Electron microscope analysis of tissue components identified and located by computer-assisted 3-D reconstructions: ultrastructural segmentation of the developing human proximal tubule

Tissue arrays as fiducial markers for section alignment in 3-D reconstruction technology

Combination of conventional histology and the three-dimensional spatial view of tissue structures offers new prospects for understanding and diagnosing nature and development of human diseases. The essential technical problem related to three-dimensional reconstruction in histopathology is represented by the correct alignment of serial sections. During the past years several methods have been proposed but failed to become popular because of their limits in terms of time consume and restricted applicability. We aimed to overcome this problem by applying the technology of Tissue Array, thus by positioning adequate fiducial markers from specific "donor" blocks into the "recipient" paraffin block of interest. Digitized pictures of serially cut sections were aligned according to the tissue markers embedded by Tissue Array, and then processed with specific softwares for three-dimensional reconstruction. Thirteen models, including fetal hearts, breast and thyroid carcinomas, were elaborated. We found the procedure to be easy, fast and reproducible. Moreover, by selectively embedding the fiducial markers according to specific angles, the Tissue Arrays can be exploited in order to establish the distance between sections. This original methodology of incorporating Tissue Arrays into paraffin blocks as fiducial markers for three-dimensional reconstruction has a potential impact on histology for research purposes and diagnostic applications.

Use of "reference series" to realign histological serial sections for three-dimensional reconstructions of the positions of cellular events in the developing brain

The present study demonstrates how, predominantly by external fiducials, histological serial sections used to reconstruct patterns of individually marked cellular events in large organs or whole embryos can be realigned with the help of "reference series". Resin-embedded embryos were cut at 1 microm and consecutive sections were alternately placed on two sets of slides. For cytological diagnosis and acquisition of embryonic contours, stained sections of the first series, termed "working series", were scanned with the x 100 objective using "Huge Image", a recently established image acquisition system. For acquisition of the contours of the resin block, adjacent unstained sections of the second series, termed "reference series", were scanned with the x 5 objective. Thereafter, "hybrid sections" were created which combined vectorized embryonic contours and cellular events taken from the working series with vectorized block contours taken from the reference series. For realignment, consecutive "hybrid sections" were matched by best-fit of the block contours. Stacks of realigned "hybrid sections" were shaped like truncated pyramids and, thus, reflected repeated "trimming" of the resin block during the sectioning procedure. Among 266 "hybrid sections" at intervals of 8 microm, needed to reconstruct the brain of a 15-day-old embryo of Tupaia belangeri (Scandentia), internal fiducials were required five times for realigning a total of six adjacent truncated pyramids. Application of this method provided realistic reconstructions of the positions of apoptotic cells in the entire developing brain without the need of secondary introduction of external fiducials.

External marker-based automatic congruencing: a new method of 3D reconstruction from serial sections

BACKGROUND

Computer-based three-dimensional (3D) visualizations reconstructed from sectional images represent a valuable tool in biomedical research and medical diagnosis. Particularly with those imaging techniques that provide virtual sections, such as CT, MRI, and CLSM, 3D reconstructions have become routine. Reconstructions from physical sections, such as those used in histological preparations, have not experienced an equivalent breakthrough, due to inherent shortcomings in sectional preparation that impede automated image-processing and reconstruction. The increased use of molecular techniques in morphological research, however, generates an overwhelming amount of 3D molecular information, stored within series of physical sections. This valuable information can be fully appreciated and interpreted only through an adequate method of 3D visualization.

METHODS AND RESULTS

In this paper we present a new method for a reliable and largely automated 3D reconstruction from physically sectioned material. The 'EMAC' concept (External Marker-based Automatic Congruencing) successfully approaches the three major obstacles to automated 3D reconstruction from serial physical sections: misalignment, distortion, and staining variation. It utilizes the objectivity of external markers for realignment of the sectional images and for geometric correction of distortion. A self-adapting dynamic thresholding technique compensates for artifactual staining variation and automatically selects the desired object contours.

CONCLUSIONS

Implemented on a low-cost hardware platform, EMAC provides a fast and efficient tool that largely facilitates the use of computer-based 3D visualization for the analysis of complex structural, molecular, and genetic information in morphological research. Due to its conceptual versatility, EMAC can be easily adapted for a broad range of tasks, including all modern molecular-staining techniques, such as immunohistochemistry and in situ hybridization.

