Design and implementation of a database and program for 3D reconstruction from serial sections: a data-driven approach.

This paper describes a structural approach for a standard setup of a computer program for 3D reconstruction from serial sections. Three-dimensional reconstruction as a technique increases in importance as, along with modern immunohistochemical techniques, it is a tool in the understanding of three-dimensional development patterns. In order to apply 3D reconstruction technique in a standard laboratory setup, an attempt was made to streamline the input and the manipulation of the data such that results are obtained easily. One will find a combination of two approaches in this paper: the first is a strict ordering of the complex data, and the second is an ordering of the processes that one wishes to apply on the data (together, these two approaches constitute an information analysis); because it was observed that developmental biologists tend to work from simple lines to describe their observations, the contour model was chosen as the vehicle to build a reconstruction model from. Consequently, the data is ordered in a database that has to be manipulated to get the data out in the desired format. The most important output format is a display of the reconstructed contour stack on a graphical computer screen. Together with the other data manipulation processes, such as the input, the inspection, the revision (correction), and the reconstruction, all processes are described using the reconstruction of an 11 embryonic days (ED) rat embryo as an example. Finally, the merits of the program are illustrated with an example from the development of the human embryonic heart.

3D base: a geometrical data base system for the analysis and visualisation of 3D-shapes obtained from parallel serial sections including three different geometrical representations.

In this paper we discuss a geometrical data base that includes three different geometrical representations of one and the same reconstructed 3D shape: the contour-pile, the voxel enumeration, and the triangulation of a surface. The data base is tailored for 3D shapes obtained from plan-parallel serial sections. It is explained how this geometrical data base is useful with the different processing approaches of a 3D shape, such as analysis and visualisation. Methods of conversion between the geometrical representations are discussed. Examples of the operation of the data base as it is embedded in a data base management system are given by illustrations of retrieval of geometrical information.

Deformation-corrected computer-aided three-dimensional reconstruction of immunohistochemically stained organs: application to the rat heart during early organogenesis.

The application of a computer-assisted, three-dimensional reconstruction procedure for serial sections to embryonic rat hearts during the period of cardiac looping and compartmentalization is described. The procedure relies on immunohistochemical staining for the introduction of selective contrast and on episcopic and diascopic images of each of the sections for alignment and correction of compression due to sectioning. Episcopic (reference) images are taken from the embedding block just before the cutting of a slice and are still aligned and undeformed. Diascopic images are taken from the sections after immunohistochemical processing and, hence, contain selective contrast but are deformed and no longer aligned. The three-dimensional images are visualized as shaded voxel models. This approach allowed the unequivocal delineation of the developing myocardium and the inspection of its changing architecture both from the outside and from within. Furthermore, it allowed a quantification of myocardial volume. Because standardized and hence comparable views of three different stages were generated, changes in the shape of the cardiac loop, the atria, and the ventricles as well as changes in the position of the atrioventricular canal and interventricular foramen could be accurately described. Characteristic changes in the position of both the right ventricle and the atrioventricular canal that are essential for the formation of a correctly functioning four-chambered heart could be observed. These changes in shape occur while the myocardial size increases dramatically.

Toward computerized morphometric facilities: a review of 58 software packages for computer-aided three-dimensional reconstruction, quantification, and picture generation from parallel serial sections.

This review gives an inventory of 58 computer-aided three-dimensional reconstruction applications in the domain of biomedical research. It is devoted to the formulation of a set of recommendations thought to be necessary for improved performance of software packages in this field. These recommendations can be used to select packages and to guide future developments of existing reconstruction systems. The survey is restricted to three-dimensional reconstructions based upon a series of parallel sections of an object. Subjects treated are programming languages, resolution and sampling, input preparation, realignment, local deformation of slices, numerical quantifications, topological complexity, internal representation, display complexity (hidden surfaces, shading, smoothing), structure extraction, descriptive elements, database, data compression, time efficiency of systems and algorithms, hardware configuration, input devices, input media, interactive aids, display devices, and output devices. Information for this survey comes from articles that appeared between 1965 and 1985.

Computerized pattern recognition used for grain counting in high resolution autoradiographs with low grain densities.

Using a video-image system coupled to a minicomputer with commercial image handling software, autoradiographic grains displayed in dark-field are counted with a fast (ca. 3.5 min for 120,000 microns 2) and reliable (false scores less than 5%) grain-recognizing FORTRAN program executed in the users memory. The grain counts are printed in a raster of adjustable size overlying a bright-field image, so that the counts can be related directly to the underlying histological structures.