Virtual and augmented reality for biomedical applications.

3D visualization technologies such as virtual reality (VR), augmented reality (AR), and mixed reality (MR) have gained popularity in the recent decade. Digital extended reality (XR) technologies have been adopted in various domains ranging from entertainment to education because of their accessibility and affordability. XR modalities create an immersive experience, enabling 3D visualization of the content without a conventional 2D display constraint. Here, we provide a perspective on XR in current biomedical applications and demonstrate case studies using cell biology concepts, multiplexed proteomics images, surgical data for heart operations, and cardiac 3D models. Emerging challenges associated with XR technologies in the context of adverse health effects and a cost comparison of distinct platforms are discussed. The presented XR platforms will be useful for biomedical education, medical training, surgical guidance, and molecular data visualization to enhance trainees' and students' learning, medical operation accuracy, and the comprehensibility of complex biological systems.

A 3D Bioprinted In Vitro Model of Pulmonary Artery Atresia to Evaluate Endothelial Cell Response to Microenvironment.

Vascular atresia are often treated via transcatheter recanalization or surgical vascular anastomosis due to congenital malformations or coronary occlusions. The cellular response to vascular anastomosis or recanalization is, however, largely unknown and current techniques rely on restoration rather than optimization of flow into the atretic arteries. An improved understanding of cellular response post anastomosis may result in reduced restenosis. Here, an in vitro platform is used to model anastomosis in pulmonary arteries (PAs) and for procedural planning to reduce vascular restenosis. Bifurcated PAs are bioprinted within 3D hydrogel constructs to simulate a reestablished intervascular connection. The PA models are seeded with human endothelial cells and perfused at physiological flow rate to form endothelium. Particle image velocimetry and computational fluid dynamics modeling show close agreement in quantifying flow velocity and wall shear stress within the bioprinted arteries. These data are used to identify regions with greatest levels of shear stress alterations, prone to stenosis. Vascular geometry and flow hemodynamics significantly affect endothelial cell viability, proliferation, alignment, microcapillary formation, and metabolic bioprofiles. These integrated in vitro-in silico methods establish a unique platform to study complex cardiovascular diseases and can lead to direct clinical improvements in surgical planning for diseases of disturbed flow.

Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks.

Comorbidities such as anemia or hypertension and physiological factors related to exertion can influence a patient's hemodynamics and increase the severity of many cardiovascular diseases. Observing and quantifying associations between these factors and hemodynamics can be difficult due to the multitude of co-existing conditions and blood flow parameters in real patient data. Machine learning-driven, physics-based simulations provide a means to understand how potentially correlated conditions may affect a particular patient. Here, we use a combination of machine learning and massively parallel computing to predict the effects of physiological factors on hemodynamics in patients with coarctation of the aorta. We first validated blood flow simulations against in vitro measurements in 3D-printed phantoms representing the patient's vasculature. We then investigated the effects of varying the degree of stenosis, blood flow rate, and viscosity on two diagnostic metrics - pressure gradient across the stenosis (ΔP) and wall shear stress (WSS) - by performing the largest simulation study to date of coarctation of the aorta (over 70 million compute hours). Using machine learning models trained on data from the simulations and validated on two independent datasets, we developed a framework to identify the minimal training set required to build a predictive model on a per-patient basis. We then used this model to accurately predict ΔP (mean absolute error within 1.18 mmHg) and WSS (mean absolute error within 0.99 Pa) for patients with this disease.

Hemodynamic and morphological characteristics of a growing cerebral aneurysm.

