Development and validation of a graphic method for spatial interpretation and evaluation of biplanar coronary angiograms]

Visual evaluation and measurement of the lesion geometry is impaired by the foreshortening of the radiographically displayed target coronary segment. For this reason, we developed and validated a simple graphic procedure that facilitates the spatial interpretation and allows an objectifiable assessment of the view of the target coronary segment. The method computes a spatial axis of the coronary segment imaged in two planes and determines its inclination in the radiation path of each projection view. A triangle made up of the axis of the imaged segment, the unforeshortened axis of the imaged segment and the foreshortening height is displayed in each projection plane. The shape of the triangle indicates the degree of foreshortening while its position in the angiogram indicates the orientation of the spatial axis relative to the observer. The method was validated by comparing calculated and true foreshortening in the radiographic views of a centimetre grid obtained in the usual angiographic projections. The method has an accuracy and precision of 0.05 +/- 0.62%. It is applied clinically to evaluate biplane segmental visualization during coronary interventions and to select valid segmental views for measurements during quantitative biplane coronary angiography. This application may considerably facilitate the interpretation and assessment of biplane angiograms.     

Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions

This paper examines a new technique for the visualization of and the interaction with trees, objects frequently used to convey hierarchical relationships in biological data. Motivated by the quality of 2D tree interaction, we adapt the planar tree-of-life metaphor to a virtual, semi-immersive 3D environment. A 3D environment extends the utility of this metaphor by allowing the user to view an entire data set in a single screen. Interrogation of the tree is implemented using 3D input devices. This real-time interrogation of the tree itself provides a quick means by which to qualitatively analyse the hierarchical data. In this paper, we describe the techniques underlying the implementation of such an environment. We conclude by considering the utility of tree metaphors as a basis for the representation of highly dimensional data sets. AVAILABILITY: Arbor3D (source code, a binary executable for SGI IRIX 6.4, Perl parsers, and sample Newick data files) are available via the Internet (http://xian.tamu.edu/Arbor3D/). Arbor3D can be displayed in "CAVE simulator" mode on an SGI workstation screen, or as an interactive virtual environment on a projection workbench. CONTACT: druths@rice.edu; echen@cs.rice.edu; leland@xian.tamu.edu     

Effect of segmentation errors on 3D-to-2D registration of implant models in X-ray images

In many biomedical applications, it is desirable to estimate the three-dimensional (3D) position and orientation (pose) of a metallic rigid object (such as a knee or hip implant) from its projection in a two-dimensional (2D) X-ray image. If the geometry of the object is known, as well as the details of the image formation process, then the pose of the object with respect to the sensor can be determined. A common method for 3D-to-2D registration is to first segment the silhouette contour from the X-ray image; that is, identify all points in the image that belong to the 2D silhouette and not to the background. This segmentation step is then followed by a search for the 3D pose that will best match the observed contour with a predicted contour. Although the silhouette of a metallic object is often clearly visible in an X-ray image, adjacent tissue and occlusions can make the exact location of the silhouette contour difficult to determine in places. Occlusion can occur when another object (such as another implant component) partially blocks the view of the object of interest. In this paper, we argue that common methods for segmentation can produce errors in the location of the 2D contour, and hence errors in the resulting 3D estimate of the pose. We show, on a typical fluoroscopy image of a knee implant component, that interactive and automatic methods for segmentation result in segmented contours that vary significantly. We show how the variability in the 2D contours (quantified by two different metrics) corresponds to variability in the 3D poses. Finally, we illustrate how traditional segmentation methods can fail completely in the (not uncommon) cases of images with occlusion.     

