The NIH/NIGMS
Center for Integrative Biomedical Computing

Performing exploratory analysis and visualization of large-scale time-varying computational science applications is challenging due to inaccuracies that arise from under-resolved data. In recent years, Lagrangian representations of the vector field computed using in situ processing are being increasingly researched and have emerged as a potential solution to enable exploration. However, prior works have offered limited estimates of the encumbrance on the simulation code as they consider “theoretical” in situ environments. Further, the effectiveness of this approach varies based on the nature of the vector field, benefitting from an in-depth investigation for each application area. With this study, an extended version of Sane et al. (2021), we contribute an evaluation of Lagrangian analysis viability and efficacy for simulation codes executing at scale on a supercomputer. We investigated previously unexplored cosmology and seismology applications as well as conducted a performance benchmarking study by using a hydrodynamics mini-application targeting exascale computing. To inform encumbrance, we integrated in situ infrastructure with simulation codes, and evaluated Lagrangian in situ reduction in representative homogeneous and heterogeneous HPC environments. To inform post hoc accuracy, we conducted a statistical analysis across a range of spatiotemporal configurations as well as a qualitative evaluation. Additionally, our study contributes cost estimates for distributed-memory post hoc reconstruction. In all, we demonstrate viability for each application — data reduction to less than 1% of the total data via Lagrangian representations, while maintaining accurate reconstruction and requiring under 10% of total execution time in over 90% of our experiments.

Prior knowledge about the imaging physics provides a mechanistic forward operator that plays an important role in image reconstruction, although myriad sources of possible errors in the operator could negatively impact the reconstruction solutions. In this work, we propose to embed the traditional mechanistic forward operator inside a neural function, and focus on modeling and correcting its unknown errors in an interpretable manner. This is achieved by a conditional generative model that transforms a given mechanistic operator with unknown errors, arising from a latent space of self-organizing clusters of potential sources of error generation. Once learned, the generative model can be used in place of a fixed forward operator in any traditional optimization-based reconstruction process where, together with the inverse solution, the error in prior mechanistic forward operator can be minimized and the potential source of error uncovered. We apply the presented method to the reconstruction of heart electrical potential from body surface potential. In controlled simulation experiments and in-vivo real data experiments, we demonstrate that the presented method allowed reduction of errors in the physics-based forward operator and thereby delivered inverse reconstruction of heart-surface potential with increased accuracy.

Importance. Medical images are essential for modern medicine and an important research subject in visualization. However, medical experts are often not aware of the many advanced three-dimensional (3D) medical image visualization techniques that could increase their capabilities in data analysis and assist the decision-making process for specific medical problems. Our paper provides a review of 3D visualization techniques for medical images, intending to bridge the gap between medical experts and visualization researchers. Highlights. Fundamental visualization techniques are revisited for various medical imaging modalities, from computational tomography to diffusion tensor imaging, featuring techniques that enhance spatial perception, which is critical for medical practices. The state-of-the-art of medical visualization is reviewed based on a procedure-oriented classification of medical problems for studies of individuals and populations. This paper summarizes free software tools for different modalities of medical images designed for various purposes, including visualization, analysis, and segmentation, and it provides respective Internet links. Conclusions. Visualization techniques are a useful tool for medical experts to tackle specific medical problems in their daily work. Our review provides a quick reference to such techniques given the medical problem and modalities of associated medical images. We summarize fundamental techniques and readily available visualization tools to help medical experts to better understand and utilize medical imaging data. This paper could contribute to the joint effort of the medical and visualization communities to advance precision medicine.

