Automatic segmentation and quantification of electron micrographs: Extracellular components

Extracellular glycosaminoglycans when precipitated by tannic acid, appear in electron micrographs as amorphous reticulate masses or fragments sometimes finely beaded and often associated with collagen fibrils. An algorithm for automatic classification, segmentation, and quantification of the amount of tannic acid-precipitable material (TAPM) and collagen in electron microscopic images is presented. Small patches of a region are initially located and the patch boundaries are traced using a binary contour tracing algorithm. The patches are then grown out and merged together to form one large area. This area is classified using a two-dimensional feature vector into one of two classes: a region with TAPM and collagen, or one with cell bodies and/or processes. Once these areas are classified and segmented, the distribution of TAPM is measured. The algorithm was tested on several TAPM images displaying varying amounts and configurations of TAPM with good results. It may also be adapted to process other electron microscopic images containing elements of interest which have complex or amorphous form.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25488/1/0000029.pd

A Relation-Centric Query Engine for the Foundational Model of Anatomy

The Foundational Model of Anatomy (FMA), a detailed representation of the structural organization of the human body, was constructed to support the development of software applications requiring knowledge of anatomy. The FMA's focus on the structural relationships between anatomical entities distinguishes it from other current anatomical knowledge sources. We developed Emily, a query engine for the FMA, to enable users to explore the richness and depth of these relationships. Preliminary analysis suggests that Emily is capable of correctly processing real world anatomical queries provided they have been translated into a constrained form suitable for processing by the query engine

The FaceBase Consortium: A comprehensive program to facilitate craniofacial research

The FaceBase Consortium consists of ten interlinked research and technology projects whose goal is to generate craniofacial research data and technology for use by the research community through a central data management and integrated bioinformatics hub. Funded by the National Institute of Dental and Craniofacial Research (NIDCR) and currently focused on studying the development of the middle region of the face, the Consortium will produce comprehensive datasets of global gene expression patterns, regulatory elements and sequencing; will generate anatomical and molecular atlases; will provide human normative facial data and other phenotypes; conduct follow up studies of a completed genome-wide association study; generate independent data on the genetics of craniofacial development, build repositories of animal models and of human samples and data for community access and analysis; and will develop software tools and animal models for analyzing and functionally testing and integrating these data. The FaceBase website (http://www.facebase.org) will serve as a web home for these efforts, providing interactive tools for exploring these datasets, together with discussion forums and other services to support and foster collaboration within the craniofacial research community

Changes in cell distribution during mouse secondary palate closure in vivo and in vitro : I. Epithelial cells

The distribution of epithelial cells around the perimeter of mouse secondary palatal shelves was observed before and after shelf reorientation in vivo and in vitro. Changes in shelf perimeter, cells per micrometer, and cell layering were measured for each of three shelf regions: anterior and posterior presumptive hard and presumptive soft palate at developmental stages which were 30, 24, and 18 hr prior to expected in vivo elevation, after in vivo elevation, and during the course of in vitro elevation. Pronounced increases in numerical cell density and cell layering accompanying shelf reorientation were noted in the superior nasal and mid-oral portions of the shelf perimeter in all three shelf regions with greatest changes noted in the posterior hard palate region. These changes were not attributable to cell division or to perimeter changes. The localized nature of the changes in cell distribution suggest that the underlying mechanisms may also be localized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24885/1/0000312.pd

The role of the mesenchyme in mouse neural fold elevation. II. Patterns of hyaluronate synthesis and distribution in embryos developing in vitro

Hyaluronate (HA) distribution patterns were examined in the cranial mesenchyme underlying the mesencephalic neural folds of mouse embryos maintained in roller tube culture. Using standard image-processing techniques, the digitized images of Alcian blue-stained or 3 H-glucosamine-labeled sections digested with an enzyme specific for HA, were subtracted from adjacent, undigested sections. The resultant difference picture images (DPI) accurately depicted the distribution of stained or labeled HA within the cranial mesenchyme. 3 H-glucosamine-labeled HA was distributed uniformly throughout the cranial mesenchyme as 12, 18, and 24 hr of culture. By contrast, the mesenchyme was uniformly stained with Alcian blue at 12 hr, but stain intensity decreased in the central regions of the mesenchyme at 18 and 24 hr. HA distribution patterns were also examined in the cranial mesenchyme of embryos cultured in the presence of diazo-oxo-norleucine (DON), a glutamine analogue that inhibits glycosaminoglycan and glycoprotein synthesis. In DON-treated mesenchyme, Alcian blue staining of HA was decreased from that in controls at 12, 18, and 24 hr. However, incorporation of 3 H-glucosamine into HA was increased. The distribution of labeled HA within treated mesenchyme as 12, 18, and 24 hr resembled that in controls at 12 hr. These results indicate that the distribution of HA within the cranial mesenchyme of normal mouse embryos during neural fold elevation and convergence is not determined solely by regional differences in HA synthesis. We propose that HA distribution patterns result from the expansion of the HA-rich extracellular matrix of the central mesenchyme regions. This expansion may play a major role in fold elevation. These results also suggest that DON treatment reversibly inhibits HA synthesis, since treated mesenchymal cells retain the capability of synthesizing HA when provided with a glucosamine substrate. Patterns of 3 H-glucosamine incorporation by DON-treated mesenchyme are similar to those observed in control mesenchyme prior to mesenchymal expansion at 12 hr.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49697/1/1001880204_ftp.pd