Computer assisted three-dimensional reconstruction of brain regions from serial section digitized images. Application to the organization of striato-nigral relationships in the rat

We have developed a software which allows the three-dimensional reconstruction of brain regions from serial section digitized images. This software, which generates wire-frame three dimensional models, requires at least a 486 PC microcomputer running Microsoft Windows (3.x or 95). Mosaics of high resolution images, covering large brain areas, digitized by means of a camera fitted on a microscope equipped with a motorized stage, are handled by our software as single high resolution images. Serial sets of such images may be segmented and manually aligned. We have utilized this software to study the organization of striatal efferences within the substantia nigra pars reticulata, as well as the distribution of neuronal cell bodies within the substantia nigra pars compacta after micro-ionophoretic application of wheat germ agglutinin conjugated to horseradish peroxidase into the orofacial sensorimotor region of the striatum. The three dimensional representation of anterogradely labeled striatal efferences confirmed and determined the lamellar organization previously postulated from serial plane section micrographs. The distribution in the rat brain of retrogradely labeled nigro-striatal cell bodies, which had not yet been studied after injection of tracer into functionally identified regions of the striatum, revealed two subpopulations: a first one rather dense, located in the anterior half of the substantia nigra pars compacta, which was in close register with the striatal efferences, and a second one, much more scattered and less numerous, located in the posterior part of the structure which extended far from the substantia nigra along the medio-lateral axis. Our three dimensional reconstruction software will now be used to study the neuronal connectivity within the basal ganglia and other brain regions.

Embedding prolene for the development of fiducial markers

A simple, inexpensive method is described for embedding Prolene with tissue samples to provide landmarks for fiducial points to align serial sections in tissue reconstructions. Prolene is a monofilament suture material that can be easily sectioned with diamond knives to provide circular markers in each section. The sections are photographed, the negatives are projected through an enlarger and the contours, Prolene circles, and scratches from the diamond knife are traced onto paper. These landmarks establish a framework for assigning fiducial points that are necessary for the correct alignment of the contours. No special equipment is needed for embedding the Prolene and the method is adaptable for both automated and nonautomated computer systems. An example of this method for tissue alignment is given using embryonic limb tissue to determine the spatial organization of developing blood vessels as demonstrated by computer reconstruction.

Three-dimensional computerized reconstruction of histologic serial sections for orthopedic research

New programs in image processing and computer graphics can now render three-dimensional images from serial tissue slices. Although neuroanatomists have used these techniques most intensively, there are exciting applications of this methodology in orthopedic research and investigative embryology. Three-dimensional reconstructions of histologic sections from newborn clubfeet have been used to determine the rotational alignment of the hindfoot bones. Similar studies could be undertaken to improve understanding of the normal and pathologic perinatal development of the spine, hip, and hand.

Lithium-induced structural changes in the cortical distal nephron localized by computer-assisted three-dimensional reconstruction

Lithium treatment is known to cause tubule dilation in distal nephron segments both in rat and in man. However, due to the heterogeneous cell composition of the distal nephron and the cellular changes following lithium treatment, it has been difficult to identify the structurally changed segments. In this study we have therefore applied computer-assisted reconstruction of cortical distal nephron segments. Tubule dilation was demonstrated in connecting and initial collecting tubules and in the first part of cortical collecting ducts (CCD) whereas it was absent from distal straight and distal convoluted tubules. Principal cells (P cells) in the CCD showed swelling of the cytoplasm, accumulation of actin-like microfilaments, and abnormal arrangements of basolateral membranes. Connecting tubule cells (CNT cells) showed similar but less pronounced changes. Intercalated cells (I cells) showed an accumulation of vesicles in the apical cytoplasm and a reduced luminal surface area. Lesions in P and CNT cells may, at least in part, explain the diabetes insipidus and sodium loss found during lithium treatment. Proton secretion in I cells is probably mediated by an ATPase present in the luminal membrane. The reduction in area of this membrane may explain why lithium-treated animals have a lowered ability to excrete an acid load.

Ultrastructural investigation of renal biopsies: a discussion of artifacts and special methodology

The aim of this presentation is to draw attention to the problems inherent in evaluating the ultrastructure of percutaneous renal biopsies and to discuss some of the special techniques which are useful in this area. It is important to realize that the ultrastructure as it appears in this kind of material does not necessarily reflect conditions in vivo. Comparison with suitable reference material may, however, permit reliable conclusions in terms of pathological diagnosis and pathogenesis. It is advocated that purely qualitative methods, which until now have predominated in ultrastructure work with renal biopsies, be replaced by morphometry and semiquantitative methods when it is possible and practical to do so in any research situation.