Correspondence-based shape models are key to various medical imaging applications that rely on a statistical analysis of anatomies. Such shape models are expected to represent consistent anatomical features across the population for population-specific shape statistics. Early approaches for correspondence placement rely on nearest neighbor search for simpler anatomies. Coordinate transformations for shape correspondence hold promise to address the increasing anatomical complexities. Nonetheless, due to the inherent shape-level geometric complexity and population-level shape variation, the coordinate-wise correspondence often does not translate to the anatomical correspondence. An alternative, group-wise approach for correspondence placement explicitly models the trade-off between geometric description and the population's statistical compactness. However, these models achieve limited success in resolving nonlinear shape correspondence. Recent works have addressed this limitation by adopting an application-specific notion of correspondence through lifting positional data to a higher dimensional feature space. However, they heavily rely on manual expertise to create domain-specific features and consistent landmarks. This paper proposes an automated feature learning approach, using deep convolutional neural networks to extract correspondence-friendly features from shape ensembles. Further, an unsupervised domain adaptation scheme is introduced to augment the pretrained geometric features with new anatomies. Results on anatomical datasets of human scapula, femur, and pelvis bones demonstrate that …

We present a nonparametric statistical framework for the quantification, analysis, and propagation of data uncertainty in direct volume rendering (DVR). The state-of-the-art statistical DVR framework allows for preserving the transfer function (TF) of the ground truth function when visualizing uncertain data; however, the existing framework is restricted to parametric models of uncertainty. In this paper, we address the limitations of the existing DVR framework by extending the DVR framework for nonparametric distributions. We exploit the quantile interpolation technique to derive probability distributions representing uncertainty in viewing-ray sample intensities in closed form, which allows for accurate and efficient computation. We evaluate our proposed nonparametric statistical models through qualitative and quantitative comparisons with the mean-field and parametric statistical models, such as uniform and Gaussian, as well as Gaussian mixtures. In addition, we present an extension of the state-of-the-art rendering parametric framework to 2D TFs for improved DVR classifications. We show the applicability of our uncertainty quantification framework to ensemble, downsampled, and bivariate versions of scalar field datasets.

Developmental dysplasia of the hip (DDH) is commonly described as reduced femoral head coverage due to anterolateral acetabular deficiency. Although reduced coverage is the defining trait of DDH, more subtle and localized anatomic features of the joint are also thought to contribute to symptom development and degeneration. These features are challenging to identify using conventional approaches. Herein, we assessed the morphology of the full femur and hemi-pelvis using an articulated statistical shape model (SSM). The model determined the morphological and pose-based variations associated with DDH in a population of Japanese females and established which of these variations predict coverage. Computed tomography images of 83 hips from 47 patients were segmented for input into a correspondence-based SSM. The dominant modes of variation in the model initially represented scale and pose. After removal of these factors through individual bone alignment, femoral version and neck-shaft angle, pelvic curvature, and acetabular version dominated the observed variation. Femoral head oblateness and prominence of the acetabular rim and various muscle attachment sites of the femur and hemi-pelvis were found to predict 3D CT-based coverage measurements (R²=0.5-0.7 for the full bones, R²=0.9 for the joint).

Background
Electrocardiographic forward problems are crucial components for noninvasive electrocardiographic imaging (ECGI) that compute torso potentials from cardiac source measurements. Forward problems have few sources of error as they are physically well posed and supported by mature numerical and computational techniques. However, the residual errors reported from experimental validation studies between forward computed and measured torso signals remain surprisingly high.

Objective
To test the hypothesis that incomplete cardiac source sampling, especially above the atrioventricular (AV) plane is a major contributor to forward solution errors.

Methods
We used a modified Langendorff preparation suspended in a human-shaped electrolytic torso-tank and a novel pericardiac-cage recording array to thoroughly sample the cardiac potentials. With this carefully controlled experimental preparation, we minimized possible sources of error, including geometric error and torso inhomogeneities. We progressively removed recorded signals from above the atrioventricular plane to determine how the forward-computed torso-tank potentials were affected by incomplete source sampling.

Results
We studied 240 beats total recorded from three different activation sequence types (sinus, and posterior and anterior left-ventricular free-wall pacing) in each of two experiments. With complete sampling by the cage electrodes, all correlation metrics between computed and measured torso-tank potentials were above 0.93 (maximum 0.99). The mean root-mean-squared error across all beat types was also low, less than or equal to 0.10 mV. A precipitous drop in forward solution accuracy was observed when we included only cage measurements below the AV plane.

