Confocal microscopy as a tool for the study of the intranuclear topography of chromosomes

A scanning confocal microscope was used to investigate the spatial positions of specific regions within blood cell nuclei. These centromeric regions were fluorescently labelled by in-situ hybridization to suspended nuclei with a centromere-1-specific DNA probe. The 3-D image data sets, obtained by optical sectioning of the cells, were used to determine the spatial position of the centromeric regions in the nuclei by means of specially developed software. The centromeres were found to be localized near the nuclear boundary. This spatial pattern was tested against a random distribution model by means of the Kolmogorov—Smirnov test. The difference between the two patterns was at a P < 0?01 significance level.     

Application of confocal laser microscopy and three-dimensional Voronoi diagrams for volume and surface estimates of interphase chromosomes

This study demonstrates the use of Voronoi tessellation procedures to obtain quantitative morphological data for chromosome territories in the cell nucleus. As a model system, chromosomes 7 and X were visualized in human female amniotic fluid cell nuclei by chromosomal in situ suppression hybridization with chromosome-specific composite probes. Light optical serial sections of 18 nuclei were obtained with a confocal scanning laser fluorescence microscope. A three-dimensional (3-D) tessellation of the image volumes defined by the stack of serial sections was then performed. For this purpose a Voronoi diagram, which consists of convex polyhedra structured in a graph environment, was built for each nucleus. The chromosome territories were extracted by applying the Delaunay graph, the dual of the Voronoi diagram, which describes the neighbourhood in the Voronoi diagram. The chromosome territories were then described by three morphological parameters, i.e. volume, surface area and a roundness factor (shape factor). The complete evaluation of a nucleus, including the calculation of the Voronoi diagram, 3-D visualization of extracted territories using computer graphic methods and parameterization was carried out on a Silicon Graphics workstation and was generally completed within 5 min. The geometric information obtained by this procedure revealed that both X- and 7-chromosome territories were similar in volume. Roundness factors indicated a pronounced variability in interphase shape for both pairs of chromosomes. Surface estimates showed a significant difference between the two X-territories but not between chromosome 7-territories.     

Three-dimensional optical microscopy using tilted views

The resolution of an optical microscope is considerably less in the direction of the optical axis (z) than in the x–y plane. This is true of conventional or confocal microscopes. To alleviate this problem we used multiple tilted views to supply the ‘missing data’ and thus increase the resolution in z. A special tilting stage was constructed which allowed specimens to be rotated through large angles. The relative, translation, rotation and z-spacing between data sets were determined by a novel Wiener/phase cross-correlation function. Once brought to a common coordinate system the data sets can be combined by Fourier space techniques similar to those used in X-ray crystallography. We applied this technique to metaphase chromosomes from intact embryos of Drosophila melanogaster. As determined from significant intensity in the Fourier transform, the resolution of the final reconstruction was about 0?25 μm in x and y, and 0?4 μm in z.     

Information recovery in missing angular data cases: an approach by the convex projections method in three dimensions

We have studied the method of projections on to convex sets (POCS) for the restoration of three-dimensional signals, especially applied for the degraded information obtained in three-dimensional (3-D) reconstructions by electron microscopy due to the limited tilting angular range of the sample that is obtainable in practice. A computer generated specimen has been used as a test object. Several noise levels were added to the specimen, obtaining signal-to-noise ratios (signal power/noise power) of between 12 and 0·5 dB. Different missing data angular regions of 30° and 10° zenithal angle have been considered. Our results illustrate the possibilities of POCS to restore incomplete 3-D data in the absence and the presence of noise, and offer ways for further applications to improve the quality of 3-D reconstructions based on real data.     