The growth of cerebral aneurysms is linked to local hemodynamic conditions, but the driving mechanisms of the growth are poorly understood. The goal of this study was to examine the association between intraaneurysmal hemodynamic features and areas of aneurysm growth, to present the key hemodynamic parameters essential for an accurate prediction of the growth, and to gain a deeper understanding of the underlying mechanisms. Patient-specific images of a growing cerebral aneurysm in 3 different growth stages acquired over a period of 40 months were segmented and reconstructed. A unique aspect of this patient-specific case study was that while one side of the aneurysm stayed stable, the other side continued to grow. This unique case enabled the authors to examine their aims in the same patient with parent and daughter arteries under the same inlet flow conditions. Pulsatile flow in the aneurysm models was simulated using computational fluid dynamics and was validated with in vitro experiments using particle image velocimetry measurements. The authors' detailed analysis of intrasaccular hemodynamics linked the growing regions of aneurysms to flow instabilities and complex vortex structures. Extremely low velocities were observed at or around the center of the unstable vortex structure, which matched well with the growing regions of the studied cerebral aneurysm. Furthermore, the authors observed that the aneurysm wall regions with a growth greater than 0.5 mm coincided with wall regions of lower (< 0.5 Pa) time-averaged wall shear stress (TAWSS), lower instantaneous (< 0.5 Pa) wall shear stress (WSS), and high (> 0.1) oscillatory shear index (OSI). To determine which set of parameters can best identify growing and nongrowing aneurysms, the authors performed statistical analysis for consecutive stages of the growing CA. The results demonstrated that the combination of TAWSS and the distance from the center of the vortical structure has the highest sensitivity and positive predictive value, and relatively high specificity and negative predictive value. These findings suggest that an unstable, recirculating flow structure within the aneurysm sac created in the region adjacent to the aneurysm wall with low TAWSS may be introduced as an accurate criterion to explain the hemodynamic conditions predisposing the aneurysm to growth. The authors' findings are based on one patient's data set, but the study lays out the justification for future large-scale verification. The authors' findings can assist clinicians in differentiating stable and growing aneurysms during preinterventional planning.

Improving the Accuracy of Two-Color Multiview (2CMV) Advanced Geospatial Information (AGI) Products Using Unsupervised Feature Learning and Optical Flow.

In two-color multiview (2CMV) advanced geospatial information (AGI) products, temporal changes in synthetic aperture radar (SAR) images acquired at different times are detected, colorized, and overlaid on an initial image such that new features are represented in cyan, and features that have disappeared are represented in red. Accurate detection of temporal changes in 2CMV AGI products can be challenging because of 'speckle noise' susceptibility and false positives that result from small orientation differences between objects imaged at different times. Accordingly, 2CMV products are often dominated by colored pixels when changes are detected via simple pixel-wise cross-correlation. The state-of-the-art in SAR image processing demonstrates that generating efficient 2CMV products, while accounting for the aforementioned problem cases, has not been well addressed. We propose a methodology to address the aforementioned two problem cases. Before detecting temporal changes, speckle and smoothing filters mitigate the effects of speckle noise. To detect temporal changes, we propose using unsupervised feature learning algorithms in conjunction with optical flow algorithms that track the motion of objects across time in small regions of interest. The proposed framework for distinguishing between actual motion and misregistration can lead to more accurate and meaningful change detection and improve object extraction from an SAR AGI product.

Numerical study of hemodynamics in brain aneurysms treated with flow diverter stents using porous medium theory.

Conventional approaches of implementing computational fluid dynamics to study aneurysmal hemodynamics after treatment with a flow diverter stent are computationally expensive. Cumbersome meshing and lengthy simulation runtimes are common. To address these issues, we present a novel volume penalization method that considers flow diverters as heterogeneous porous media. The proposed model requires a considerably smaller number of mesh elements, leading to faster simulation runtimes. Three patient-specific aneurysms were virtually treated with flow diverters and aneurysmal hemodynamics were simulated. The results of the virtual deployments including aneurysmal hemodynamics were compared to corresponding results from conventional approaches. The comparisons showed that the proposed approach led to 9.12 times increase in the speed of simulations on average. Further, aneurysmal kinetic energy and inflow rate metrics for the proposed approach were consistent with those from conventional approaches, differing on average by 3.52% and 3.78%, respectively.

An Optical Flow-Based Approach for Minimally Divergent Velocimetry Data Interpolation.