Conclusion
First, our forward computed potentials using complete cardiac source measurements set a benchmark for similar studies. Second, this study validates the importance of complete cardiac source sampling above the AV plane to produce accurate forward computed torso potentials. Testing ECGI systems and techniques with these more complete and highly accurate datasets will improve inverse techniques and noninvasive detection of cardiac electrical abnormalities.

In current biological and medical research, statistical shape modeling (SSM) provides an essential framework for the characterization of anatomy/morphology. Such analysis is often driven by the identification of a relatively small number of geometrically consistent features found across the samples of a population. These features can subsequently provide information about the population shape variation. Dense correspondence models can provide ease of computation and yield an interpretable low-dimensional shape descriptor when followed by dimensionality reduction. However, automatic methods for obtaining such correspondences usually require image segmentation followed by significant preprocessing, which is taxing in terms of both computation as well as human resources. In many cases, the segmentation and subsequent processing require manual guidance and anatomy specific domain expertise. This paper proposes a self-supervised deep learning approach for discovering landmarks from images that can directly be used as a shape descriptor for subsequent analysis. We use landmark-driven image registration as the primary task to force the neural network to discover landmarks that register the images well. We also propose a regularization term that allows for robust optimization of the neural network and ensures that the landmarks uniformly span the image domain. The proposed method circumvents segmentation and preprocessing and directly produces a usable shape descriptor using just 2D or 3D images. In addition, we also propose two variants on the training loss function that allows for prior shape information to be integrated into the model. We apply this framework on several 2D and 3D datasets to obtain their shape descriptors. We analyze these shape descriptors in their efficacy of capturing shape information by performing different shape-driven applications depending on the data ranging from shape clustering to severity prediction to outcome diagnosis.

Statistical shape modeling (SSM) characterizes anatomical variations in a population of shapes generated from medical images. SSM requires consistent shape representation across samples in shape cohort. Establishing this representation entails a processing pipeline that includes anatomy segmentation, re-sampling, registration, and non-linear optimization. These shape representations are then used to extract low-dimensional shape descriptors that facilitate subsequent analyses in different applications. However, the current process of obtaining these shape descriptors from imaging data relies on human and computational resources, requiring domain expertise for segmenting anatomies of interest. Moreover, this same taxing pipeline needs to be repeated to infer shape descriptors for new image data using a pre-trained/existing shape model. Here, we propose DeepSSM, a deep learning-based framework for learning the functional mapping from images to low-dimensional shape descriptors and their associated shape representations, thereby inferring statistical representation of anatomy directly from 3D images. Once trained using an existing shape model, DeepSSM circumvents the heavy and manual pre-processing and segmentation and significantly improves the computational time, making it a viable solution for fully end-to-end SSM applications. In addition, we introduce a model-based data-augmentation strategy to address data scarcity. Finally, this paper presents and analyzes two different architectural variants of DeepSSM with different loss functions using three medical datasets and their downstream clinical application. Experiments showcase that DeepSSM performs comparably or better to the state-of-the-art SSM both quantitatively and on application-driven downstream tasks. Therefore, DeepSSM aims to provide a comprehensive blueprint for deep learning-based image-to-shape models.

Objectives
The spinal cord injury (SCI) patient population is overwhelmingly affected by neuropathic pain (NP), a secondary condition for which therapeutic options are limited and have a low degree of efficacy. The objective of this study was to identify novel deep brain stimulation (DBS) targets that may theoretically benefit those with NP in the SCI patient population. We hypothesize that localized changes in white matter identified in SCI subjects with NP compared to those without NP could be used to develop an evidence‐based approach to DBS target identification.