Registration of serial sections of mouse liver cell nuclei

Image registration of biological tissue is essential for 3D reconstruction, which is important for visualizing and quantifying the 3D relationships between internal structures of an object. The biological role of DNA organization, which is an extremely complex 3D architecture within the cell nucleus, has come into focus since it has become clear that the chromatin structure in itself functions as a regulator of DNA. Thus, 3D reconstruction of cell nuclei based on consecutive series of high-resolution ultrathin slices may provide new information about the chromatin structure and its organizational changes during carcinogenesis. This work focuses mainly on the problem of registering successive serial transmission electron micrographs of ultrathin sections of mouse liver cell nuclei to analyse the 3D chromatin structure. A five-step semiautomatic interactive registration method is proposed. The first two steps of the procedure correct the rotation and translation components by using the phase correlation. The third, fourth and fifth steps correct the global distortion, employing a point mapping method based on different ways of selecting the control points. In step three, the control points were automatically computed by phase correlating corresponding subimages of the reference and sensed image. A semiautomatic method is used in the fourth step to select the control points, i.e. an automated method for computing the centre of mass of manually identified anatomical structures in neighbouring slices. For the sections which could not be properly corrected by the four steps, a final step is introduced, where control points are manually selected in the reference and sensed images. An algorithm is proposed to examine the spatial distribution of selected control points. Four sets of serial sections of mouse liver cell nuclei, each with approximately 100 sections, are registered by the proposed method and also registered manually for the comparison of registration accuracy. Artificial X–Z and Z–Y sections of registered series were visually compared for the smoothness of the nuclear membrane. To quantify the registration accuracy and the extent of registration, the correlation coefficient (C) and the overlap index (C₀) were computed over the registered structure of interest. In addition to the visual comparison and the comparison of C and C₀, the registered serial sets were compared by 3D GLCM-based texture features in the Z direction. The results demonstrate that the proposed semiautomatic registration technique achieved accurate results comparable to the manual registration. The proposed registration method relies only on the operator for rough pinpointing of cellular structures. Therefore, it should provide better reproducibility, and allow the user to operate the system faster and in a more relaxed manner than in a manual registration.     

A unique mechanism of nuclear division in <i>Giardia lamblia</i> involves components of the ventral disk and the nuclear envelope

The fine structure of the binucleate, parasitic protist Giardia lamblia during interphase and divisional stages was studied by serial thin sectioning and three-dimensional reconstructions. The earlier sign of nuclear division is the development of a few peripheral areas of densely packed chromatin directly attached to the inner nuclear envelope. An intracytoplasmic sheet of ventral disk components grows from the cell periphery towards one of the nuclei, apparently constricting this nucleus, which becomes located at a ventral bulge. After the basal bodies become duplicated, a full nuclear division occurs in trophozoites, giving two pairs of parent-daughter nuclei. This full division occurs in a dorsal-ventral direction, with the resulting nuclear pairs located at the sides of the two sets of basal bodies. A new ventral disk is formed from the diskderived sheets in the cell harboring the four nuclei. Cytokinesis is polymorphic, but at early stages is dorsalto-dorsal. Encysting trophozoites show the development of Golgi cisternae stacks and dense, specific secretory granules. 3-D reconstructions show that cysts contain a single pair of incompletely strangled nuclei. The dividing Giardia lacks a typical, microtubular spindle either inside or outside the nuclei. The nuclear envelope seems to be the only structure involved in the final division of the parent-daughter nuclei.     

Second-order stereology for pores in translucent alumina studied by confocal scanning laser microscopy

The three-dimensional (3-D) arrangement of pores in translucent alumina was investigated with a confocal scanning laser microscope (CSLM). By moving the focal plane of the CSLM down into the material, a stack of serial thin optical sections was obtained to produce a 3-D image of the pores. Computer-based image analysis was used to obtain the coordinates of the pore centroids. The distance distribution function G(r) and the second-order functions K(r), L(r), H(r) and g(r) were used to analyse the spatial point pattern of the pore centroids. Estimates of the preceding functions obtained from eight stacks of sections were compared with the corresponding functions for a 3-D stationary Poisson point process, which served as a reference model for complete spatial randomness. The analysis suggested that the pore centroids were arranged in an aggregated pattern within a range of about 10 μm.     

Synthesis and turnover of DNA in hepatocytes of neonatal rats

The incorporation of ³H-thymidine has been studied in the hepatocytes nuclei of rats during the first 3 days of life. The synthesis of DNA which occurs in 18% of nuclei after a single injection of the labelled precursors 2 h after birth, cannot be considered as premitotic since:

• (i) The hepatic cell number is constant during the first 3 days of life.
• (ii) The mitotic index is less than 0·1%, 20 times lower than that expected on the basis of the labelling index and of the length of cellular cycle.
• (iii) The percentage of labelled nuclei does not increase in the following 3 days.
• (iv) The average number of grains per nucleus is unchanged for 18 h after the injection, a period longer than an entire cellular cycle (13 h).

This synthesis is better explained as due to an increase of DNA content per nucleus, previously described, in the hepatocytes during the first 3 days of life. After 20 h of life (18 h after label injection) a decrease of label of about 30% takes place without variation of DNA-Feulgen dye content per nucleus. It is concluded that synthesis and turnover of DNA are present in the hepatocytes nuclei and that these processes are probably related to the functional maturation of the cells.     