Three-dimensional (3D) biomedical image sets are often acquired with in-plane pixel spacings that are far less than the out-of-plane spacings between images. The resultant anisotropy, which can be detrimental in many applications, can be decreased using image interpolation. Optical flow and/or other registration-based interpolators have proven useful in such interpolation roles in the past. When acquired images are comprised of signals that describe the flow velocity of fluids, additional information is available to guide the interpolation process. In this paper, we present an optical-flow based framework for image interpolation that also minimizes resultant divergence in the interpolated data.

Suitability of lattice Boltzmann inlet and outlet boundary conditions for simulating flow in image-derived vasculature.

The lattice Boltzmann method (LBM) is a popular alternative to solving the Navier-Stokes equations for modeling blood flow. When simulating flow using the LBM, several choices for inlet and outlet boundary conditions exist. While boundary conditions in the LBM have been evaluated in idealized geometries, there have been no extensive comparisons in image-derived vasculature, where the geometries are highly complex. In this study, the Zou-He (ZH) and finite difference (FD) boundary conditions were evaluated in image-derived vascular geometries by comparing their stability, accuracy, and run times. The boundary conditions were compared in four arteries: a coarctation of the aorta, dissected aorta, femoral artery, and left coronary artery. The FD boundary condition was more stable than ZH in all four geometries. In general, simulations using the ZH and FD method showed similar convergence rates within each geometry. However, the ZH method proved to be slightly more accurate compared with experimental flow using three-dimensional printed vasculature. The total run times necessary for simulations using the ZH boundary condition were significantly higher as the ZH method required a larger relaxation time, grid resolution, and number of time steps for a simulation representing the same physiological time. Finally, a new inlet velocity profile algorithm is presented for complex inlet geometries. Overall, results indicated that the FD method should generally be used for large-scale blood flow simulations in image-derived vasculature geometries. This study can serve as a guide to researchers interested in using the LBM to simulate blood flow.

Computing the ankle-brachial index with parallel computational fluid dynamics.

The ankle-brachial index (ABI), a ratio of arterial blood pressure in the ankles and upper arms, is used to diagnose and monitor circulatory conditions such as coarctation of the aorta and peripheral artery disease. Computational simulations of the ABI can potentially determine the parameters that produce an ABI indicative of ischemia or other abnormalities in blood flow. However, 0- and 1-D computational methods are limited in describing a 3-D patient-derived geometry. Thus, we present a massively parallel framework for computational fluid dynamics (CFD) simulations in the full arterial system. Using the lattice Boltzmann method to solve the Navier-Stokes equations, we employ highly parallelized and scalable methods to generate the simulation domain and efficiently distribute the computational load among processors. For the first time, we compute an ABI with 3-D CFD. In this proof-of-concept study, we investigate the dependence of ABI on the presence of stenoses, or narrowed regions of the arteries, by directly modifying the arterial geometry. As a result, our framework enables the computation a hemodynamic factor characterizing flow at the scale of the full arterial system, in a manner that is extensible to patient-specific imaging data and holds potential for treatment planning.

A New Method for Simulating Embolic Coils as Heterogeneous Porous Media.

PURPOSE: To gain insight into the influence of coils on aneurysmal hemodynamics, computational fluid dynamics (CFD) can be used. Conventional methods of modeling coils consider the explicit geometry of the deployed devices within the aneurysm and discretize the fluid domain. However, the complex geometry of a coil mass leads to cumbersome domain discretization along with a significant number of mesh elements. These problems have motivated a homogeneous porous medium coil model, whereby the explicit geometry of the coils is greatly simplified, and relevant homogeneous porous medium parameters are approximated. Unfortunately, since the coils are not distributed uniformly in the aneurysm, the homogeneity assumption is no longer valid. METHODS: In this paper, a novel heterogeneous porous medium approach is introduced. To verify the model, we performed CFD simulations to calculate the pressure drop caused by actual deployed coils in a straight cylinder. Next, we considered three different anatomical aneurysm geometries virtually treated with coils and studied the hemodynamics using the presented heterogeneous porous medium model. RESULTS: We show that the blood kinetic energy predicted by the heterogeneous model is in strong agreement with the conventional approach. The homogeneity assumption, on the other hand, significantly over-predicts the blood kinetic energy within the aneurysmal sac. CONCLUSIONS: These results indicate that the benefits of the porous medium assumption can be retained if a heterogeneous approach is applied. Implementation of the presented method led to a substantial reduction in the total number of mesh elements compared to the conventional method, and greater accuracy was enabled by considering heterogeneity compared to the homogenous approach.

