Spatial visualization of DNA in solution.

An image analysis method is presented which allows for the reconstruction of the three-dimensional path of filamentous objects from two of their projections. Starting with stereo pairs, this method is used to trace the trajectory of DNA molecules embedded in vitreous ice and leads to a faithful representation of their three-dimensional shape in solution. This computer-aided reconstruction is superior to the subjective three-dimensional impression generated by observation of stereo pairs of micrographs because it enables one to look at the reconstructed molecules from any chosen direction and distance and allows quantitative analysis such as determination of distances, curvature, persistence length, and writhe of DNA molecules in solution.     

Three-dimensional reconstruction of the actin cytoskeleton from stereo images

In eucaryotic cells, actin filaments are abundant components in the cytoskeleton where they form a complex three dimensional (3D) structural network that provides the cell with its shape and mechanical properties. However, understanding the structural and mechanical properties of actin filaments composing the cell cytoskeleton is often hampered by the inability to faithfully reconstruct the three-dimensional geometric relationships. This paper presents a vision-based reconstruction approach that automatically reconstitutes the three-dimensional structures of cytoskeletal polymers from stereo image pairs taken at the different tilt angles. The approach finds corresponding points between two images and recovers the depth information about the structures. The computational process consists of three major procedures: feature representation, stereo matching, and disparity refinement, implemented in a multi-resolution manner based on a coarse-to-fine strategy. The reconstruction depicts the three-dimensional structure of cytoskeletal polymers and their geometric relationships. New and useful information becomes available and allows quantitative analysis of the structure. Measurement of the cytoskeleton geometrical properties and the filament concentration in a defined volume are obtained by direct calculation.     

Improved coordinate reconstruction from stereo diagrams

A program has been written that reconstructs three-dimensional coordinates for a protein structure given a stereo C_α diagram. Initial three-dimensional coordinates are determined using an algorithm similar to the one used by Rossmann in the program STEREO. Thereafter the coordinates are refined such that the stereo image based on the reconstructed three-dimensional coordinates optimally fits the scanned stereo image while normal C_α stereochemistry is enforced.     

Alternative electron density models for structural biochemistry.

Computer graphics can depict intrinsically three-dimensional structures. Restriction to plane sections of an electron density, or even to the widely used cagecontouring technique is not necessary. By detecting two-dimensional and three-dimensional density maxima, the algorithm discussed here offers new possibilities for describing the trace of linked density maxima. The core-tracing technique is described and illustrated by means of stereo views.     

Computer 3-dimensional reconstruction of intraglandular lymph vessels and ductal systems of the human submandibular gland.

Computer three-dimensional reconstruction of serial sections is currently an active area of research. In this paper we combine computer graphics, image processing and biomedical techniques to reconstruct a stereo model of intraglandular lymphatic vessels, veins, arteries and ducts from serial microsections of the human submandibular gland.     

Efficiently measuring complex sessile epibenthic organisms using a novel photogrammetric technique

This paper describes a stereo photogrammetry method that allows accurate measurements of volume for sessile epibenthic organisms. It represents a novel approach based on multiple views (five stereo image pairs) from a purpose built stereo digital still camera system combined with a three-dimensional reconstruction software program (CAM). The bias, accuracy, precision and efficiency of the method were assessed in the laboratory using models with three levels of morphological complexity (simple, moderate and complex morphologies) and two sizes (large and small). The technique did not show any biases to observer experience, with no significant difference among observers (p > 0.05). Volume measurements made with CAM were very accurate when compared with the water displacement volume of each model, with an overall mean error of about − 3% (S.E. ± 1%). The CAM volume measurements were more accurate on complex models and moderately complex models than on models with simple morphologies. Also, large models had a higher accuracy than small models. Volume measurements made with CAM were also highly precise with the lowest precision observed being ± 2% of the volume estimate. The time required for a volume estimation using the CAM method was also highly efficient, and the longest time taken for a volume estimation was on average 1 h and 36 min, making it the fastest reported three-dimensional reconstruction method. In field applications, volume estimations of four sponges were all within the observed accuracy, precision and efficiency established during laboratory trials. The accuracy, precision and efficiency demonstrated by the CAM method make this technique highly suitable for routine measurements of the volume of sessile epibenthic organisms.     

