Volumetric modeling and interactive cutting of deformable bodies

A new approach for the interactive simulation of viscoelastic object cutting is presented. Two synchronized geometrical models at different resolutions are used, both derived from medical images. In contrast with most previous approaches, the blade deforms the object, and cutting occurs once a contact pressure threshold is exceeded. Moreover, we achieve interactive simulation rates by embedding a high-resolution geometry within a regular grid with arbitrary resolution. This allows to trade off accuracy for speed in the computation of deformations. The input data is a high-resolution volumetric model of the objects. The surface model of the object, used for rendering as well as collision detection and response, is a polygonal level set of the volumetric data. It is embedded in the volume model using barycentric coordinates.Cutting is performed by removing voxels at the fine level, and updating the surface and volume models accordingly. We introduce a new data structure, which we call a Dynamic Branched Grid, in order to preserve the fine-level topology at the coarse level. When an element of the coarse volumetric model is cut, it is replaced by a number of superimposed elements with the same size and at the same rest position as the original one. Each new element is assigned a part of material contained in the original one, and the mass and stiffness are recomputed accordingly. The well-known problem of creating small, ill-shaped finite elements while remeshing is thus completely avoided.     

Analytically defined surfaces to analyze molecular interaction properties

Molecular surfaces are widely used for characterizing molecules and displaying and quantifying their interaction properties. Here we consider molecular surfaces defined as isocontours of a function (a sum of exponential functions centered on each atom) that approximately represents electron density. The smoothness is advantageous for surface mapping of molecular properties (e.g., electrostatic potential). By varying parameters, these surfaces can be constructed to represent the van der Waals or solvent-accessible surface of a molecular with any accuracy. We describe numerical algorithms to operate on the analytically defined surfaces. Two applications are considered: (1) We define and locate extremal points of molecular properties on the surfaces. The extremal points provide a compact representation of a property on a surface, obviating the necessity to compute values of the property on an array of surface points as is usually done; (2) a molecular surface patch or interface is projected onto a flat surface (by introducing curvilinear coordinates) with approximate conservation of area for analysis purposes. Applications to studies of protein-protein interactions are described.     

Quantification and visualization of molecular surface flexibility

Two new methods for the quantification and visualization of the flexibility of molecular surfaces are presented. Both methods rely on results of molecular dynamics (MD) simulations. Whereas method I is based on a simple but fast grid-counting algorithm, method II uses a mapping function that allows for a sharp and clear visualization of atomic RMS fluctuations on a molecular surface. To demonstrate the scope of the methods, MD simulations of two proteins, PTI and ubiquitin, were performed. The flexibility data are mapped onto the molecular surfaces of the proteins and visualized using texture mapping technology available on modern workstations.     

Texture mapping: A new tool for molecular graphics

The real-time texture mapping capabilities of modern graphics workstations are explored with respect to their applications in a variety of relevant scenarios in interactive molecular modeling techniques. The common usage of texture mapping to reduce geometric complexity while enhancing realism is extended, opening new ways to visualize large amounts of molecular data in a comprehensive fashion. Thus, texture mapping may be employed to (1) display and filter multichannel information of structural properties on molecular surfaces, (2) improve the quality and accuracy of highly complex isodensity contours, (3) increase the rendering speed of space-filling atomic representations by two orders of magnitude and (4) apply volume-rendering techniques to large, three-dimensional density distributions in real time. Implementation of these novel techniques requires only moderate modifications or extensions to existing molecular modeling applications.     

ProteinShader: illustrative rendering of macromolecules

Background

Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings.

Results

The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline.

Conclusion

By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images.     

Approximation and visualization of large-scale motion of protein surfaces

We present a method for the approximation and real-time visualization of large-scale motion of protein surfaces. A molecular surface is represented by an expansion of spherical harmonic functions, and the motion of protein atoms around their equilibrium positions is computed by normal mode analysis. The motion of the surface is approximated by projecting the normal mode vectors of the solvent-accessible atoms to the spherical harmonic representation of the molecular surface. These surface motion vectors are represented by a separated spherical harmonic expansion. Representing the surface geometry and the surface motion vectors by spherical harmonic expansions allows variable-resolution analysis and real-time display of the large-scale surface motion. This technique has been applied to interactive visualization, interactive surface manipulation, and animation.     

A real-time malleable molecular surface

We describe a method for generating a molecular surface using a parametric patch representation. Unlike previous methods, this algorithm generates a parametric patch surface which is smooth and G¹ continuous and manipulable in real-time. Crucial to our approach is the creation of a net of approximately equilateral triangles from which we generate the control points used as the basis for describing the surface. We present in detail the method used for generating the triangular net and accompanying control points, along with examples of the resulting surfaces.     

