Volumetric Visualization Research Articles

ZeVis: A Visual Analytics System for Exploration of a Larval Zebrafish Brain in Serial-Section Electron Microscopy Images

The automation and improvement of nano-scale electron microscopy imaging technologies have expanded a push in neuroscience to understand brain circuits at the scale of individual cells and their connections. Most of this research effort, called `connectomics', has been devoted to handling, processing, and segmenting large-scale image data to reconstruct graphs of neuronal connectivity. However, connectomics datasets contain a wealth of high-resolution information about the brain that could be leveraged to understand its detailed anatomy beyond just the connections between neurons, such as cell morphologies and distributions. This study introduces a novel visualization system, ZeVis, for the interactive exploration of a whole larval zebrafish brain using a terabyte-scale serial-section electron microscopy dataset. ZeVis combines 2D cross-sectional views and 3D volumetric visualizations of the input serial-section electron microscopy data with overlaid segmentation results to facilitate the analyses of various brain structures and their interpretations. The system also provides a graph-based data processing interface to generate subsets of feature segmentation data easily. The segmentation data can be filtered by morphological features or anatomical constraints, allowing statistical analysis and comparisons across regions. We applied ZeVis to actual data of a terabyte-scale whole-brain larval zebrafish and analyzed cell nucleus distributions in several anatomical regions.

Spherical Visualization Database Prototype for Education and Scientific Research: Designing and Managing

The article describes methods for spherical visualizing of data as global geophysical, environmental, atmospheric processes on the surface of planets and different kinds of processes on the surface of spherical bodies. Such data can be demonstrated through virtual globes and spherical screens. Volumetric visualization significantly increases the degree of visibility, comprehension and assimilation of the demonstrated content and may be used in the scientific and educational process. The main goal of this research is to develop database requirements for spherical visualization. The requirements are based on the modern educational and science research representation approaches. The following tasks have been formed and accomplished: a strict classification of data; a convenient way to interact at the stage of adding data to the database and analyzing; their representativeness; introduction of additional data classifications; the possibility of individual user navigation and a high degree of inter-activity. For the proposed model, the basic functions of the database management system are described. Requirements to a basic hierarchical data model were substantiated. The main object of hierarchical data model is a spherical Slide representing a separate topic of particular discipline. The superstructure is used above the hierarchical model in the form of an individual route map representing a directory with links to the main database.

MASK GENERATOR FOR ORTHOGONAL REGULAR MESH

Existing mesh generators are focused mainly on obtaining non-orthogonal irregular grids designed to describe the curved boundaries of streamlined bodies. However, the thickening of the grid leads to an increase in the calculation time, and the non-conformity of the grid leads to unphysical effects. The software package (SP) developed by the authors for the simulation of gas-thermodynamic processes is oriented toward a much simpler description of the geometry, i. e., uses a different principle of increasing the smoothness of the solution in places with a complex surface structure. This principle consists in superimposing on the flow such sources of momentum and energy, which are equivalent in their effect on the flow to the interaction with the solid wall. SP contains a mask generator of an orthogonal regular grid. The initial data for building the mask is a 3D model created in any CAD application, which is saved in the STL format and placed in the project directory. Each cell contains information about the presence of a three-dimensional solid, the permeability of each face of the hexahedron, and the direction of the normal vector to the streamlined surface. In this regard, the generator creates three types of masks: volumetric, surface full and incomplete permeability, as well as a mask of guiding cosines. To obtain a volume (solid) mask from the center of each cell along the axes, a straight line is drawn and its intersection is checked with each triangle approximating the surface of the body under study. An odd number of intersections of triangles and a straight line indicates the presence of a volume mask in the cells. A surface impermeable mask is formed in three directions at the free cell section and the occupied volume mask. If it is necessary to introduce a semipermeable mask, its localization and measure are assigned by the user. The mask of the guiding cosines is assigned in the cell, which is adjacent to the surface impermeable mask. The values of the guiding cosines are assigned equal to the corresponding values of the nearby triangle approximating the surface of the 3D model. The generated masks are formed as separate files. A SolidWorks application has been developed that allows for volumetric visualization. In the decisive program, the information about the presence of the volume mask is used as follows: the volume mask is excluded from the solution area, self-similar problems are solved near the surface, and if there are guiding properties, an isentropic flow rotation is performed.

