Virtual histology of transgenic mouse embryos for high-throughput phenotyping.

A bold new effort to disrupt every gene in the mouse genome necessitates systematic, interdisciplinary approaches to analyzing patterning defects in the mouse embryo. We present a novel, rapid, and inexpensive method for obtaining high-resolution virtual histology for phenotypic assessment of mouse embryos. Using osmium tetroxide to differentially stain tissues followed by volumetric X-ray computed tomography to image whole embryos, isometric resolutions of 27 mum or 8 mum were achieved with scan times of 2 h or 12 h, respectively, using mid-gestation E9.5-E12.5 embryos. The datasets generated by this method are immediately amenable to state-of-the-art computational methods of organ patterning analysis. This technique to assess embryo anatomy represents a significant improvement in resolution, time, and expense for the quantitative, three-dimensional analysis of developmental patterning defects attributed to genetically engineered mutations and chemically induced embryotoxicity.

Morphometric and qualitative analysis of congenital occipitocervical instability in children: implications for patients with Down syndrome.

OBJECT: Congenital occipitocervical (OC) instability is uncommon in healthy children but can occur in many children with Down syndrome. A simple morphometric method of evaluating the OC joint in children with OC instability is presented, supported by a qualitative image analysis based on computed tomography (CT). METHODS: Thin-cut CT scans of the OC joint were obtained in eight patients with Down syndrome and one patient with congenital OC instability. These patients' CT scans were compared with those of 15 healthy age-matched control individuals. Morphometric analysis was performed by measuring the depth and length of the superior articular surface (SAS) of C-1, and these values were normalized for a comparison between groups. Qualitative data were acquired using a surface-rendering technique for a visual comparison of the C-1 SAS. Morphometric analysis demonstrated an absence of the concave C-1 SAS anatomy in patients with congenital OC instability compared with age-matched control individuals (0.083 compared with 0.202, p < 0.001). Three-dimensional (3D) image analysis of the C-l SAS supported this finding. CONCLUSIONS: Congenital differences in the shape of the OC joint are highly associated with atraumatic OC instability in children with Down syndrome. High-resolution CT imaging combined with 3D rendering techniques and surface mapping provides support for this assessment. It appears that abnormal OC joint shape is a contributing factor to congenital OC instability, especially in patients with Down syndrome.

Case study: an evaluation of user-assisted hierarchical watershed segmentation.

This paper evaluates the effectiveness of an interactive, three-dimensional image segmentation technique that relies on watersheds. This paper presents two user-based case studies, which include two different groups of domain experts. Subjects manipulate a graphics-based front end to a hierarchy of segmented regions generated from a watershed segmentation algorithm, which is implemented in the Insight Toolkit. In the first study, medical students segment several different anatomical structures from the Visible Human Female head and neck color cryosection data. In the second study, radiologists use the interactive tool to produce models of brain tumors from MRI data. This paper presents a quantitative and qualitative comparison against hand contouring. To quantify accuracy, we estimate ground truth from the hand-contouring data using the Simultaneous Truth and Performance Estimation algorithm. We also apply metrics from the literature to estimate precision and efficiency. The watershed segmentation technique showed improved subject interaction times and increased inter-subject precision over hand contouring, with quality that is visually and statistically comparable. The analysis also identifies some failures in the watershed technique, where edges were poorly defined in the data, and note a trend in the hand-contouring results toward systematically larger segmentations, which raises questions about the wisdom of using expert segmentations to define ground truth.

Optimization of volumetric computed tomography for skeletal analysis of model genetic organisms.

Forward and reverse genetics now allow researchers to understand embryonic and postnatal gene function in a broad range of species. Although some genetic mutations cause obvious morphological change, other mutations can be more subtle and, without adequate observation and quantification, might be overlooked. For the increasing number of genetic model organisms examined by the growing field of phenomics, standardized but sensitive methods for quantitative analysis need to be incorporated into routine practice to effectively acquire and analyze ever-increasing quantities of phenotypic data. In this study, we present platform-independent parameters for the use of microscopic x-ray computed tomography (microCT) for phenotyping species-specific skeletal morphology of a variety of different genetic model organisms. We show that microCT is suitable for phenotypic characterization for prenatal and postnatal specimens across multiple species.

Practical vessel imaging by computed tomography in live transgenic mouse models for human tumors.

Contrast-enhanced small-animal computed tomography is an economical and highly quantitative tool for serially examining tumor development in situ, for analyzing the network of blood vessels that nourish them, and for following the response of tumors to preclinical therapeutic intervention(s). We present practical considerations for visualizing the vascular network of transgenic mouse tumors. Using a long-acting iodinated triglyceride blood-pool contrast agent, we present optimized scanner acquisition parameters and volume-rendering techniques for examining the intermediate and large vessels of complex spontaneous tumors (e.g., alveolar rhabdomyosarcomas) in transgenic mice. Our findings indicate that multiple-frame, 360-720 view acquisitions were mandatory for clarifying bone and soft tissue from vessel contrast. This finding was consistent in visualizations using a one-dimensional transfer function where voxel color and opacity was assigned in proportion to CT value and a two-dimensional transfer function where voxel color and opacity was assigned in proportion to CT value and gradient magnitude. This study lays a groundwork for the qualitative and quantitative assessment of anti-angiogenesis preclinical studies using transgenic mice.