The effects of chlorcyclizine-induced glycosaminoglycan alterations on palatal mesenchyme-basal lamina relationships in the mouse

The relationships of mesenchymal cells to the basal lamina underlying regions of the palatal-shelf epithelium that are known to increase in cell density during shelf reorientation are quantitatively different from those of cells underlying neighboring regions that do not increase in cell density. Chlorcyclizine-induced alterations of the extracellular matrix were used to investigate the possible contribution of extracellular matrix to these differences. Chlorcyclizine causes hyaluronate and the chondroitin sulfates to be degraded into pieces with smaller molecular weights and lower charge densities, with little or no effect on their synthesis, and also results in cleft palate. Pregnant CD-1 mice were gavaged with chlorcylizine on days 10.5, 11.5, and 12.5 of gestation, and the fetuses were harvested on day 13.5. Some palatal shelves were excised immediately and fixed for electron microscopy; other heads were partially dissected and incubated for 4 hr prior to fixation. In normal heads differences in mesenchymal cell configurations are detectable after 4 hr in vitro . Electron micrographs were taken of the epithelial-mesenchymal interface in nasal and oral regions that increased in epithelial cell density and in nasal and oral regions which did not. Several variables of mesenchymal cell configuration were measured in a 500-nm-wide zone delimited on photographic prints. Chlorcyclizine-induced glycosaminoglycan alterations resulted in quantifiable, region-specific differences in mesenchymal cell relationships to the basal lamina and in the ultrastructural appearance of the zone immediately subjacent to the basal lamina. These results suggest that the epithelial-mesenchymal interface and sublaminar zone of the nasal and oral regions as well as their active and inactive segments may be constitutively different.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49691/1/1001760310_ftp.pd

Visible Human, Know Thyself: The Digital Anatomist Structural Abstraction

The Visible Human data sets have stimulated a great deal of activity in the graphical representation of anatomy. A major challenge is to enhance this resource of image-based information with knowledge of its own structure. There is a need for a symbolic model of the structural organization of the human body, which could invest with meaning the graphical information extractable from the clusters of voxels and their geometric coordinates that make up the Visible Human data sets. The objective of this communication is to examine the elements of structural information such a symbolic model should encompass, and to assess the extent to which the Anatomical Structural Abstraction (ASA) of the Digital Anatomist Foundational Model of Anatomy (Fm) meets this objective

A Visual Database Environment for Scientific Research

The paper describes a visual database environment designed to be used for scientific research in the imaging sciences. It provides hierarchical relational structures that allow the user to model data as entities possessing properties, parts and relationships, and it supports multi-level queries on these structures. A schema constructor interface allows users to define for each structure, not only its components, but also its visualization, which is built from its components using graphical primitives. Finally, an experiment management subsystem allows users to construct and run computational experiments that apply imaging operators to data from the database. The experiment management system keeps track of the experimental procedures developed by the user and the results generated by executing these procedures

A Visual Database System for Data and Experiment Management in Model-Based Computer Vision

We present the design of a visual database system for data and experiment management. Our system was designed as a general scientific database system, but motivated by and intended for use in model-based computer vision. We provide a unified data model, a highly graphical user interface, an advanced query facility, and an interactive laboratory notebook. We hope that the system, when completed, will aid in scientific experimentation and will promote data sharing in the computer vision research community

Visible Human, Construct Thyself: The Digital Anatomist Dynamic Scene Generator

The Visible Human data sets have stimulated a great deal of activity in the graphical representation of anatomy. A major challenge is to enhance this resource of image-based information with knowledge of its own structure. There is a need for a symbolic model of the structural organization of the human body, which could invest with meaning the graphical information extractable from the clusters of voxels and their geometric coordinates that make up the Visible Human data sets. The objective of this communication is to examine the elements of structural information such a symbolic model should encompass, and to assess the extent to which the Anatomical Structural Abstraction (ASA) of the Digital Anatomist Foundational Model of Anatomy (Fm) meets this objective