Automatic determination of the handedness of single-particle maps of macromolecules solved by CryoEM

Single-Particle Analysis by Cryo-Electron Microscopy is a well-established technique to elucidate the three-dimensional (3D) structure of biological macromolecules. The orientation of the acquired projection images must be initially estimated without any reference to the final structure. In this step, algorithms may find a mirrored version of all the orientations resulting in a mirrored 3D map. It is as compatible with the acquired images as its unmirrored version from the image processing point of view, only that it is not biologically plausible.In this article, we introduce HaPi (Handedness Pipeline), the first method to automatically determine the hand of electron density maps of macromolecules solved by CryoEM. HaPi is built by training two 3D convolutional neural networks. The first determines α-helices in a map, and the second determines whether the α-helix is left-handed or right-handed. A consensus strategy defines the overall map hand. The pipeline is trained on simulated and experimental data. The handedness can be detected only for maps whose resolution is better than 5 Å. HaPi can identify the hand in 89% of new simulated maps correctly. Moreover, we evaluated all the maps deposited at the Electron Microscopy Data Bank and 11 structures uploaded with the incorrect hand were identified.     

A Simple Geometrical Pattern for the Branching Distribution of the Bronchial Tree, Useful to Estimate Optimality Departures

The design of the bronchial tree has largely been proposed as a model of optimal design from a physical-functional perspective. However, the distributive function of the airway may be more related to a geometrical than a physical problem. The bronchial tree must distribute a three dimensional volume of inspired air on a two dimensional alveolar surface, included in a limited volume. It is thus valid to ask whether an optimal bronchial tree from a physical perspective is also optimum from a geometrical point of view. In this paper we generate a simple geometric model for the branching pattern of the bronchial tree, deducing relationships that permit estimation of the departures from the geometrical optimum of each bifurcation. We also, for comparative purposes, estimate the departures from the physical optimum. From the geometrical assumptions: i) a symmetrical dichotomic fractal design, ii) with minimum volume and iii) maximum dispersion of the terminal points; and several simulations we suggest that the optimality is characterized by a bifurcation angle theta approximately 60 degrees and a length reduction scale gamma = (1/2)(1/3) = 0.7937. We propose distances from the physical and geometrical optimality defined as Euclidean distances from the expected optima. We show how the advanced relationships and the distances can be used to estimate departures from the optimality in bronchographs of four species. We found lower physical and geometrical departures in the distal zone than those of the proximal zones, as well as lower physical than geometrical departures from optimality.     

XMIPP: a new generation of an open-source image processing package for electron microscopy

X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.     

Impact of coronary tortuosity on coronary pressure: numerical simulation study

Background

Coronary tortuosity (CT) is a common coronary angiographic finding. Whether CT leads to an apparent reduction in coronary pressure distal to the tortuous segment of the coronary artery is still unknown. The purpose of this study is to determine the impact of CT on coronary pressure distribution by numerical simulation.

Methods

21 idealized models were created to investigate the influence of coronary tortuosity angle (CTA) and coronary tortuosity number (CTN) on coronary pressure distribution. A 2D incompressible Newtonian flow was assumed and the computational simulation was performed using finite volume method. CTA of 30°, 60°, 90°, 120° and CTN of 0, 1, 2, 3, 4, 5 were discussed under both steady and pulsatile conditions, and the changes of outlet pressure and inlet velocity during the cardiac cycle were considered.

Results

Coronary pressure distribution was affected both by CTA and CTN. We found that the pressure drop between the start and the end of the CT segment decreased with CTA, and the length of the CT segment also declined with CTA. An increase in CTN resulted in an increase in the pressure drop.

Conclusions

Compared to no-CT, CT can results in more decrease of coronary blood pressure in dependence on the severity of tortuosity and severe CT may cause myocardial ischemia.     