Alternative methods for virtual heart transplant-Size matching for pediatric heart transplantation with and without donor medical images available.

BACKGROUND: Listed pediatric heart transplant patients have the highest solid-organ waitlist mortality rate. The donor-recipient body weight (DRBW) ratio is the clinical standard for allograft size matching but may unnecessarily limit a patient's donor pool. To overcome DRBW ratio limitations, two methods of performing virtual heart transplant fit assessments were developed that account for patient-specific nuances. Method 1 uses an allograft total cardiac volume (TCV) prediction model informed by patient data wherein a matched allograft 3-D reconstruction is selected from a virtual library for assessment. Method 2 uses donor images for a direct virtual transplant assessment. METHODS: Assessments were performed in medical image reconstruction software. The allograft model was developed using allometric/isometric scaling assumptions and cross-validation. RESULTS: The final predictive model included gender, height, and weight. The 25th-, 50th-, and 75th-percentiles for TCV percentage errors were -13% (over-prediction), -1%, and 8% (under-prediction), respectively. Two examples illustrating the potential of virtual assessments are presented. CONCLUSION: Transplant centers can apply these methods to perform their virtual assessments using existing technology. These techniques have potential to improve organ allocation. With additional experience and refinement, virtual transplants may become standard of care for determining suitability of donor organ size for an identified recipient.

Corrigendum to "Structural alterations of the brainstem in migraine" (Neuroimage Clin. 2017; 13: 223-227).

[This corrects the article DOI: 10.1016/j.nicl.2016.10.023.].

The Effect of Stents in Cerebral Aneurysms: A Review.

The etiology of up to 95% of cerebral aneurysms may be accounted for by hemodynamically-induced factors that create vascular injury. The purpose of this review is to describe key physical properties that stents have and how they affect cerebral aneurysms. We performed a two-step screening process. First, a structured search was performed using the PubMed database. The following search terms and keywords were used: "Hemodynamics," "wall shear stress (WSS)," "velocity," "viscosity," "cerebral aneurysm," "intracranial aneurysm," "stent," "flow diverter," "stent porosity," "stent geometry," "stent configuration," and "stent design." Reports were considered if they included original data, discussed hemodynamic changes after stent-based treatment of cerebral aneurysms, examined the hemodynamic effects of stent deployment, and/or described the geometric characteristics of both stents and the aneurysms they were used to treat. The search strategy yielded a total of 122 articles, 61 were excluded after screening the titles and abstracts. Additional articles were then identified by cross-checking reference lists. The final collection of 97 articles demonstrates that the geometric characteristics and configurations of deployed stents influenced hemodynamic parameters such as aneurysmal WSS, inflow, and pressure. The geometric characteristics of the aneurysm and its position also had significant influences on intra-aneurysmal hemodynamics after treatment. In conclusion, changes in specific aneurysmal hemodynamic parameters that result from stenting relate to a number of factors including the geometric properties and configurations of deployed stents, the geometric properties of the aneurysm, and the pretreatment hemodynamics.

3D printing for congenital heart disease: a single site's initial three-yearexperience.