The relative merits of direct morphometry of reconstructions of whole cells, and statistical morphometry by stereology of random sections of cells.

Stereology, or the derivation of quantitative, three-dimensional (3-D) data about cells by statistical analysis of the structures of random sections, is widely used in cytology and pathology. However, there are situations where this approach is inadequate, and only an analysis of a homogeneous population of whole cells will give the required results. This involved 3-D reconstruction from physical or optical sections, or tomography or photogrammetry of whole-cell mounts. Use of stereo views of individual sections or projections adds considerably to the information available for both contouring and reconstruction. Recent image-processing advances in clinical radiography have shown, for the first time, that rapid, high-resolution digitization and contrast enhancement enable nearly all structural details to be routinely extracted from the micrographs and adequately portrayed. Three-D whole-cell reconstructions provide the digital data for many kinds of morphometric measurements on both whole cells and their individual organelles and membranes. Rapid fixation or freezing allows improved quantitative structure/function correlations of organelles with disturbances in cell metabolism or gene expression.     

Use of Low Temperature Scanning Electron Microscopy to Observe Frozen Hydrated Specimens of Nematodes

Frozen hydrated specimens of Pratylenchus agilis and dauer larvae of Steinernema carpocapsae were observed with low-temperature field emission scanning electron microscopy. This new technique provides information about the surface features of nematodes and also allows specimens to be fractured to reveal their internal structure. Furthermore, both halves of fractured specimens can be retained, examined, and photographed either as two-dimensional micrographs or as three-dimensional images for stereo observation (stereology) or quantitative measurements (stereometry). This technique avoids artifacts normally associated with procedures required to prepare nematodes for examination in the transmission and scanning electron microscopes, such as chemical fixation, dehydration, and sectioning or critical point drying.     

Three-dimensional displays and stereo vision

Procedures for three-dimensional image reconstruction that are based on the optical and neural apparatus of human stereoscopic vision have to be designed to work in conjunction with it. The principal methods of implementing stereo displays are described. Properties of the human visual system are outlined as they relate to depth discrimination capabilities and achieving optimal performance in stereo tasks. The concept of depth rendition is introduced to define the change in the parameters of three-dimensional configurations for cases in which the physical disposition of the stereo camera with respect to the viewed object differs from that of the observer's eyes.     

Computational studies of the extraction of visual spatial information from binocular and motion cues

This paper reviews some of the contributions that work in computational vision has made to the study of biological vision systems. We concentrate on two areas where there has been strong interaction between computational and experimental studies: the use of binocular stereo to recover the distances to surfaces in space, and the recovery of the three-dimensional shape of objects from relative motion in the image. With regard to stereo, we consider models proposed for solving the stereo correspondence problem, focussing on the way in which physical properties of the world constrain possible methods of solution. We also show how critical observations regarding human stereo vision have helped to shape these models. With regard to the recovery of structure from motion, we focus on how the constraint of object rigidity has been used in computational models of this process.     

A stereo imaging system for measuring structural parameters of plant canopies

Plants constantly adapt their leaf orientation in response to fluctuations in the environment, to maintain radiation use efficiency in the face of varying intensity and incidence direction of sunlight. Various methods exist for measuring structural canopy parameters such as leaf angle distribution. However, direct methods tend to be labour-intensive, while indirect methods usually give statistical information on stand level rather than on individual leaves. We present an area-based, binocular stereo system composed of commercially available components that allows three-dimensional reconstruction of small- to medium-sized canopies on the level of single leaves under field conditions. Spatial orientation of single leaves is computed with automated processes using modern, well-established stereo matching and segmentation techniques, which were adapted for the properties of plant canopies, providing high spatial and temporal resolution (angle measurements with an accuracy of approx. +/-5 degrees and a maximum sampling rate of three frames per second). The applicability of our approach is demonstrated in three case studies: (1) the dihedral leaflet angle of an individual soybean was tracked to monitor nocturnal and daytime leaf movement showing different frequencies and amplitudes; (2) drought stress was diagnosed in soybean by quantifying changes in the zenith leaflet angle distribution; and (3) the diurnal course of the zenith leaf angle distribution of a closed soybean canopy was measured.     