An experimental study on volumetric visualization of black oil reservoir models

Volume rendering techniques are essential to inspect volume data. In this work, we consider volume rendering for unstructured meshes. We focus on the visualization of black oil reservoir simulation models, represented by irregular hexahedral meshes with geometry distortions and discontinuities. We conduct an experimental study comparing three different strategies to compute the volume integration. The first strategy resamples the model in a regular grid; the second linearizes the model geometry and the variation of the scalar field within a hexahedron cell; the third uses an accurate evaluation of the scalar field at each sample. We compare performance and image quality delivered by each strategy by running a set of experiments with different models. We also investigate the gain in perception applying directional ambient occlusion shading effects. All strategies were entirely implemented on the graphics card.

Simultaneous in-situ measurements of gas temperature and pyrolysis of biomass smoldering via X-ray computed tomography

In-situ X-ray computed tomography (XCT) imaging is employed to investigate the smoldering dynamics of biomass at the sub-millimeter scale. This technique provides simultaneous and spatially-resolved information about the gas temperature and the biomass density, thereby enabling tracking of the pyrolysis and char oxidation fronts. To achieve well-controlled heating and flow conditioning, oak biomass samples are instrumented above a diffusion flame inside a tube, with total oxygen concentrations of 6% and 11% per volume. Experiments are performed on a laboratory XCT system. The flow is diluted with Kr to increase X-ray attenuation in the gas phase thus allowing for simultaneous 3D measurements of sample density and surrounding temperature. XCT scans are acquired every 90 s at a spatial resolution of 135 µm. The high spatial resolution enables the volumetric visualization of the smoldering process that is associated with pyrolysis and char oxidation. These measurements show how the grain structure affects flame stabilization and induces fingering of the pyrolysis front, while crack formation accelerates the char oxidation locally. Evaluations of the sample mass via XCT are compared with load cell measurements, showing good agreement. A low-order model is developed to evaluate the propagation speeds of pyrolysis and oxidation fronts from the X-ray data over time, and comparisons are made with the surface recess speed.

INTRAOPERATIVE OPTICAL COHERENCE TOMOGRAPHY (OCT) GUIDANCE OF VITREORETINAL SURGERY

Background: Multiple studies have described the utility of intraoperative spectral-domain OCT (SD-OCT) with two dimensional (2D) B-scan imaging in the management of numerous vitreoretinal disorders including macular holes, vitreomacular traction disorders, epiretinal membranes and retinal detachment. Some of these studies also described post-processing of the 2D B-scans to obtain 3D images. With the advancement of intraoperative OCT technology, live volumetric (4D, i.e. 3D over time) visualization of different anterior and posterior segment surgeries has been described in recent studies using intraoperative swept-source microscope-integrated OCT (SS-MIOCT). Our study aims to explore the potential utility of SS-MIOCT during vitrectomy for complications of proliferative diabetic retinopathy. Aim of the work: To evaluate the use of live volumetric (4D) intraoperative swept-source microscope-integrated OCT (SS-MIOCT) in vitrectomy for proliferative diabetic retinopathy (PDR) complications.Patient and Methods: In this prospective study, we analyzed a subgroup of cases with PDR complications that required vitrectomy and that were imaged by the research SS-MIOCT system. In near real time, images were displayed in stereo heads-up display facilitating intraoperative surgeon feedback. Postoperative review included scoring image quality, identifying different diabetic retinopathy (DR)-associated pathologies and reviewing the intraoperatively documented surgeon feedback.Results: Twenty eyes were included. Indications for vitrectomy were tractional retinal detachment (TRD, 16 eyes), combined tractional-rhegmatogenous retinal detachment (2 eyes) and vitreous hemorrhage (2 eyes). Useful, good quality 2D (B-scans) and 4D images were obtained in 16/20 eyes (80%). In these eyes, multiple DR pathologies could be imaged. SS-MIOCT provided surgical guidance, e.g. in identifying dissection planes under fibrovascular membranes, and in determining residual membranes and traction that would benefit from additional peeling. In 4/20 eyes (20%) acceptable images were captured, but they were not useful due to high TRD elevation which was challenging for imaging.Conclusion: SS-MIOCT can provide important guidance during surgery for PDR complications through intraoperative identification of different pathologies and facilitation of intraoperative decision making.