BACKGROUND: 3D printing is an ideal manufacturing process for creating patient-matched models (anatomical models) for surgical and interventional planning. Cardiac anatomical models have been described in numerous case studies and journal publications. However, few studies attempt to describe wider impact of the novel planning augmentation tool. The work here presents the evolution of an institution's first 3 full years of 3D prints following consistent integration of the technology into clinical workflow (2012-2014) - a center which produced 79 models for surgical planning (within that time frame). Patient outcomes and technology acceptance following implementation of 3D printing were reviewed. METHODS: A retrospective analysis was designed to investigate the anatomical model's impact on time-based surgical metrics. A contemporaneous cohort of standard-of-care pre-procedural planning (no anatomical models) was identified for comparative analysis. A post-surgery technology acceptance assessment was also employed in a smaller subset to measure perceived efficacy of the anatomical models. The data was examined. RESULTS: Within the timeframe of the study, 928 primary-case cardiothoracic surgeries (encompassing both CHD and non-CHD surgeries) took place at the practicing pediatric hospital. One hundred sixty four anatomical models had been generated for various purposes. An inclusion criterion based on lesion type limited those with anatomic models to 33; there were 113 cases matching the same criterion that received no anatomical model. Time-based metrics such as case length-of-time showed a mean reduction in overall time for anatomical models. These reductions were not statistically significant. The technology acceptance survey did demonstrate strong perceived efficacy. Anecdotal vignettes further support the technology acceptance. DISCUSSION & CONCLUSION: The anatomical models demonstrate trends for reduced operating room and case length of time when compared with similar surgeries in the same time-period; in turn, these reductions could have significant impact on patient outcomes and operating room economics. While analysis did not yield robust statistical powering, strong Cohen's d values suggest poor powering may be more related to sample size than non-ideal outcomes. The utility of planning with an anatomical model is further supported by the technology acceptance study which demonstrated that surgeons perceive the anatomical models to be an effective tool in surgical planning for a complex CHD repair. A prospective multi-center trial is currently in progress to further validate or reject these findings.

Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease.

Noninvasive engineering models are now being used for diagnosing and planning the treatment of cardiovascular disease. Techniques in computational modeling and additive manufacturing have matured concurrently, and results from simulations can inform and enable the design and optimization of therapeutic devices and treatment strategies. The emerging synergy between large-scale simulations and 3D printing is having a two-fold benefit: first, 3D printing can be used to validate the complex simulations, and second, the flow models can be used to improve treatment planning for cardiovascular disease. In this review, we summarize and discuss recent methods and findings for leveraging advances in both additive manufacturing and patient-specific computational modeling, with an emphasis on new directions in these fields and remaining open questions.

Mathematical Analysis of Glioma Growth in a Murine Model.

Five immunocompetent C57BL/6-cBrd/cBrd/Cr (albino C57BL/6) mice were injected with GL261-luc2 cells, a cell line sharing characteristics of human glioblastoma multiforme (GBM). The mice were imaged using magnetic resonance (MR) at five separate time points to characterize growth and development of the tumor. After 25 days, the final tumor volumes of the mice varied from 12 mm3 to 62 mm3, even though mice were inoculated from the same tumor cell line under carefully controlled conditions. We generated hypotheses to explore large variances in final tumor size and tested them with our simple reaction-diffusion model in both a 3-dimensional (3D) finite difference method and a 2-dimensional (2D) level set method. The parameters obtained from a best-fit procedure, designed to yield simulated tumors as close as possible to the observed ones, vary by an order of magnitude between the three mice analyzed in detail. These differences may reflect morphological and biological variability in tumor growth, as well as errors in the mathematical model, perhaps from an oversimplification of the tumor dynamics or nonidentifiability of parameters. Our results generate parameters that match other experimental in vitro and in vivo measurements. Additionally, we calculate wave speed, which matches with other rat and human measurements.

Three-dimensional printing: changing clinical care or just a passing fad?

PURPOSE OF REVIEW: Advances in medical imaging and three-dimensional (3D) reconstruction software have enabled a proliferation of 3D modeling and 3D printing for clinical applications. In particular, 3D printing has garnered an extraordinary media presence over the past few years. There is growing optimism that 3D printing can address patient specificity and complexity for improved interventional and surgical planning. Will this relatively untested technology bring about a paradigm shift in the clinical environment, or is it just a transient fad? RECENT FINDINGS: Case studies and series centered around 3D printing are omnipresent in clinical and engineering journals. These primarily qualitative studies support the potential efficacy of the emerging technology. Few studies analyze the value of 3D printing, weighing its potential benefits against increasing costs (e.g., institutional overhead, labor, and materials). SUMMARY: Clinical integration of 3D printing is growing rapidly, and its adoption into clinical practice presents unique workflow challenges. There are numerous clinical trials on the horizon that will finally help to elucidate the measured impact of 3D printing on clinical outcomes through quantitative analyses of clinical and economic metrics. The contrived integration of 3D printing into clinical practice seems all but certain as the value of this technology becomes more and more evident.