Modelling and analysis of 3-D arrangements of particles by point processes with examples of application to biological data obtained by confocal scanning light microscopy

Within the concept of point processes, a review is presented of quantities which can be used in studies of three-dimensional (3-D) aggregates of particles. Suitable characteristics and estimators are given for both unmarked and marked point processes. To demonstrate the feasibility of such quantitative approaches, an application in histology, dealing with 3-D arrangements of cell nuclei in rat liver, is described. Using a confocal scanning light microscope, 3-D images are recorded and image analysis used to obtain the coordinates of the centroid, together with the volume and DNA content, of each cell nucleus. Examples of results are given, using both unmarked and marked point processes. In the latter case, cell type, nuclear volume and ploidy group are suitable marks.     

Statistical analysis of labelling patterns of mammary carcinoma cell nuclei on histological sections

It is of central interest for tumour biology to explore the mechanisms of tumour cell proliferation. In this study, methods of spatial statistics were used to study the spatial distribution of proliferating cells within tumour tissue quantitatively and objectively. Mammary cancer tissue was studied as an example. It was attempted to clarify whether cell division occurs entirely at random (random labelling), i.e. the process of division occurs at random, independently from the state of the neighbouring nuclei, or whether the spatial distribution of proliferation is more complex, e.g. in the form of actively proliferating clusters alternating with relatively silent zones. In the case of random labelling, the reduced second moment functions K(r) of the labelled and the unlabelled nuclei would be identical. The same would hold for the pair correlation functions g(r) . The alternative hypothesis is that the second‐order properties of the processes of the labelled and the unlabelled nuclei are different. Twenty cases of invasive ductal mammary carcinomas were studied. The nuclei of proliferating cells were stained immunohistochemically with the monoclonal antibody MIB‐1, which detects specifically the proliferation‐associated nuclear antigen Ki 67. The planar coordinates of the tumor cell nucleus profiles from two rectangular visual fields per case were recorded. For each visual field, the following investigations were performed: estimation of the explorative summary characteristics K(r) and g(r) , fitting of the parameters of a stationary Strauss hard‐core model to the observed point patterns, estimation of two distance‐dependent Simpson indices and Monte Carlo tests of all individual patterns on the null hypothesis of random labelling. Significant differences between the mean K‐functions and the mean g‐functions of the labelled and the unlabelled nuclei were found. Moreover, the mean interaction parameter γ of the stationary Strauss hard‐core model was significantly higher for the labelled nuclei than for the unlabelled nuclei. The estimates of the two distance‐dependent Simpson indices showed a tendency of points with the same label towards a positive spatial correlation. In the Monte Carlo tests, the null hypothesis of random labelling was rejected for the majority of the visual fields. These four lines of investigation led to the concordant conclusion that the labelling of mammary carcinoma nuclei by MIB‐1 is not simply random. The data suggest that the second‐order properties of the point process of the labelled nuclei are significantly different from those of the unlabelled nuclei. In particular, the process of the labelled nuclei shows a higher degree of clustering (increased strength of interaction) than the process of the unlabelled points.     

Three-dimensional analysis of cell nucleus structures visualized by confocal scanning laser microscopy

Studies of the three-dimensional (3-D) organization of cell nuclei are becoming increasingly important for the understanding of basic cellular events such as growth and differentiation. Modern methods of molecular biology, including in situ hybridization and immunofluorescence, allow the visualization of specific nuclear structures and the study of spatial arrangements of chromosome domains in interphase nuclei. Specific methods for labelling nuclear structures are used to develop computerized techniques for the automated analysis of the 3-D organization of cell nuclei. For this purpose, a coordinate system suitable for the analysis of tri-axial ellipsoidal nuclei is determined. High-resolution 3-D images are obtained using confocal scanning laser microscopy. The results demonstrate that with these methods it is possible to recognize the distribution of visualized structures and to obtain useful information regarding the 3-D organization of the nuclear structure of different cell systems.     