Sub-60-nm 3D super-resolution imaging via saturated I5S

To investigate fine structure in biological samples, over recent decades, super-resolution methods in light microscopy have been honed. Here, we report a technique integrating nonlinearity arising from fluorophore saturation with a new version of I5S to produce quasi-isotropic three-dimensional (3D) wide-field (WF) super-resolution imaging. This extended technique—saturated I5S (SI5S)—promises lateral and axial resolutions below 60 nm when the illuminating light intensity approaches the saturation threshold in simulation. A linear processing algorithm is used to acquire SI5S image reconstructions, and comparisons with 3D structured illumination microscopy (3D-SIM) and I5S show that a substantial improvement in resolution can be realized using SI5S. The notable improvement in 3D resolution means that SI5S could facilitate volumetric visualization of intracellular fine structure within biological samples.

Three-dimensional visualization of opacifications in the murine crystalline lens by in vivo optical coherence tomography.

Diagnostic classification techniques used to diagnose cataracts, the world's leading cause of blindness, are currently based on subjective methods. Here, we present optical coherence tomography as a noninvasive tool for volumetric visualization of lesions formed in the crystalline lens. A custom-made swept-source optical coherence tomography (SS-OCT) system was utilized to investigate the murine crystalline lens. In addition to imaging cataractous lesions in aged wildtype mice, we studied the structure and shape of cataracts in a mouse model of Alzheimer's disease. Hyperscattering opacifications in the crystalline lens were observed in both groups. Post mortem histological analysis were performed to correlate findings in the anterior and posterior part of the lens to 3D OCT in vivo imaging. Our results showcase the capability of OCT to rapidly visualize cataractous lesions in the murine lens and suggest that OCT might be a valuable tool that provides additional insight for preclinical studies of cataract formation.

Interactive synthesis and visualisation of vast areas with geometrically diverse trees

This paper summarises a Doctoral Thesis which proposes a new approach for large- scale forest visualisation with geometrically diverse trees. The main contribution of the proposed method is an interactive visualisation of numerous trees without generating geometric data in advance, which is achieved by a new method for on-the-fly tree skeleton synthesis with a specific level of detail, and by a new procedural volumetric tree crown visualisation which avoids geometry formation altogether. The proposed method enables visualisation of forests with millions of trees, thus allowing rendering more trees than geometry-based visualisation methods.

Fully automated segmentation of left ventricular scar from 3D late gadolinium enhancement magnetic resonance imaging using a cascaded multi-planar U-Net (CMPU-Net).

Three-dimensional (3D) late gadolinium enhancement magnetic resonance (LGE-MR) imaging enables the quantification of myocardial scar at high resolution with unprecedented volumetric visualization. Automated segmentation of myocardial scar is critical for the potential clinical translation of this technique given the number of tomographic images acquired. In this paper, we describe the development of cascaded multi-planar U-Net (CMPU-Net) to efficiently segment the boundary of the left ventricle (LV) myocardium and scar from 3D LGE-MR images. In this approach, two subnets, each containing three U-Nets, were cascaded to first segment the LV myocardium and then segment the scar within the presegmented LV myocardium. The U-Nets were trained separately using two-dimensional (2D) slices extracted from axial, sagittal, and coronal slices of 3D LGE-MR images. We used 3D LGE-MR images from 34 subjects with chronic ischemic cardiomyopathy. The U-Nets were trained using 8430 slices, extracted in three orthogonal directions from 18 images. In the testing phase, the outputs of U-Nets of each subnet were combined using the majority voting system for final label prediction of each voxel in the image. The developed method was tested for accuracy by comparing its results to manual segmentations of LV myocardium and LV scar from 7250 slices extracted from 16 3D LGE-MR images. Our method was also compared to numerous alternative methods based on machine learning, energy minimization, and intensity-thresholds. Our algorithm reported a mean dice similarity coefficient (DSC), absolute volume difference (AVD), and Hausdorff distance (HD) of 85.14%±3.36%, 43.72±27.18cm3 , and 19.21±4.74mm for determining the boundaries of LV myocardium from LGE-MR images. Our method also yielded a mean DSC, AVD, and HD of 88.61%±2.54%, 9.33±7.24cm3 , and 17.04±9.93mm for LV scar segmentation on the unobserved test dataset. Our method significantly outperformed the alternative techniques in segmentation accuracy (P<0.05). The CMPU-Net method provided fully automated segmentation of LV scar from 3D LGE-MR images and outperformed the alternative techniques.