K-ary clustering with optimal leaf ordering for gene expression data

MOTIVATION: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical clustering allows a user to view relationships in scales ranging from single genes to large sets of genes, while at the same time providing a global view of the expression data. However, hierarchical clustering is very sensitive to noise, it usually lacks of a method to actually identify distinct clusters, and produces a large number of possible leaf orderings of the hierarchical clustering tree. In this paper we propose a new hierarchical clustering algorithm which reduces susceptibility to noise, permits up to k siblings to be directly related, and provides a single optimal order for the resulting tree. RESULTS: We present an algorithm that efficiently constructs a k-ary tree, where each node can have up to k children, and then optimally orders the leaves of that tree. By combining k clusters at each step our algorithm becomes more robust against noise and missing values. By optimally ordering the leaves of the resulting tree we maintain the pairwise relationships that appear in the original method, without sacrificing the robustness. Our k-ary construction algorithm runs in O(n(3)) regardless of k and our ordering algorithm runs in O(4(k)n(3)). We present several examples that show that our k-ary clustering algorithm achieves results that are superior to the binary tree results in both global presentation and cluster identification. AVAILABILITY: We have implemented the above algorithms in C++ on the Linux operating system.     

A model-based parallel origin and orientation refinement algorithm for cryoTEM and its application to the study of virus structures

We present a model-based parallel algorithm for origin and orientation refinement for 3D reconstruction in cryoTEM. The algorithm is based upon the Projection Theorem of the Fourier Transform. Rather than projecting the current 3D model and searching for the best match between an experimental view and the calculated projections, the algorithm computes the Discrete Fourier Transform (DFT) of each projection and searches for the central section ("cut") of the 3D DFT that best matches the DFT of the projection. Factors that affect the efficiency of a parallel program are first reviewed and then the performance and limitations of the proposed algorithm are discussed. The parallel program that implements this algorithm, called PO(2)R, has been used for the refinement of several virus structures, including those of the 500 Angstroms diameter dengue virus (to 9.5 Angstroms resolution), the 850 Angstroms mammalian reovirus (to better than 7A), and the 1800 Angstroms paramecium bursaria chlorella virus (to 15 Angstroms).     

栽培药材川续断地上部分体积估算的最优样方选择

以贵州省黔南州龙里县内人工栽培的川续断(Dipsacus asperoides)为研究对象, 就如何选择最优样方的面积和数目来估算川续断地上部分体积进行了研究。首先运用球缺模型计算栽培川续断的地上体积, 然后利用基于套状样方的样带调查法研究估算川续断体积时的最优样方面积, 最后利用方差法计算最优采样数目。结果表明: (1)在只考虑相对平均值和相对消耗时, 25 m × 25 m是最优样方面积; 在此基础上进一步考虑到样方的边界效应和单位面积地上体积相对平均值的变化, 得出25 m × 50 m是最优样方面积。(2)如果预计置信度1-α是0.9, 绝对误差限度d是0.12, 总体方差S²按照常规取0.25, 则25 m × 50 m对应的最佳样方数目是25。(3)该研究实际采集了25个25 m × 50 m的样方, 计算后得到整个栽培园地(面积为72696.24 m ²)川续断的总体积90%的近似置信区间为[1909.798 m³, 2214.762 m³]。     

Constructing tree stem form from digitized surface measurements by a programming approach within discrete mathematics

Key message

The main message of this work is the demonstration of possibility of creation of stem shape from digitized points using integer-programming approach. The points are digitized by magnetic motion tracker which in contrast to the laser scanning allows the reconstruction of complete cross-section of stem even in the “hidden (invisible)” part.

Abstract

Three-dimensional information on tree stem form plays an important role in understanding the structure and strength of a standing tree against the forces of wind, snow, and other natural pressure. It also contributes to precision in volume measurement compared to conventional two-dimensional measurement. We investigate approaches for obtaining three-dimensional information of tree stem form from partially organized surface measurements, acquired using a three-dimensional digitizing device (Polhemus FASTRAK^® motion tracking device). We then propose a new programming approach from discrete mathematics to construct tree stem form. Our method is based on an optimal connection of neighbor triangles for surface construction, which is created by locally possible combination of three digitized points on the stem surface. We compare the proposed method to the existing heuristic methods of contour tracing and region growing. Our analysis shows that the proposed method provides a consistent construction of tree stem form, for even stems with extremely irregular structure such as those from bent trees and mangrove trees with unique root spread, while the other methods are incapable for constructing such tree stems.     