Imaging Transient Blood Vessel Fusion Events in Zebrafish by Correlative Volume Electron Microscopy

The study of biological processes has become increasingly reliant on obtaining high-resolution spatial and temporal data through imaging techniques. As researchers demand molecular resolution of cellular events in the context of whole organisms, correlation of non-invasive live-organism imaging with electron microscopy in complex three-dimensional samples becomes critical. The developing blood vessels of vertebrates form a highly complex network which cannot be imaged at high resolution using traditional methods. Here we show that the point of fusion between growing blood vessels of transgenic zebrafish, identified in live confocal microscopy, can subsequently be traced through the structure of the organism using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) and Serial Block Face/Scanning Electron Microscopy (SBF/SEM). The resulting data give unprecedented microanatomical detail of the zebrafish and, for the first time, allow visualization of the ultrastructure of a time-limited biological event within the context of a whole organism.     

Interactive processing and visualization of image data for biomedical and life science applications

Background

Applications in biomedical science and life science produce large data sets using increasingly powerful imaging devices and computer simulations. It is becoming increasingly difficult for scientists to explore and analyze these data using traditional tools. Interactive data processing and visualization tools can support scientists to overcome these limitations.

Results

We show that new data processing tools and visualization systems can be used successfully in biomedical and life science applications. We present an adaptive high-resolution display system suitable for biomedical image data, algorithms for analyzing and visualization protein surfaces and retinal optical coherence tomography data, and visualization tools for 3D gene expression data.

Conclusion

We demonstrated that interactive processing and visualization methods and systems can support scientists in a variety of biomedical and life science application areas concerned with massive data analysis.

     

Visual analysis of trabecular bone structure

Acquiring image data of bone biopsies by a micro-CT scanner is today a common technique. The amount of data to be assessed is huge. The task to assess quantitative measures requires a concise visualization. We present visualization techniques that can be used interactively on state-of-the-art PCs and demonstrate how the frontier can be pushed further. A skeletonization process is applied to the image of the bone to create the central surface. After triangulation this surface can be renderd at interactive frame rates. When the surface is additionally colored by local measures (mean grey value of image data, local thickness) the overall structure and details can be recognized at the same time. This can facilitate the exploration of the biopsy and can help finding special features.     

SwarmPS: rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.     

High-resolution confocal imaging and three-dimensional rendering

Intrinsic opacity and inhomeogeniety of most biological tissues have prevented the efficient light penetration and signal detection for high-resolution confocal imaging of thick tissues. Here, we summarize recent technical advances in high-resolution confocal imaging for visualization of cellular structures and gene expression within intact whole-mount thick tissues. First, we introduce features of the FocusClear technology that render biological tissue transparent and thus improve the light penetration and signal detection. Next, a universal fluorescence staining method that labels all nuclei and membranes is described. We then demonstrate the postrecording image processing techniques for 3D visualization. From these images, regions of interest in the whole-mount brain can be segmented and volume rendered. Together, these technical advances in confocal microscopy allow visualization of structures within whole-mount tissues up to 1mm thick at a resolution similar to that of the observation of single cells in culture. Practical uses and limitations of these techniques are discussed.     

Protein surface representation and analysis by dimension reduction

Background

Protein structures are better conserved than protein sequences, and consequently more functional information is available in structures than in sequences. However, proteins generally interact with other proteins and molecules via their surface regions and a backbone-only analysis of protein structures may miss many of the functional and evolutionary features. Surface information can help better elucidate proteins' functions and their interactions with other proteins. Computational analysis and comparison of protein surfaces is an important challenge to overcome to enable efficient and accurate functional characterization of proteins.

Methods

In this study we present a new method for representation and comparison of protein surface features. Our method is based on mapping the 3-D protein surfaces onto 2-D maps using various dimension reduction methods. We have proposed area and neighbor based metrics in order to evaluate the accuracy of this surface representation. In order to capture functionally relevant information, we encode geometric and biochemical features of the protein, such as hydrophobicity, electrostatic potential, and curvature, into separate color channels in the 2-D map. The resulting images can then be compared using efficient 2-D image registration methods to identify surface regions and features shared by proteins.

Results

We demonstrate the utility of our method and characterize its performance using both synthetic and real data. Among the dimension reduction methods investigated, SNE, LandmarkIsomap, Isomap, and Sammon's mapping provide the best performance in preserving the area and neighborhood properties of the original 3-D surface. The enriched 2-D representation is shown to be useful in characterizing the functional site of chymotrypsin and able to detect structural similarities in heat shock proteins. A texture mapping using the 2-D representation is also proposed as an interesting application to structure visualization.