Shadow extension for ray casting enhances volumetric visualization in real-time 4D-OCT

Progress in swept source laser technology and graphics processing unit (GPU) have led to the realization of real time four-dimensional optical coherence tomography (4D-OCT). Various rendering algorithms have been introduced for volumetric OCT leading to enhanced spatial comprehension. These algorithms still cannot provide sufficient visual realism. Shadowing is one of the advanced rendering techniques used to provide realistic spatial comprehension for objects in space. We developed and implemented a shadow extension for ray casting for real-time 4D-OCT, using both a swept source (SS)-OCT and spectral domain (SD)-OCT. Our technique builds upon previously developed ray casting techniques, adding an additional shadowing computation. The shadow extension for ray casting yields greater three-dimensionality of objects via self-shadowing, and also improves depth perception of objects. We imaged a beveled needle hovering over a flat surface and found that the positioning of a beveled needle can be accurately determined in relation to the environment. The shadowing algorithm was implemented using texture memory of the GPU, which realized video rendering rate. The complete processing pipeline requires 47 ms with a volume size of 1024 × 256 × 100, with a 100 kHz sweep rate SS-OCT. This new algorithm may enhance interactive surgical guidance during ophthalmic microsurgery.

Large-scale volumetric flow visualization of the unsteady wake of a flapping-wing micro air vehicle

The objective of this experimental investigation is the volumetric visualization of the near wake topology of the vortex structures generated by a flapping-wing micro air vehicle. To achieve the required visualization domain (which in the present experiments amounts to a size of 60,000 cm3), use is made of robotic particle image velocimetry, which implements coaxial illumination and imaging in combination with the use of helium-filled soap bubbles as tracer particles. Particle trajectories are determined via Lagrangian particle tracking and information of different phases throughout the flapping cycle is obtained by means of a phase-averaging procedure applied to the particle tracks. Experiments have been performed at different settings (flow speed, flapping frequency, and body angle) that are representative of actual flight conditions, and the effect of reduced frequency on the wake topology is investigated. Furthermore, experiments have been carried out in both tethered and free-flight conditions, allowing an unprecedented comparison between the aerodynamics of the two conditions.Graphic abstract

Rotational Three-dimensional OCTA: a Notable New Imaging Tool to Characterize Type 3 Macular Neovascularization

This study explored whether rotational three-dimensional (3D) visualization of optical coherence tomography angiography (OCTA) volume data may yield valuable information regarding type 3 macular neovascularization (MNV). In this retrospective, cross-sectional study, we collected data from 15 eyes (13 patients) with treatment-naïve type 3 MNV in their post-nascent stage and age-related macular degeneration (AMD). Subjects were imaged with the SS-OCT system (PLEX Elite 9000, Carl Zeiss Meditec Inc., Dublin, CA, USA). The OCTA volume data were processed with a prototype volume projection removal algorithm and then analyzed using volumetric visualization techniques in order to obtain a 3D visualization of the region occupied by type 3 MNV. The two-dimensional and three-dimensional OCTA images were investigated. Mean ± SD age was 75.1 ± 7.4 years. BCVA was 0.42 ± 0.21 LogMAR in the study eyes. Considering the cohort of analyzed eyes, on rotational 3D OCTA images, a total of 35 neovascular lesions (vs 22 lesions detected on 2D OCTA images) rising from the deep vascular complex and variably spanning the outer retinal layers and eventually reaching the RPE/sub-RPE space were detected. Nine of 35 lesions had a saccular shape, while the remaining cases had a filiform shape. On rotational 3D OCTA images, these lesions were inclined on the three planes, instead of perpendicular to the RPE/Bruch’s membrane. In conclusion, this study used an algorithm to obtain rotational three-dimensional visualization of type 3 MNV. This approach seems to increase the detection rate for these lesions and to be useful to offer new insight into type 3 MNV.