Fractal properties of perfusion heterogeneity in optimized arterial trees: a model study

Regional blood flows in the heart muscle are remarkably heterogeneous. It is very likely that the most important factor for this heterogeneity is the metabolic need of the tissue rather than flow dispersion by the branching network of the coronary vasculature. To model the contribution of tissue needs to the observed flow heterogeneities we use arterial trees generated on the computer by constrained constructive optimization. This method allows to prescribe terminal flows as independent boundary conditions, rather than obtaining these flows by the dispersive effects of the tree structure. We study two specific cases: equal terminal flows (model 1) and terminal flows set proportional to the volumes of Voronoi polyhedra used as a model for blood supply regions of terminal segments (model 2). Model 1 predicts, depending on the number Nterm of end-points, fractal dimensions D of perfusion heterogeneities in the range 1.20 to 1.40 and positively correlated nearest-neighbor regional flows, in good agreement with experimental data of the normal heart. Although model 2 yields reasonable terminal flows well approximated by a lognormal distribution, it fails to predict D and nearest-neighbor correlation coefficients r1 of regional flows under normal physiologic conditions: model 2 gives D = 1.69 +/- 0.02 and r1 = -0.18 +/- 0.03 (n = 5), independent of Nterm and consistent with experimental data observed under coronary stenosis and under the reduction of coronary perfusion pressure. In conclusion, flow heterogeneity can be modeled by terminal positions compatible with an existing tree structure without resorting to the flow-dispersive effects of a specific branching tree model to assign terminal flows.     

Statistical learning methods as a preprocessing step for survival analysis: evaluation of concept using lung cancer data

Background

Despite its superb lateral resolution, flat-panel-detector (FPD) based tomosynthesis suffers from low contrast and inter-plane artifacts caused by incomplete cancellation of the projection components stemming from outside the focal plane. The incomplete cancellation of the projection components, mostly due to the limited scan angle in the conventional tomosynthesis scan geometry, often makes the image contrast too low to differentiate the malignant tissues from the background tissues with confidence.

Methods

In this paper, we propose a new method to suppress the inter-plane artifacts in FPD-based tomosynthesis. If 3D whole volume CT images are available before the tomosynthesis scan, the CT image data can be incorporated into the tomosynthesis image reconstruction to suppress the inter-plane artifacts, hence, improving the image contrast. In the proposed technique, the projection components stemming from outside the region-of-interest (ROI) are subtracted from the measured tomosynthesis projection data to suppress the inter-plane artifacts. The projection components stemming from outside the ROI are calculated from the 3D whole volume CT images which usually have lower lateral resolution than the tomosynthesis images. The tomosynthesis images are reconstructed from the subtracted projection data which account for the x-ray attenuation through the ROI. After verifying the proposed method by simulation, we have performed both CT scan and tomosynthesis scan on a phantom and a sacrificed rat using a FPD-based micro-CT.

Results

We have measured contrast-to-noise ratio (CNR) from the tomosynthesis images which is an indicator of the residual inter-plane artifacts on the focal-plane image. In both cases of the simulation and experimental imaging studies of the contrast evaluating phantom, CNRs have been significantly improved by the proposed method. In the rat imaging also, we have observed better visual contrast from the tomosynthesis images reconstructed by the proposed method.

Conclusions

The proposed tomosynthesis technique can improve image contrast with aids of 3D whole volume CT images. Even though local tomosynthesis needs extra 3D CT scanning, it may find clinical applications in special situations in which extra 3D CT scan is already available or allowed.     