Ultrastructure of three-dimensionally localized distal nephron segments in superficial cortex of the rat kidney

The ultrastructure of superficial distal nephron segments was analyzed after precise localization of tubule cross sections using computer-assisted three-dimensional reconstructions. Five systems of tubules, each with three interconnected distal tubules, were reconstructed and the lengths of the post macula densa segment of the distal straight tubule (DST), the distal convoluted tubule (DCT), the connecting tubule (CNT), and the initial collecting tubule (ICT) were determined. Each cortical collecting duct (CCD) was in continuity with only one tubule in contact with the renal capsule. In three of the five reconstructions, the two nonsubcapsular tubules fused and had a common connection to the subcapsular tubule. The length, between the macula densa (MD) and the confluence, of subcapsular tubules (2.68 +/- 0.15 mm) significantly exceeded the length of tubules not in contact with the renal capsule (2.05 +/- 0.10 mm). This difference was mainly due to a longer ICT in subcapsular tubules. Subcapsular tubules always contacted the renal capsule in the early DCT and often again in the ICT. Cells in the early DCT showed more microvilli on the luminal surface and more infoldings of basolateral membranes than cells in the late DCT. The ultrastructure of intercalated cells (I cells) varied within a range of different manifestations and the ultrastructural variation of I cells was similar in all the analyzed tubule segments. Connecting tubule cells and principal cells were similar in ultrastructure in all tubule segments and cortical levels analyzed.

Computer programs for neuroanatomy: three-dimensional reconstruction and analysis of populations of cortical neurons and other bodies with a laminar distribution

The program is designed for analysis of serial microtome sections containing biological structures (bodies, particles), each of which may be represented as one point. Any subset of sections may quickly be selected for reconstruction. In addition to rotation, translation, scaling etc. two particular features are offered. (1) Section-independent parts of reconstructions may be isolated ("windows") and then reconstructed, analyzed and subdivided, like the parent data. (2) Curved, bandshaped parts may be unfolded, for inspection of distribution pattern, determination of density etc. The program is written in Pascal (source 121 Kb, compiled program 65 Kb). User-friendliness, robustness and speed were key aims.

Three-dimensional representation and analysis of brain energy metabolism

Quantitative autoradiography of brain glucose metabolism has been combined with digital image processing to represent the brain as a three-dimensional (3-D) reconstruction of brain energy use. Autoradiographs contain enormous amounts of potentially useful data, but conventional analyses, based on tedious manual methods, can sample and analyze only a small portion of this information. Computer 3-D reconstruction provides a mechanism for observing and analyzing all the data; therefore, a system of computer programs was developed for this purpose. The programs use digital imaging methods for image registration, superimpose whole brain data sets, and allow resampling of the 3-D data in arbitrary planes for pixel-by-pixel comparisons among multiple 3-D sets. These programs operate on the mathematical properties of the images alone, obviating the need for manual image alignment. Various statistical analyses can be applied to the data directly to study the patterns of metabolic changes in different experiments. The system is applied to data from experiments on the influence of injectable anesthetics on cerebral glucose metabolism.

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.

Three-dimensional reconstructions of objects from serial sections using a microcomputer graphics system

A computer graphics system for constructing 3-dimensional models of tissues from serial sections has been designed around a Motorola 68000 CPU. The system consists of a Dual Systems 16-bit microcomputer running the UNIX operating system. A Scion Corporation MicroAngelo color graphics system drives the color monitor. Three-dimensional imaging is enhanced by hidden line removal and area filling by color. A computer-drawn model of a cherry angioma is compared with a previously constructed physical model of the same angioma to illustrate how the system operates.

Three-dimensional reconstruction of median eminence microvascular modules

To test the hypothesis that the median eminence microvasculature has a direct regulatory role in the hormonal communication between the brain and the pituitary gland, it is necessary to determine whether the physical means for such control (e.g. smooth muscle sphincters strategically located in the capillary plexus) actually exists. Our approach is to search for such structures in transmission electron micrographs of thin serial sections of the median eminence. The complexity of these images and the anticipated need to include large numbers of them in the study led us to consider computer reconstruction for this problem. We report here the successful three-dimensional reconstruction of capillary modules using digital image processing techniques for capillary feature detection/extraction, for construction of montages (mosaics) of overlapping images of the same section, and for automatic image registration by two independent methods without the use of fiducial marks. These tasks have been performed manually in nearly all the published neurobiological reconstructions; here they are performed by programs using only the mathematical properties of the images. Methods like those described here provide the only practical means for executing large scale reconstructions and gaining significant new information about the regulation of blood flow in this region of the brain.