Three-dimensional reconstruction from serial section images by computer graphics

A method is described that allows a three-dimensional object to be reconstructed from micrographs of serial sections by means of computer graphics. The reconstructed object, which can be rotated three-dimensionally, is displayed on a colour visual display unit, and the object is shaded in order to provide an illusion of a three-dimensional structure. Moreover, the technique makes it possible to observe an inner structure as seen through an outer one.     

Serial sectioning and digitization of porous media for two- and three-dimensional analysis and reconstruction

A procedure is proposed for serial sectioning of impregnated porous media, for photographing the sections under the microscope, and for digitizing the image using an IBM PC (XT) with a digitizing board. The result is a three-dimensional matrix containing the enhanced digitized image in a binary form of O's and I's which represent solid and pore spaces respectively. The procedure was tested on three different porous materials: (1) a pack of glass beads, 170–350 μm; (2) Berca sandstone; and (3) Elora clay loam soil. Each of these was impregnated, forty-six to eighty cross-sections were prepared by close parallel polishing of 10–50 μm per section, and then the sections were photographed and digitized. Examples of the real and digitized cross-sectioned samples are given as well as an example of reconstructed images in a plane perpendicular to the plane of sampling. It is proposed that the method of serial sectioning and automated digitization of porous media provides a powerful tool for further three-dimensional geometrical and topological investigation of pore space to be used in models of fluid transport phenomena.     

Study of the structure of the air and blood capillaries of the gas exchange tissue of the avian lung by serial section three-dimensional reconstruction

We have previously reconstructed the gas exchange tissue of the adult muscovy duck, Cairina moschata using a method of manually aligning sections and tracing the contours of the components of the gas exchange tissue. This reconstruction method demonstrated that the air capillaries are comprised of an expanded globular part interconnected by narrow air channels. The blood capillaries completely surround the air capillaries forming an anastomosing meshwork of short segments. However, the resulting reconstruction was limited in scope because of the laborious process of tracing the profiles of each component through the sequence of micrographs. We have now reconstructed a larger proportion of the exchange tissue by using a cross-correlation based alignment strategy and have demonstrated that the staining intensity of each of the exchange tissue components is sufficiently different to allow them to be identified by simple filtering and thresholding. The resulting reconstructions sample a much larger proportion of the exchange tissue and demonstrate the heterogeneity of structures from different locations in the parabronchus. We have shown that a sheet-flow-type arrangement of blood capillaries surrounds the infundibulum; this represents an unexpected functional convergence with the arrangement of blood capillaries surrounding the mammalian alveoli. It is feasible, using this reconstruction strategy, to analyse the exchange tissue of a large number of avian species in order to determine structural correlates of function. The resulting reconstructions could be analysed in order to determine the basis of the functional efficiency and rigidity of the avian lung.     

Optical sectioning with a fluorescence confocal SLM: procedures for determination of the 2-D digital modulation transfer function and for 3-D reconstruction by tessellation

We have determined the operational parameters of a confocal scanning laser microscope (CSLM) used for fluorescence imaging. The system performance was characterized by the modulation transfer function (MTF), calculated from an edge response function (ERF) corresponding to a standard test pattern overlaying fluorescence solutions on a microscopic slide. Signal truncation error was avoided by making the ERF continuous at its limits through superposition of a suitable linear curve. We determined an appropriate scanning step density by defining a compromise between the requirements of the sampling theorem with respect to aliasing and the need for minimal suppression of higher spatial frequencies. These procedures for choosing the sampling density of the total digital CSLM permit a systematic optimization of the image acquisition parameters. A reproducible digital image was obtained, an important prerequisite for subsequent 3-D image reconstruction. The latter was accomplished by first developing and applying a maximally automated algorithm for finding closed and distinct contours (corresponding to objects in the 2-D optical sections). The missing information between contour loops was then interpolated by tessellation (triangulation) using a minimal polygon edge length criterion capable of describing closed surfaces even for adjacent contours with highly dissimilar geometries. In this procedure, we define an average shift length which compensates for the inherent disadvantage of run length encoding algorithms applied to different starting points in successive planes. The surface segments were used to calculate 3-D representations by applying a shading model, in the present applications specifically to chromosome I and the nucleolus of polytenized Chironomus thummi salivary gland nuclei.