, Shan; Kirveslahti, Henry; Boyer, Doug M; Summers, Adam P.; Maga, A. Murat

doi:10.1111/2041-210x.13669

Cited by 91 publications

(66 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To place pseudo-landmark points (pLMs) on each of our specimens, we first created 3D models of from our CT volumes using the Segment Editor module of 3D Slicer ( Fedorov et al, 2012 ). To generate a set of pLMs on our atlas model, we used the PseudoLMGenerator module in the SlicerMorph extension of 3D Slicer which uses the original mesh geometry and a sagittal plane as the axis of symmetry, to generate a dense symmetric set of surface points ( Rolfe et al, 2021 ). One author (K.M.D.)…”

Section: Methodsmentioning

confidence: 99%

“…One author (K.M.D.) then went through the pLMs and removed points that were on both jaws and the pectoral girdle using the MarkupEditor tool in 3D Slicer ( Rolfe et al, 2021 ; Fig. 5 ).…”

Section: Methodsmentioning

confidence: 99%

“…We also ran separate principal components analyses on both the symmetric and asymmetric components of variation from the symmetry analysis using the geomorph ( Adams and Otárola-Castillo, 2013 ). Visualizations were created in the SlicerMorph extension of 3D Slicer ( Rolfe et al, 2021 ) and using ggplot in R ( Wickham, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

et al. 2022

Self Cite

View full text Add to dashboard Cite

Due to the complexity of fish skulls, previous attempts to classify craniofacial phenotypes have relied on qualitative features or sparce 2D landmarks. In this work we aim to identify previously unknown 3D craniofacial phenotypes with a semiautomated pipeline in adult zebrafish mutants. We first estimate a synthetic ‘normative’ zebrafish template using microCT scans from a sample pool of wildtype animals using the Advanced Normalization Tools (ANTs). We apply a computational anatomy (CA) approach to quantify the phenotype of zebrafish with disruptions in bmp1a, a gene implicated in later skeletal development and whose human ortholog when disrupted is associated with Osteogenesis Imperfecta. Compared to controls, the bmp1a fish have larger otoliths, larger normalized centroid sizes, and exhibit shape differences concentrated around the operculum, anterior frontal, and posterior parietal bones. Moreover, bmp1a fish differ in the degree of asymmetry. Our CA approach offers a potential pipeline for high-throughput screening of complex fish craniofacial shape to discover novel phenotypes for which traditional landmarks are too sparce to detect. The current pipeline successfully identifies areas of variation in zebrafish mutants, which are an important model system for testing genome to phenome relationships in the study of development, evolution, and human diseases.

show abstract

Section: Methodsmentioning

confidence: 99%

“…One author (K.M.D.) then went through the pLMs and removed points that were on both jaws and the pectoral girdle using the MarkupEditor tool in 3D Slicer ( Rolfe et al, 2021 ; Fig. 5 ).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…Scans were reconstructed using NRecon software with the following settings: misalignment between −2 and +2, dynamic range mode, min 0.01, max 0.2. Reconstructed slices were imported and visualized using the SlicerMorph extension ( Rolfe et al 2021 ) of the 3D Slicer biomedical visualization program.…”

Section: Methodsmentioning

confidence: 99%

The arginine methyltransferase Carm1 is necessary for heart development

Jamet

et al. 2022

G3 Genes|Genomes|Genetics

Self Cite

View full text Add to dashboard Cite

To discover genes implicated in human congenital disorders, we performed ENU mutagenesis in the mouse and screened for mutations affecting embryonic development. In this work we report defects of heart development in mice homozygous for a mutation of Coactivator-associated Arginine Methyltransferase 1 (Carm1). While Carm1 has been extensively studied, it has never been previously associated with a role in heart development. Phenotype analysis combining histology and micro-computed tomography (micro-CT) imaging shows a range of cardiac defects. Most notably, many affected mid-gestation embryos appear to have cardiac rupture and hemorrhaging in the thorax. Mice that survive to late gestation show a variety of cardiac defects, including Ventricular Septal Defects (VSDs), Double Outlet Right Ventricle (DORV), and Persistent Truncus Arteriosus (PTA). Transcriptome analyses of the mutant embryos by mRNA-seq reveal the perturbation of several genes involved in cardiac morphogenesis and muscle development and function. In addition, we observe the mis-localization of cardiac neural crest cells at E12.5 in the outflow tract. The cardiac phenotype of Carm1 mutant embryos is similar to that of Pax3 null mutants, and PAX3 is a putative target of CARM1. However, our analysis does not support the hypothesis that developmental defects in Carm1 mutant embryos are primarily due to a functional defect of PAX3.

show abstract

“…For µCT scanned specimens, the resulting isolated specimen image stacks were viewed and manipulated for lighting and opacity using CTvox v3.0 (Bruker) or the SlicerMorph module ( Rolfe et al, 2021 ) in 3D Slicer v4.13.0 ( Fedorov et al, 2012 ). Hard tissues were coded and imaged using the tools in CTvox, with custom transfer functions, or in 3D Slicer by modifying the region of interest (ROI) box in the “volume rendering” module.…”

Section: Methodsmentioning

confidence: 99%

Phylogenetics of Archerfishes (Toxotidae) and Evolution of the Toxotid Shooting Apparatus

Girard

Davis

Tan

et al. 2022

Integrative Organismal Biology

View full text Add to dashboard Cite

Archerfishes (Toxotidae) are variously found in the fresh- and brackish-water environments of Asia Pacific and are well known for their ability to shoot water at terrestrial prey. These shots of water are intended to strike their prey and cause it to fall into the water for capture and consumption. While this behavior is well known, there are competing hypotheses (blowpipe vs. pressure tank hypothesis) of how archerfishes shoot and which oral structures are involved. Current understanding of archerfish shooting structures is largely based on two species, Toxotes chatareus and T. jaculatrix. We do not know if all archerfishes possess the same oral structures to shoot water, if anatomical variation is present within these oral structures, or how these features have evolved. Additionally, there is little information on the evolution of the Toxotidae as a whole, with all previous systematic works focusing on the interrelationships of the family. We first investigate the limits of archerfish species using new and previously published genetic data. Our analyses highlight that the current taxonomy of archerfishes does not conform to the relationships we recover. Toxotes mekongensis and T. siamensis are placed in synonymy of T. chatareus, Toxotes carpentariensis is recognized as a species and removed from synonymy of T. chatareus, and the genus Protoxotes is recognized for T. lorentzi based on the results of our analyses. We then take an integrative approach, using a combined analysis of discrete hard- and soft-tissue morphological characters with genetic data, to construct a phylogeny of the Toxotidae. Using the resulting phylogenetic hypothesis, we then characterize the evolutionary history and anatomical variation within the archerfishes. We discuss the variation in the oral structures and the evolution of the mechanism with respect to the interrelationships of archerfishes, and find that the oral structures of archerfishes support the blowpipe hypothesis but soft-tissue oral structures may also play a role in shooting. Finally, by comparing the morphology of archerfishes to their sister group, we find that the Leptobramidae has relevant shooting features in the oral cavity, suggesting that some components of the archerfish shooting mechanism are examples of co-opted or exapted traits.

show abstract

SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution-NonCo mmercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 91 publications

References 63 publications

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

Computational anatomy and geometric shape analysis enables analysis of complex craniofacial phenotypes in zebrafish

The arginine methyltransferase Carm1 is necessary for heart development

Phylogenetics of Archerfishes (Toxotidae) and Evolution of the Toxotid Shooting Apparatus

Contact Info

Product

Resources

About