3D MRI heart segmentation of mouse embryos

Three-dimensional microCT imaging of mouse heart development from early post-implantation to late fetal stages

Comprehensive detailed characterization of new mouse models can be challenging due to the individual focus involved in developing these models. Often models are engineered to test a specific hypothesis in a limited number of tissues, stages, and/or other contexts. Whether or not the model produces the desired phenotypes, phenotyping beyond the desired context can be extremely work intensive and these studies are often not undertaken. However, the general information resulting from broader phenotyping can be invaluable to the wider scientific community. The International Mouse Phenotyping Consortium (IMPC) and its subsidiaries, like the Knockout Mouse Project (KOMP), has made great strides in streamlining this process. In particular, the use of microCT has been an invaluable resource in examining internal organ systems throughout fetal/developmental stages. Here, we provide several novel vignettes demonstrating the utility of microCT in uncovering cardiac phenotypes both based on human disease correlations and those that are unpredicted.

A step-wise approach for analysis of the mouse embryonic heart using 17.6Tesla MRI

BACKGROUND

The mouse embryo is ideal for studying human cardiac development. However, laboratory discoveries do not easily translate into clinical findings partially because of histological diagnostic techniques that induce artifacts and lack standardization.

AIM

To present a step-wise approach using 17.6T MRI, for evaluation of mice embryonic heart and accurate identification of congenital heart defects.

SUBJECTS

17.5-embryonic days embryos from low-risk (non-diabetic) and high-risk (diabetic) model dams.

STUDY DESIGN

Embryos were imaged using 17.6Tesla MRI. Three-dimensional volumes were analyzed using ImageJ software.

OUTCOME MEASURES

Embryonic hearts were evaluated utilizing anatomic landmarks to locate the four-chamber view, the left- and right-outflow tracts, and the arrangement of the great arteries. Inter- and intra-observer agreement were calculated using kappa scores by comparing two researchers' evaluations independently analyzing all hearts, blinded to the model, on three different, timed occasions. Each evaluated 16 imaging volumes of 16 embryos: 4 embryos from normal dams, and 12 embryos from diabetic dams.

RESULTS

Inter-observer agreement and reproducibility were 0.779 (95% CI 0.653-0.905) and 0.763 (95% CI 0.605-0.921), respectively. Embryonic hearts were structurally normal in 4/4 and 7/12 embryos from normal and diabetic dams, respectively. Five embryos from diabetic dams had defects: ventricular septal defects (n=2), transposition of great arteries (n=2) and Tetralogy of Fallot (n=1). Both researchers identified all cardiac lesions.

CONCLUSION

A step-wise approach for analysis of MRI-derived 3D imaging provides reproducible detailed cardiac evaluation of normal and abnormal mice embryonic hearts. This approach can accurately reveal cardiac structure and, thus, increases the yield of animal model in congenital heart defect research.

Automatic classification framework for ventricular septal defects: a pilot study on high-throughput mouse embryo cardiac phenotyping

Intensive international efforts are underway toward phenotyping the entire mouse genome by modifying all its [Formula: see text] genes one-by-one for comparative studies. A workload of this scale has triggered numerous studies harnessing image informatics for the identification of morphological defects. However, existing work in this line primarily rests on abnormality detection via structural volumetrics between wild-type and gene-modified mice, which generally fails when the pathology involves no severe volume changes, such as ventricular septal defects (VSDs) in the heart. Furthermore, in embryo cardiac phenotyping, the lack of relevant work in embryonic heart segmentation, the limited availability of public atlases, and the general requirement of manual labor for the actual phenotype classification after abnormality detection, along with other limitations, have collectively restricted existing practices from meeting the high-throughput demands. This study proposes, to the best of our knowledge, the first fully automatic VSD classification framework in mouse embryo imaging. Our approach leverages a combination of atlas-based segmentation and snake evolution techniques to derive the segmentation of heart ventricles, where VSD classification is achieved by checking whether the left and right ventricles border or overlap with each other. A pilot study has validated our approach at a proof-of-concept level and achieved a classification accuracy of 100% through a series of empirical experiments on a database of 15 images.

Using optical coherence tomography to rapidly phenotype and quantify congenital heart defects associated with prenatal alcohol exposure

BACKGROUND

The most commonly used method to analyze congenital heart defects involves serial sectioning and histology. However, this is often a time-consuming process where the quantification of cardiac defects can be difficult due to problems with accurate section registration. Here we demonstrate the advantages of using optical coherence tomography, a comparatively new and rising technology, to phenotype avian embryo hearts in a model of fetal alcohol syndrome where a binge-like quantity of alcohol/ethanol was introduced at gastrulation.

RESULTS

The rapid, consistent imaging protocols allowed for the immediate identification of cardiac anomalies, including ventricular septal defects and misaligned/missing vessels. Interventricular septum thicknesses and vessel diameters for three of the five outflow arteries were also significantly reduced. Outflow and atrioventricular valves were segmented using image processing software and had significantly reduced volumes compared to controls. This is the first study to our knowledge that has 3D reconstructed the late-stage cardiac valves in precise detail to examine their morphology and dimensions.

CONCLUSIONS

We believe, therefore, that optical coherence tomography, with its ability to rapidly image and quantify tiny embryonic structures in high resolution, will serve as an excellent and cost-effective preliminary screening tool for developmental biologists working with a variety of experimental/disease models.