Ciliary beating in three dimensions: Steps of a quantitative description

We document a novel approach for quantitative assessment of ciliary activity, exemplified in rapid three-dimensional cyclic motion of the frontal cirri of Stylonychia. Cells held under voltage-clamp control are stimulated by step pulses to elicit reproducible hyperpolarization- or depolarization-induced ciliary motor responses. High-speed video recording at 200 fields per second is used for imaging ciliary organelles of the same cell in two perspectives: the axial view and, following cell rotation by 90 degrees, the lateral view. From video sequences of typically 1 s, the contours of the cirral images are determined and digitized. Computer programs are established to (1) reduce an observed image to a "ciliary axis", (2) sort series of axes by template to generate an averaged ciliary cycle in 2D-projection, and (3) to associate the generalized axial and lateral 2D-images for generation of a sequence of three-dimensional images, which quantitatively represent the cycle in space and time. The method allows us to produce predetermined perspectives of images selected from the ciliary cycle, and to generate stereo views for graphical representation of ciliary motion. The approach includes a potential for extraction of the complete microtubular sliding program of a cilium under reproducible electric stimulation of the ciliary membrane.     

Establishment of a Human Multiple Myeloma Xenograft Model in the Chicken to Study Tumor Growth,Invasion and Angiogenesis

Multiple myeloma (MM), a malignant plasma cell disease, remains incurable and novel drugs are required to improve the prognosis of patients. Due to the lack of the bone microenvironment and auto/paracrine growth factors human MM cells are difficult to cultivate. Therefore, there is an urgent need to establish proper in vitro and in vivo culture systems to study the action of novel therapeutics on human MM cells. Here we present a model to grow human multiple myeloma cells in a complex 3D environment in vitro and in vivo. MM cell lines OPM-2 and RPMI-8226 were transfected to express the transgene GFP and were cultivated in the presence of human mesenchymal cells and collagen type-I matrix as three-dimensional spheroids. In addition, spheroids were grafted on the chorioallantoic membrane (CAM) of chicken embryos and tumor growth was monitored by stereo fluorescence microscopy. Both models allow the study of novel therapeutic drugs in a complex 3D environment and the quantification of the tumor cell mass after homogenization of grafts in a transgene-specific GFP-ELISA. Moreover, angiogenic responses of the host and invasion of tumor cells into the subjacent host tissue can be monitored daily by a stereo microscope and analyzed by immunohistochemical staining against human tumor cells (Ki-67, CD138, Vimentin) or host mural cells covering blood vessels (desmin/ASMA).In conclusion, the onplant system allows studying MM cell growth and angiogenesis in a complex 3D environment and enables screening for novel therapeutic compounds targeting survival and proliferation of MM cells.     

Laboratory cryo soft X-ray microscopy

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.     

Stereographic reconstruction of human brain CT series

A relatively simple method for the three-dimensional reconstruction of brain contours from a series of CT scans is presented. A procedure is described for storing the structural information obtained from the CT series and for organizing and displaying the data. Furthermore, it is shown how additional features such as standardized artery information taken from an atlas can be superimposed on the spatially reconstructed brain model. It is proposed that three-dimensional representations in the form of computed stereo pairs are quite suitable for morphological documentation of specific neuropsychological issues, such as the localization of aphasic syndromes.     