Impairment of cytoskeleton-dependent vesicle and organelle translocation in green algae: combined use of a microfocused infrared laser as microbeam and optical tweezers

A Nd‐YAG laser at 1064 nm is used as optical tweezers to move intracellular objects and a laser microbeam to cause impairment of cytoskeleton tracks and influence intracellular motions in desmidiaceaen green algae. Naturally occurring migrations of large nuclei are inhibited in Micrasterias denticulata and Pleurenterium tumidum when the responsible microtubules are targeted with a laser microbeam generating 180 mW power in the focal plane. Impairment of the microtubule tracks appears to be irreversible, as the nucleus cannot pass the former irradiated area in Pleurenterium or remains abnormally dislocated in Micrasterias. The actin filament‐dependent movement of secretory vesicles and smaller particles can be manipulated by the same IR‐laser at 90 mW when functioning as optical tweezers. In Closterium lunula particles are displaced from their cytoplasmic tracks for up to 10 µm but return to their tracks immediately after removing the light pressure gained by the optical tweezers. The cytoplasmic tracks consist of actin filament cables running parallel to the longitudinal axis of Closterium cells as depicted by Alexa phalloidin staining and confocal laser scanning microscopy. Dynamics and extensibility of the cytoplasmic strands connecting particles to the tracks are also demonstrated in the area of large vacuoles which are surrounded by actin filament bundles. In Micrasterias trapping of secretory vesicles by the optical tweezers causes irreversible malformations of the cell shape. The vesicle accumulation itself dissipates within 30 s after removing the optical tweezers, also indicating reversibility of the effects induced, in the case of actin filament‐mediated processes.     

Improvement in the resolution of three-dimensional data sets collected using optical serial sectioning

In this paper an approach for improving the quality of 3-D microscopic images obtained through optical serial sectioning is described and implemented. A serially sectioned image is composed of a sequence of 2-D images obtained by incrementing the focusing plane of the microscope through the specimen of interest; ideally, the image obtained at each focusing plane should be in focus, and should contain information lying only within that plane. In practice, however, the images obtained contain redundant information from neighbouring focusing planes and are blurred by a three-dimensional low-pass distortion. These degradations are a consequence of the limited aperture of any optical system; using principles of geometric optics and allowing for the passage of light through the specimen, we are able to demonstrate that the microscope distortion can be described as a linear system, if the absorption of the specimen is assumed to be linear and non-diffractive. The transfer function of the microscope is found to zero a biconic region of 3-D spatial frequencies orientated along the optical axis; a closed-form expression is derived for the low-pass transfer function of the microscope outside the region of missing frequencies. The planar resolution of the serial sections can be greatly improved by convolving the image obtained with the inverse of the low-pass distortion function, although the missing cone of frequencies is not recoverable. The reconstruction technique is demonstrated using both simulated images, to demonstrate more clearly the effects of the distortion and the accuracy of the subsequent reconstruction, and actual experiments with a pollen grain and a stained preparation of human cerebellum tissue.     

Confocal laser microscopy and three-dimensional reconstruction of nucleus-associated microtubules in the division plane of vacuolated plant cells

The way in which transvacuolar strands radiating from the cell nucleus reorganize to form the phragmosome, within which division occurs, has been thoroughly studied in epidermal explants of Nautilocalyx lynchii. In recent years it has been established that the movement of the nucleus into the centre of large vacuolated cells such as these, in preparation for division, involves actin filaments. In the present study, the appearance and gradual reorganization of nucleus-associated microtubules (NAMTs) over the premitotic period is described. Epidermal explants fluorescently labelled with anti-tubulin were optically sectioned by confocal scanning laser microscopy, the sections reconstructed by an image processing computer and projected as rotating stereo pairs. This revealed that the NAMTs are a major component of the phragmosome, and that they change from a radiating to a planar distribution concomitantly with the ‘bunching’ of cortical MTs to form the pre-prophase band. The continuity of the two sets of MTs indicates that the band contains newly polymerized microtubules. Other recent studies on the division of vacuolated cells are reviewed and factors affecting the alignment of the division plane are discussed.     

Three-dimensional imaging of corneal cells using in vivo confocal microscopy

Confocal microscopy is a unique and powerful imaging paradigm which allows optical sectioning through intact tissue. Real-time tandem scanning confocal microscopy has previously been used to generate high-magnification two-dimensional (2-D) images of cells in living organ systems. Inherent problems with movement, however, have prevented the in vivo acquisition of complete 3-D datasets. The development of a new objective lens, used in combination with specialized real-time image acquisition procedures, has allowed sequential serial sections to be obtained in vivo from the rabbit cornea for the first time. These sections can be digitially registered and stacked on the computer to provide a 3-D reconstruction of the corneal cells. This technique should serve as a useful method for studying 3-D structures and analysing 4-D phenomena at the cellular level in living animals. Three-dimensional images of a stromal nerve in normal rabbit cornea and of fibroblasts within a rabbit corneal wound are presented as examples of current capabilities.     