Analysis of the factors that stabilize a designed two-stranded antiparallel beta-sheet

Autonomously folding beta-hairpins (two-strand antiparallel beta-sheets) have become increasingly valuable tools for probing the forces that control peptide and protein conformational preferences. We examine the effects of variations in sequence and solvent on the stability of a previously designed 12-residue peptide (1). This peptide adopts a beta-hairpin conformation containing a two-residue loop (D-Pro-Gly) and a four-residue interstrand sidechain cluster that is observed in the natural protein GB1. We show that the conformational propensity of the loop segment plays an important role in beta-hairpin stability by comparing 1 with (D)P--> N mutant 2. In addition, we show that the sidechain cluster contributes both to conformational stability and to folding cooperativity by comparing 1 with mutant 3, in which two of the four cluster residues have been changed to serine. Thermodynamic analysis suggests that the high loop-forming propensity of the (D)PG segment decreases the entropic cost of beta-hairpin formation relative to the more flexible NG segment, but that the conformational rigidity of (D)PG may prevent optimal contacts between the sidechains of the GB1-derived cluster. The enthalpic favorability of folding in these designed beta-hairpins suggests that they are excellent scaffolds for studying the fundamental mechanisms by which amino acid sidechains interact with one another in folded proteins.     

Recognition of 3D flexible objects by GRBF

Recently Poggio and Edelman have shown that for each object there exists a smooth mapping from an arbitrary view to its standard view and that the mapping can be learned from a sparse data set. In this paper, we extend their scheme further to deal with 3D flexible objects. We show the mappings from an arbitrary view to the standard view, and its rotated view can be synthesized even for a flexible object by learning from examples. To classify 3D flexible objects, we propose two methods, which do not require any special knowledge on the target flexible objects. They are: (1) learning the characteristic function of the object and (2) learning the view-change transformation. We show their performance by computer simulations. Received: 1 March 1993/Accepted in revised form: 7 June 1993     

GPU-Accelerated Framework for Intracoronary Optical Coherence Tomography Imaging at the Push of a Button

Frequency domain optical coherence tomography (FD-OCT) has become one of the important clinical tools for intracoronary imaging to diagnose and monitor coronary artery disease, which has been one of the leading causes of death. To help more accurate diagnosis and monitoring of the disease, many researchers have recently worked on visualization of various coronary microscopic features including stent struts by constructing three-dimensional (3D) volumetric rendering from series of cross-sectional intracoronary FD-OCT images. In this paper, we present the first, to our knowledge, "push-of-a-button" graphics processing unit (GPU)-accelerated framework for intracoronary OCT imaging. Our framework visualizes 3D microstructures of the vessel wall with stent struts from raw binary OCT data acquired by the system digitizer as one seamless process. The framework reports the state-of-the-art performance; from raw OCT data, it takes 4.7 seconds to provide 3D visualization of a 5-cm-long coronary artery (of size 1600 samples x 1024 A-lines x 260 frames) with stent struts and detection of malapposition automatically at the single push of a button.     

Development of a 3D optical scanner for evaluating patient-specific dose distributions

PurposeThis paper describes the hardware and software characteristics of a 3D optical scanner (P3DS) developed in-house. The P3DS consists of an LED light source, diffuse screen, step motor, CCD camera, and scanner management software with 3D reconstructed software.Materials and methodWe performed optical simulation, 2D and 3D reconstruction image testing, and pre-clinical testing for the P3DS. We developed the optical scanner with three key characteristics in mind. First, we developed a continuous scanning method to expand possible clinical applications. Second, we manufactured a collimator to improve image quality by reducing scattering from the light source. Third, we developed an optical scanner with changeable camera positioning to enable acquisition of optimal images according to the size of the gel dosimeter.ResultsWe confirmed ray-tracing in P3DS with optic simulation and found that 2D projection and 3D reconstructed images were qualitatively similar to the phantom images. For pre-clinical tests, the dose distribution and profile showed good agreement among RTP, optical CT, and external beam radiotherapy film data for the axial and coronal views. The P3DS has shown that it can scan and reconstruct for evaluation of the gel dosimeter within 1 min. We confirmed that the P3DS system is a useful tool for the measurement of 3D dose distributions for 3D radiation therapy QA. Further experiments are needed to investigate quantitative analysis for 3D dose distribution.     