     

EzMol: A Web Server Wizard for the Rapid Visualization and Image Production of Protein and Nucleic Acid Structures

EzMol is a molecular visualization Web server in the form of a software wizard, located at http://www.sbg.bio.ic.ac.uk/ezmol/. It is designed for easy and rapid image manipulation and display of protein molecules, and is intended for users who need to quickly produce high-resolution images of protein molecules but do not have the time or inclination to use a software molecular visualization system. EzMol allows the upload of molecular structure files in PDB format to generate a Web page including a representation of the structure that the user can manipulate. EzMol provides intuitive options for chain display, adjusting the color/transparency of residues, side chains and protein surfaces, and for adding labels to residues. The final adjusted protein image can then be downloaded as a high-resolution image. There are a range of applications for rapid protein display, including the illustration of specific areas of a protein structure and the rapid prototyping of images.     

Targeted regeneration of bone in the osteoporotic human femur

We have recently developed image processing techniques for measuring the cortical thicknesses of skeletal structures in vivo, with resolution surpassing that of the underlying computed tomography system. The resulting thickness maps can be analysed across cohorts by statistical parametric mapping. Applying these methods to the proximal femurs of osteoporotic women, we discover targeted and apparently synergistic effects of pharmaceutical osteoporosis therapy and habitual mechanical load in enhancing bone thickness.     

Volumetric feature extraction and visualization of tomographic molecular imaging

Electron tomography is useful for studying large macromolecular complex within their cellular context. The associate problems include crowding and complexity. Data exploration and 3D visualization of complexes require rendering of tomograms as well as extraction of all features of interest. We present algorithms for fully automatic boundary segmentation and skeletonization, and demonstrate their applications in feature extraction and visualization of cell and molecular tomographic imaging. We also introduce an interactive volumetric exploration and visualization tool (Volume Rover), which encapsulates implementations of the above volumetric image processing algorithms, and additionally uses efficient multi-resolution interactive geometry and volume rendering techniques for interactive visualization.     

Quantum dots as a sensor for quantitative visualization of surface charges on single living cells with nano-scale resolution

We developed a technique using quantum dot (QD) as a sensor for quantitative visualization of the surface charge on biological cells with nano-scale resolution. The QD system was designed and synthesized using amino modified CdSe/ZnS nanoparticles. In a specially designed buffer solution, they are positively charged and can homogeneously disperse in the aqueous environment to label all the negative charges on the surfaces of living cells. Using a wide-field optical sectioning microscopy to achieve 2D/3D imaging of the QD-labeled cells, we determined the charge densities of different kinds of cells from normal to mutant ones. The information about the surface charge distribution is significant in evaluating the structure, function, biological behavior and even malignant transformation of cells.     

Fitting of high-resolution structures into electron microscopy reconstruction images

Dynamic macromolecular assemblies, such as ribosomes, viruses, and muscle protein complexes, are often more amenable to visualization by electron microscopy than by high-resolution X-ray crystallography or NMR. When high-resolution structures of component structures are available, it is possible to build an atomic model that gives information about the molecular interactions at greater detail than the experimental resolution, due to constraints of modeling placed upon the interpretation. There are now several competing computational methods to search systematically for orientations and positions of components that match the experimental image density, and continuing developments will be reviewed. Attention is now also moving toward the related task of optimization, with flexible and/or multifragment models and sometimes with stereochemically restrained refinement methods. This paper will review the various approaches and describe advances in the authors' methods and applications of real-space refinement.     

High Resolution Helium Ion Scanning Microscopy of the Rat Kidney

Helium ion scanning microscopy is a novel imaging technology with the potential to provide sub-nanometer resolution images of uncoated biological tissues. So far, however, it has been used mainly in materials science applications. Here, we took advantage of helium ion microscopy to explore the epithelium of the rat kidney with unsurpassed image quality and detail. In addition, we evaluated different tissue preparation methods for their ability to preserve tissue architecture. We found that high contrast, high resolution imaging of the renal tubule surface is possible with a relatively simple processing procedure that consists of transcardial perfusion with aldehyde fixatives, vibratome tissue sectioning, tissue dehydration with graded methanol solutions and careful critical point drying. Coupled with the helium ion system, fine details such as membrane texture and membranous nanoprojections on the glomerular podocytes were visualized, and pores within the filtration slit diaphragm could be seen in much greater detail than in previous scanning EM studies. In the collecting duct, the extensive and striking apical microplicae of the intercalated cells were imaged without the shrunken or distorted appearance that is typical with conventional sample processing and scanning electron microscopy. Membrane depressions visible on principal cells suggest possible endo- or exocytotic events, and central cilia on these cells were imaged with remarkable preservation and clarity. We also demonstrate the use of colloidal gold probes for highlighting specific cell-surface proteins and find that 15 nm gold labels are practical and easily distinguishable, indicating that external labels of various sizes can be used to detect multiple targets in the same tissue. We conclude that this technology represents a technical breakthrough in imaging the topographical ultrastructure of animal tissues. Its use in future studies should allow the study of fine cellular details and provide significant advances in our understanding of cell surface structures and membrane organization.