T1 and T2* mapping of the human quadriceps and patellar tendons using ultra-short echo-time (UTE) imaging and bivariate relaxation parameter-based volumetric visualization

Quantification of magnetic resonance (MR)-based relaxation parameters of tendons and ligaments is challenging due to their very short transverse relaxation times, requiring application of ultra-short echo-time (UTE) imaging sequences. We quantify both T1 and T2* in the quadriceps and patellar tendons of healthy volunteers at a field strength of 3 T and visualize the results based on 3D segmentation by using bivariate histogram analysis. We applied a 3D ultra-short echo-time imaging sequence with either variable repetition times (VTR) or variable flip angles (VFA) for T1 quantification in combination with multi-echo acquisition for extracting T2*. The values of both relaxation parameters were subsequently binned for bivariate histogram analysis and corresponding cluster identification, which were subsequently visualized. Based on manually-drawn regions of interest in the tendons on the relaxation parameter maps, T1 and T2* boundaries were selected in the bivariate histogram to segment the quadriceps and patellar tendons and visualize the relaxation times by 3D volumetric rendering. Segmentation of bone marrow, fat, muscle and tendons was successfully performed based on the bivariate histogram analysis. Based on the segmentation results mean T2* relaxation times, over the entire tendon volumes averaged over all subjects, were 1.8 ms ± 0.1 ms and 1.4 ms ± 0.2 ms for the patellar and quadriceps tendons, respectively. The mean T1 value of the patellar tendon, averaged over all subjects, was 527 ms ± 42 ms and 476 ms ± 40 ms for the VFA and VTR acquisitions, respectively. The quadriceps tendon had higher mean T1 values of 662 ms ± 97 ms (VFA method) and 637 ms ± 40 ms (VTR method) compared to the patellar tendon. 3D volumetric visualization of the relaxation times revealed that T1 values are not constant over the volume of both tendons, but vary locally. This work provided additional data to build upon the scarce literature available on relaxation times in the quadriceps and patellar tendons. We were able to segment both tendons and to visualize the relaxation parameter distributions over the entire tendon volumes.

Controlling for Artifacts in Widefield Optical Coherence Tomography Angiography Measurements of Non-Perfusion Area

The recent clinical adoption of optical coherence tomography (OCT) angiography (OCTA) has enabled non-invasive, volumetric visualization of ocular vasculature at micron-scale resolutions. Initially limited to 3 mm × 3 mm and 6 mm × 6 mm fields-of-view (FOV), commercial OCTA systems now offer 12 mm × 12 mm, or larger, imaging fields. While larger FOVs promise a more complete visualization of retinal disease, they also introduce new challenges to the accurate and reliable interpretation of OCTA data. In particular, because of vignetting, wide-field imaging increases occurrence of low-OCT-signal artifacts, which leads to thresholding and/or segmentation artifacts, complicating OCTA analysis. This study presents theoretical and case-based descriptions of the causes and effects of low-OCT-signal artifacts. Through these descriptions, we demonstrate that OCTA data interpretation can be ambiguous if performed without consulting corresponding OCT data. Furthermore, using wide-field non-perfusion analysis in diabetic retinopathy as a model widefield OCTA usage-case, we show how qualitative and quantitative analysis can be confounded by low-OCT-signal artifacts. Based on these results, we suggest methods and best-practices for preventing and managing low-OCT-signal artifacts, thereby reducing errors in OCTA quantitative analysis of non-perfusion and improving reproducibility. These methods promise to be especially important for longitudinal studies detecting progression and response to therapy.