Radiogenomics to characterize regional genetic heterogeneity in glioblastoma.

BACKGROUND: Glioblastoma (GBM) exhibits profound intratumoral genetic heterogeneity. Each tumor comprises multiple genetically distinct clonal populations with different therapeutic sensitivities. This has implications for targeted therapy and genetically informed paradigms. Contrast-enhanced (CE)-MRI and conventional sampling techniques have failed to resolve this heterogeneity, particularly for nonenhancing tumor populations. This study explores the feasibility of using multiparametric MRI and texture analysis to characterize regional genetic heterogeneity throughout MRI-enhancing and nonenhancing tumor segments. METHODS: We collected multiple image-guided biopsies from primary GBM patients throughout regions of enhancement (ENH) and nonenhancing parenchyma (so called brain-around-tumor, [BAT]). For each biopsy, we analyzed DNA copy number variants for core GBM driver genes reported by The Cancer Genome Atlas. We co-registered biopsy locations with MRI and texture maps to correlate regional genetic status with spatially matched imaging measurements. We also built multivariate predictive decision-tree models for each GBM driver gene and validated accuracies using leave-one-out-cross-validation (LOOCV). RESULTS: We collected 48 biopsies (13 tumors) and identified significant imaging correlations (univariate analysis) for 6 driver genes: EGFR, PDGFRA, PTEN, CDKN2A, RB1, and TP53. Predictive model accuracies (on LOOCV) varied by driver gene of interest. Highest accuracies were observed for PDGFRA (77.1%), EGFR (75%), CDKN2A (87.5%), and RB1 (87.5%), while lowest accuracy was observed in TP53 (37.5%). Models for 4 driver genes (EGFR, RB1, CDKN2A, and PTEN) showed higher accuracy in BAT samples (n = 16) compared with those from ENH segments (n = 32). CONCLUSION: MRI and texture analysis can help characterize regional genetic heterogeneity, which offers potential diagnostic value under the paradigm of individualized oncology.

Structural alterations of the brainstem in migraine.

Atypical brainstem modulation of pain might contribute to changes in sensory processing typical of migraine. The study objective was to investigate whether migraine is associated with brainstem structural alterations that correlate with this altered pain processing. MRI T1-weighted images of 55 migraine patients and 58 healthy controls were used to: (1) create deformable mesh models of the brainstem that allow for shape analyses; (2) calculate volumes of the midbrain, pons, medulla and the superior cerebellar peduncles; (3) interrogate correlations between regional brainstem volumes, cutaneous heat pain thresholds, and allodynia symptoms. Migraineurs had smaller midbrain volumes (healthy controls = 61.28 mm3, SD = 5.89; migraineurs = 58.80 mm3, SD = 6.64; p = 0.038), and significant (p < 0.05) inward deformations in the ventral midbrain and pons, and outward deformations in the lateral medulla and dorsolateral pons relative to healthy controls. Migraineurs had a negative correlation between ASC-12 allodynia symptom severity with midbrain volume (r = - 0.32; p = 0.019) and a positive correlation between cutaneous heat pain thresholds with medulla (r = 0.337; p = 0.012) and cerebellar peduncle volumes (r = 0.435; p = 0.001). Migraineurs with greater symptoms of allodynia have smaller midbrain volumes and migraineurs with lower heat pain thresholds have smaller medulla and cerebellar peduncles. The brainstem likely plays a role in altered sensory processing in migraine and brainstem structure might reflect severity of allodynia and hypersensitivity to pain in migraine.