Comparative evaluation of autofocus algorithms for a real-time system for automatic detection of Mycobacterium tuberculosis

Microscopy images must be acquired at the optimal focal plane for the objects of interest in a scene. Although manual focusing is a standard task for a trained observer, automatic systems often fail to properly find the focal plane under different microscope imaging modalities such as bright field microscopy or phase contrast microscopy. This article assesses several autofocus algorithms applied in the study of fluorescence-labeled tuberculosis bacteria. The goal of this work was to find the optimal algorithm in order to build an automatic real-time system for diagnosing sputum smear samples, where both accuracy and computational time are important. We analyzed 13 focusing methods, ranging from well-known algorithms to the most recently proposed functions. We took into consideration criteria that are inherent to the autofocus function, such as accuracy, computational cost, and robustness to noise and to illumination changes. We also analyzed the additional benefit provided by preprocessing techniques based on morphological operators and image projection profiling.     

Using optical full-field measurement based on digital image correlation to measure strain on a tree subjected to mechanical load

Key message

The results indicate the usability of DIC technique in tree biomechanics is advantageous compared to standard procedure since it reveals the induced strain in full-field way, accurately and noninvasively.

Abstract

The goal of this study was to analyze and measure the displacement and strain response behavior of the tree (Juglans regia L.) subjected to a mechanical load. The analysis addresses issues of tree biomechanics that call for a high-quality deformation data measured on trees’ surfaces in a noninvasive way. For these purposes, the 3D digital image correlation (3D-DIC) was proposed and tested against standard extensometers. The measured tree was subjected to a bending by a pulling test to induce strain on the tree stem. The DIC technique successfully provided strain field on a tree bark despite its highly complicated geometry. Vertical averaging of the strain field obtained by the DIC revealed that a tree stem behaves according to beam theory exhibiting compression and tension parts. The absolute values of strain measured by both techniques agree with each other in order of magnitude, DIC returning lower values (approximately 21.1 and 40.8 % for compression and tension part, respectively). The results reveal necessity for future study of stress/strain transfer from xylem to bark. The sensitivity analysis shows that the computed strain highly depends on subset size used in the DIC computation. Based on the projection error and strain, the optimal subset size was found out to be between 21 and 31 pixels. The measurement proved that the DIC method can be successfully used in tree biomechanics. In general, our results and the character of DIC technique that allows testing at different scales depending on imaging methods indicate its big potential in plant biomechanics.     

The effect of overabundant projection directions on 3D reconstruction algorithms

The experimental process of collecting images from macromolecules in an electron microscope is such that it does not allow for prior specification of the angular distribution of the projection images. As a consequence, an uneven distribution of projection directions may occur. Concerns have been raised recently about the behavior of 3D reconstruction algorithms for the case of unevenly distributed projections. It has been illustrated on experimental data that in the case of a heavily uneven distribution of projection directions some algorithms tend to elongate the reconstructed volumes along the overloaded direction so much as to make a quantitative biological analysis impossible. In answer to these concerns we have developed a strategy for quantitative comparison and optimization of 3D reconstruction algorithms. We apply this strategy to quantitatively analyze algebraic reconstruction techniques (ART) with blobs, simultaneous iterative reconstruction techniques (SIRT) with voxels, and weighted backprojection (WBP). We show that the elongation artifacts that had been previously reported can be strongly reduced. With our specific choices for the free parameters of the three algorithms, WBP reconstructions tend to be inferior to those obtained with either SIRT or ART and the results obtained with ART are comparable to those with SIRT, but at a very small fraction of the computational cost of SIRT.