Piston Motion Performance Analysis of a 3DOF Electrothermal MEMS Scanner for Medical Applications

MEMS scanners are useful for medical applications as optical coherence tomography and laser microsurgery. Although widespread design of MEMS scanners have been presented, their behavior is not well known, and thus, their motions are not easily and efficiently controlled. This deficiency induces several difficulties (limited resolution, accuracy, cycle time, etc.), and to tackle this problem, this article presents the modeling of an ISC electrothermally actuated MEMS mirror and the experimental characterization for the piston motion. Modeling and characterization are important to implement the control. A multiphysic model is proposed, and an experimental validation is performed with a good correspondence for a voltage range from 0 V to 3.5 V with a maximum displacement up to 200 µm and with a relative tilting difference of 0.1°. The article also presents a simple and efficient experimental setup to measure a displacement in dynamic and static mode, or a mirror plane tilting in static mode.     

Limitations on optical sectioning in live-cell confocal microscopy

In three-dimensional (3-D) live-cell microscopy, it has been common to treat cells as having a constant refractive index (RI). Although the variations in RI associated with the nucleus and other organelles were recognized from phase- and differential interference contrast (DIC) images, it was assumed that they were small and would not affect 3-D fluorescence images obtained using widefield/deconvolution, confocal of multiphoton imaging. This paper makes clear that this confidence was misplaced. Confocal images made using backscattered light (BSL) to image the flat, glass/water interfaces above and below living microscope specimens should reveal these structures as flat and featureless. That the image of the interface on the far side of the cells is neither flat nor featureless indicates that the "optical section" surface can be profoundly distorted by the RI irregularities associated with the presence of nuclei and other subcellar structures. This observation calls into question the reliability of images made using any of the current methods for performing 3-D light microscopy of living cells.     

The glycosomes of trypanosomes: number and distribution as revealed by electron spectroscopic imaging and 3-D reconstruction

Computer-aided 3-D reconstruction of typanosomes from 0·35-μm-thick sections imaged on the Zeiss 902 electron microscope are being used to study the dynamics of cell organization. Segregation of glycolytic enzymes into glycosomes raises questions concerning the distribution and biogenesis of these organelles. Direct counts of glycosomes from Trypanosoma evansi indicate 30–40 per cell and for the closely related T. brucei, 65 per cell. These figures contrast with the estimates of others who have used model-based morphometric methods to obtain a value of 230 per cell.     

Image processing techniques for 3-D chromosome analysis

3-D karyotype analysis is developing rapidly due to the availability of confocal microscopes and CCD video cameras, and the development of 3-D processing techniques. Here, image enhancement and visualization techniques specifically designed for 3-D karyotype analysis are described. To facilitate a good comparison between the different techniques, the same 3-D image, obtained with a confocal scanning laser microscope (CSLM), of a mitotic prophase nucleus of a root-tip cell of Crepis capillaris was used throughout. Besides well-known stereoscopic presentation, another means of improving depth perception is shown, i.e. a solid modelling algorithm, which simulates the process of fluorescence. An interactive routine to dissect objects in the image is presented as an alternative for automated segmentation algorithms, which cannot be applied to closely apposed or merging objects. As an example of a convenient way to reduce the vast amount of data (2 Mbyte per image), a partly automated 3-D cursor is presented in detail. This cursor is used to trace the central axes of chromosomes and record them as strings of Cartesian coordinates. The advantages of a computer graphics display, which facilitates real-time rotation and hence is a powerful tool in studying 3-D features of chromosomes, are also shown.     

Probing DNA structure and function with a multiwavelength fluorescence confocal laser microscope

Three levels of organization in DNA structure in the interphase cell nucleus are assessed by confocal laser scanning microscopy: (i) the conformational state of the double helix; (ii) the distribution of eu- and heterochromatin; and (iii) the localization of replication complexes throughout S phase. Multi-parameter measurements were carried out in each optical section using two laser sources and combined stereoscopic reconstructions were used to assess the co-localization of nuclear components. DNA is highly polymorphic and can adopt a variety of different helical conformations as well as unusual structures (curved, cruciform, multi-stranded). We have assessed by laser scanning microscopy the presence of left-handed Z-DNA in polytene chromosomes of Diptera as well as the spatio-temporal distribution of Z-DNA binding proteins in whole-mount Drosophila embryos and ovaries. We have determined the 3-D distribution of replication sites relative to heterochromatin regions, nucleoli and nuclear membrane by using short pulses of BrdU incorporation in synchronized mouse and human fibroblasts. Replication sites were visualized with a monoclonal anti-BrdU antibody combined with DNA fluorescent staining and antibody labelling of nuclear lamin. The implications of dynamic DNA movement and structural rearrangement to the organization of the nucleus in domains are discussed.