The relative merits of direct morphometry of reconstructions of whole cells,and statistical morphometry by stereology of random sections of cells

Stereology, or the derivation of quantitative, three-dimensional (3-D) data about cells by statistical analysis of the structures of random sections, is widely used in cytology and pathology. However, there are situations where this approach is inadequate, and only an analysis of a homogeneous population of whole cells will give the required results. This involved 3-D reconstruction from physical or optical sections, or tomography or photogrammetry of whole-cell mounts. Use of stereo views of individual sections or projections adds considerably to the information available for both contouring and reconstruction. Recent image-processing advances in clinical radiography have shown, for the first time, that rapid, high-resolution digitization and contrast enhancement enable nearly all structural details to be routinely extracted from the micrographs and adequately portrayed. Three-D whole-cell reconstructions provide the digital data for many kinds of morphometric measurements on both whole cells and their individual organelles and membranes. Rapid fixation or freezing allows improved quantitative structure/function correlations of organelles with disturbances in cell metabolism or gene expression.     

Fast and Robust Stereo Vision Algorithm for Obstacle Detection

Binocular computer vision is based on bionics, after the calibration through the camera head by double-exposure image synchronization, access to the calculation of two-dimensional image pixels of the three-dimensional depth information. In this paper, a fast and robust stereo vision algorithm is described to perform in-vehicle obstacles detection and characterization. The stereo algorithm which provides a suitable representation of the geometric content of the road scene is described, and an in-vehicle embedded system is presented. We present the way in which the algorithm is used, and then report experiments on real situations which show that our solution is accurate, reliable and efficient. In particular, both processes are fast, generic, robust to noise and bad conditions, and work even with partial occlusion.     

Probing depth in monocular images

It is generally expected that depth (distance) is the internal representational primitive that corresponds to much of the perception of 3D. We tested this assumption in monocular surface stimuli that are devoid of distance information (due to orthographic projection and the chosen surface shape, with perspective projection used as a control) and yet are vividly three-dimensional. Slant judgments were found to be in close correspondence with the actual geometric slant of the stimuli; the spatial orientation of the surfaces was perceived accurately. The apparent depth in these stimuli was then tested by superimposing a stereo depth probe over the monocular surface. In both the perspective and orthographic projection the gradient of perceived depth, measured by matching the apparent depth of the stereo probe with that of the monocular surface at a series of locations, was substantial. The experiments demonstrate that in orthographic projection the visual system can compute from local surface orientation a depth quantity that is commensurate with the relative depth derived from stereo disparity. The depth data suggests that, at least in the near field, the zero value for relative depth lies at the same absolute depth as the stereo horopter (locus of zero stereo disparity). Relative to this zero value, the depth-from-slant computation seems to provide an estimate of distance information that is independent of the absolute distance to the surface.Supproted by Office of Naval Research Contract N00014-K-84-0533. We gratefully acknowledge the suggestions of Jacob Beck regarding the experimental design, and the assistance provided by Cathryn Stanford     

Tinkerbell—A Tool for Interactive Segmentation of 3D Data

A software system for interactive manipulation of three-dimensional data has been developed, based on the Open Inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge. Once isolated, the region of interest can be conveniently analyzed and displayed.     

The computer synthesis of expressive faces.

This paper presents a methodology for the computer synthesis of realistic faces capable of expressive articulations. A sophisticated three-dimensional model of the human face is developed that incorporates a physical model of facial tissue with an anatomical model of facial muscles. The tissue and muscle models are generic, in that their structures are independent of specific facial geometries. To synthesize specific faces, these models are automatically mapped onto geometrically accurate polygonal facial representations constructed by photogrammetry of stereo facial images or by non-uniform meshing of detailed facial topographies acquired by using range sensors. The methodology offers superior realism by utilizing physical modelling to emulate complex tissue deformations in response to coordinated facial muscle activity. To provide realistic muscle actions to the face model, a performance driven animation technique is developed which estimates the dynamic contractions of a performer's facial muscles from video imagery.