Imaging techniques for visualizing and phenotyping congenital heart defects in murine models

Mouse model is ideal for investigating the genetic and developmental etiology of congenital heart disease. However, cardiovascular phenotyping for the precise diagnosis of structural heart defects in mice remain challenging. With rapid advances in imaging techniques, there are now high throughput phenotyping tools available for the diagnosis of structural heart defects. In this review, we discuss the efficacy of four different imaging modalities for congenital heart disease diagnosis in fetal/neonatal mice, including noninvasive fetal echocardiography, micro-computed tomography (micro-CT), micro-magnetic resonance imaging (micro-MRI), and episcopic fluorescence image capture (EFIC) histopathology. The experience we have gained in the use of these imaging modalities in a large-scale mouse mutagenesis screen have validated their efficacy for congenital heart defect diagnosis in the tiny hearts of fetal and newborn mice. These cutting edge phenotyping tools will be invaluable for furthering our understanding of the developmental etiology of congenital heart disease.

Automatic intra-subject registration-based segmentation of abdominal fat from water-fat MRI

PURPOSE

To develop an automatic registration-based segmentation algorithm for measuring abdominal adipose tissue depot volumes and organ fat fraction content from three-dimensional (3D) water-fat MRI data, and to evaluate its performance against manual segmentation.

MATERIALS AND METHODS

Data were obtained from 11 subjects at two time points with intermediate repositioning, and from four subjects before and after a meal with repositioning. Imaging was performed on a 3 Tesla MRI, using the IDEAL chemical-shift water-fat pulse sequence. Adipose tissue (subcutaneous--SAT, visceral--VAT) and organs (liver, pancreas) were manually segmented twice for each scan by a single trained observer. Automated segmentations of each subject's second scan were generated using a nonrigid volume registration algorithm for water-fat MRI images that used a b-spline basis for deformation and minimized image dissimilarity after the deformation. Manual and automated segmentations were compared using Dice coefficients and linear regression of SAT and VAT volumes, organ volumes, and hepatic and pancreatic fat fractions (HFF, PFF).

RESULTS

Manual segmentations from the 11 repositioned subjects exhibited strong repeatability and set performance benchmarks. The average Dice coefficients were 0.9747 (SAT), 0.9424 (VAT), 0.9404 (liver), and 0.8205 (pancreas); the linear correlation coefficients were 0.9994 (SAT volume), 0.9974 (VAT volume), 0.9885 (liver volume), 0.9782 (pancreas volume), 0.9996 (HFF), and 0.9660 (PFF). When comparing manual and automated segmentations, the average Dice coefficients were 0.9043 (SAT volume), 0.8235 (VAT), 0.8942 (liver), and 0.7168 (pancreas); the linear correlation coefficients were 0.9493 (SAT volume), 0.9982 (VAT volume), 0.9326 (liver volume), 0.8876 (pancreas volume), 0.9972 (HFF), and 0.8617 (PFF). In the four pre- and post-prandial subjects, the Dice coefficients were 0.9024 (SAT), 0.7781 (VAT), 0.8799 (liver), and 0.5179 (pancreas); the linear correlation coefficients were 0.9889, 0.9902 (SAT, and VAT volume), 0.9523 (liver volume), 0.8760 (pancreas volume), 0.9991 (HFF), and 0.6338 (PFF).

CONCLUSION

Automated intra-subject registration-based segmentation is potentially suitable for the quantification of abdominal and organ fat and achieves comparable quantitative endpoints with respect to manual segmentation.

3-dimensional imaging modalities for phenotyping genetically engineered mice

A variety of 3-dimensional (3D) digital imaging modalities are available for whole-body assessment of genetically engineered mice: magnetic resonance microscopy (MRM), X-ray microcomputed tomography (microCT), optical projection tomography (OPT), episcopic and cryoimaging, and ultrasound biomicroscopy (UBM). Embryo and adult mouse phenotyping can be accomplished at microscopy or near microscopy spatial resolutions using these modalities. MRM and microCT are particularly well-suited for evaluating structural information at the organ level, whereas episcopic and OPT imaging provide structural and functional information from molecular fluorescence imaging at the cellular level. UBM can be used to monitor embryonic development longitudinally in utero. Specimens are not significantly altered during preparation, and structures can be viewed in their native orientations. Technologies for rapid automated data acquisition and high-throughput phenotyping have been developed and continually improve as this exciting field evolves.

Imaging modalities to assess structural birth defects in mutant mouse models

Assessment of structural birth defects (SBDs) in animal models usually entails conducting detailed necropsy for anatomical defects followed by histological analysis for tissue defects. Recent advances in new imaging technologies have provided the means for rapid phenotyping of SBDs, such as using ultra-high frequency ultrasound biomicroscopy, optical coherence tomography, micro-CT, and micro-MRI. These imaging modalities allow the detailed assessment of organ/tissue structure, and with ultrasound biomicroscopy, structure and function of the cardiovascular system also can be assessed noninvasively, allowing the longitudinal tracking of the fetus in utero. In this review, we briefly discuss the application of these state-of-the-art imaging technologies for phenotyping of SBDs in rodent embryos and fetuses, showing how these imaging modalities may be used for the detection of a wide variety of SBDs.