A method for volumetric visualization of temperature distribution: three-dimensional meshed infrared thermography

In this study, a method called three-dimensional meshed infrared thermography (3D MIT) was developed to visualize the volumetric temperature of air using an infrared camera. The main operating principle of the proposed method is to image the spheres using an infrared camera and processing the images with computer software to obtain the volumetric temperature distribution. For the correct implementation of the method, an equation is proposed to determine the distance between the thermal target and the measurement target placed in the flow to be examined. The proposed method was compared with conventional measurement screen methods, namely those using a plane target and a high-porosity target, via particle image velocimetry (PIV) in terms of flow effects. The temperature measurement capability of the proposed method is presented in comparison with the results of thermocouple and conventional measurement screen-based measurements recorded using a jet flow. In addition, the volumetric temperature isosurfaces obtained via the 3D MIT method of a jet flow were compared with the volumetric velocity isosurfaces obtained via the PIV method in terms of the flow structure.

Handheld Photoacoustic Imager for Theranostics in 3D.

A handheld approach to 3D photoacoustic imaging is essential in clinical applications. To this end, we develop a 3D handheld photoacoustic imager for dynamic (temporally and spatially) volumetric visualization. In this 3D imager, the optically transmitting part and the acoustically receiving part are integrated into a single handheld probe with a compact size about 160 mm ×64 mm ×40 mm. Besides, a dedicated imaging reconstruction algorithm for the heterogeneous medium is developed based on the phase-shift migration method in the frequency domain, which deals well with the stratified condition in the designed system. Dynamic 3D imaging supporting flexible handheld operation is demonstrated with needle biopsy and in vitro temperature measurement for photothermal therapy. The development of such a 3D handheld photoacoustic system paves the way for compact and handheld-operating implementations, and its further clinical exploration is promising.

3-Dimensional Optical Clearing and Imaging of Pruritic Atopic Dermatitis and Psoriasis Skin Reveals Downregulation of Epidermal Innervation

3-Dimensional Optical Clearing and Imaging of Pruritic Atopic Dermatitis and Psoriasis Skin Reveals Downregulation of Epidermal Innervation

Interactive obstruction-free lensing for volumetric data visualization.

Occlusion is an issue in volumetric visualization as it prevents direct visualization of the region of interest. While many techniques such as transfer functions, volume segmentation or view distortion have been developed to address this, there is still room for improvement to better support the understanding of objects' vicinity. However, most existing Focus+Context fail to solve partial occlusion in datasets where the target and the occluder are very similar density-wise. For these reasons, we investigate a new technique which maintains the general structure of the investigated volumetric dataset while addressing occlusion issues. With our technique, the user interactively defines an area of interest where an occluded region or object is partially visible. Then our lens starts pushing at its border occluding objects, thus revealing hidden volumetric data. Next, the lens is modified with an extended field of view (fish-eye deformation) to better see the vicinity of the selected region. Finally, the user can freely explore the surroundings of the area under investigation within the lens. To provide real-time exploration, we implemented our lens using a GPU accelerated ray-casting framework to handle ray deformations, local lighting, and local viewpoint manipulation. We illustrate our technique with five application scenarios in baggage inspection, 3D fluid flow visualization, chest radiology, air traffic planning, and DTI fiber exploration.

In-situ computer tomography for analyzing the effect of voids on the damage behavior of composite materials

Due to their high specific stiffness and strength composites are ideally suited for applications in machine building, vehicle constructions, wind power technology and aviation. In the manufacture of composite structures voids are an unavoidable fact. Several non-destructive techniques are potentially able of detecting defects, but only the exact knowledge of the effects of defects on the mechanical properties allows the definition of thresholds for the purpose of quality management. Here, an experimental program for characterizing the effect of voids on the damage behaviour is presented. Flat specimens with glass fibre non-crimp fabric reinforcement and epoxy matrix (GF-NCF/EP) are produced using vacuum assisted resin transfer moulding. By means of a specific adjustment of the process parameters, test specimens with three different void contents are produced and compared. For detailed analysis of damage evolution in the vicinity of voids, in-situ computed tomography (in-situ CT) is used, for the volumetric visualization of the material during tensile loading.