To classify localized neurostructural changes associated with NP in the SCI population, we compared white matter fiber density (FD) and cross‐section (FC) between SCI subjects with NP (N = 17) and SCI subjects without NP (N = 15) using diffusion‐weighted magnetic resonance imaging (MRI). We then identified theoretical target locations for DBS using fiber bundles connected to significantly altered regions of white matter. Finally, we used computational models of DBS to determine if our theoretical target locations could be used to feasibly activate our fiber bundles of interest.
We identified significant increases in FC in the splenium of the corpus callosum in pain subjects when compared to controls. We then isolated five fiber bundles that were directly connected to the affected region of white matter. Our models were able to predict that our fiber bundles of interest can be feasibly activated with DBS at reasonable stimulation amplitudes and with clinically relevant implantation approaches.
Altogether, we identified neuroarchitectural changes associated with NP in the SCI cohort and implemented a novel, evidence‐driven target selection approach for DBS to guide future research in neuromodulation treatment of NP after SCI.

Introduction
Acute myocardial ischemia occurs when coronary perfusion to the heart is inadequate, which can perturb the highly organized electrical activation of the heart and can result in adverse cardiac events including sudden cardiac death. Ischemia is known to influence the ST and repolarization phases of the ECG, but it also has a marked effect on propagation (QRS); however, studies investigating propagation during ischemia have been limited.

We estimated conduction velocity (CV) and ischemic stress prior to and throughout 20 episodes of experimentally induced ischemia in order to quantify the progression and correlation of volumetric conduction changes during ischemia. To estimate volumetric CV, we 1) reconstructed the activation wavefront; 2) calculated the elementwise gradient to approximate propagation direction; and 3) estimated conduction speed (CS) with an inverse-gradient technique.
We found that acute ischemia induces significant conduction slowing, reducing the global median speed by 20 cm/s. We observed a biphasic response in CS (acceleration then deceleration) early in some ischemic episodes. Furthermore, we noted a high temporal correlation between ST-segment changes and CS slowing; however, when comparing these changes over space, we found only moderate correlation (corr. = 0.60).
This study is the first to report volumetric CS changes (acceleration and slowing) during episodes of acute ischemia in the whole heart. We showed that while CS changes progress in a similar time course to ischemic stress (measured by ST-segment shifts), the spatial overlap is complex and variable, showing extreme conduction slowing both in and around regions experiencing severe ischemia.

Objective: In this study, we have used whole heart simulations parameterized with large animal experiments to validate three techniques (two from the literature and one novel) for estimating epicardial and volumetric conduction velocity (CV). Methods: We used an eikonal-based simulation model to generate ground truth activation sequences with prescribed CVs. Using the sampling density achieved experimentally we examined the accuracy with which we could reconstruct the wavefront, and then examined the robustness of three CV estimation techniques to reconstruction related error. We examined a triangulation-based, inverse-gradient-based, and streamline-based techniques for estimating CV cross the surface and within the volume of the heart. Results: The reconstructed activation times agreed closely with simulated values, with 50-70% of the volumetric nodes and 97-99% of the epicardial nodes were within 1 ms of the ground truth. We found close agreement between the CVs calculated using reconstructed versus ground truth activation times, with differences in the median estimated CV on the order of 3-5% volumetrically and 1-2% superficially, regardless of what technique was used. Conclusion: Our results indicate that the wavefront reconstruction and CV estimation techniques are accurate, allowing us to examine changes in propagation induced by experimental interventions such as acute ischemia, ectopic pacing, or drugs. Significance: We implemented, validated, and compared the performance of a number of CV estimation techniques. The CV estimation techniques implemented in this study produce accurate, high-resolution CV fields that can be used to study propagation in the heart experimentally and clinically.

Introduction

Accurate reconstruction of cardiac activation wavefronts is crucial for clinical diagnosis, management, and treatment of cardiac arrhythmias. Furthermore, reconstruction of activation profiles within the intramural myocardium has long been impossible because electrical mapping was only performed on the endocardial surface. Recent advancements in electrocardiographic imaging (ECGI) have made endocardial and epicardial activation mapping possible. We propose a novel approach to use both endocardial and epicardial mapping in a combined approach to reconstruct intramural activation times.

To implement and validate a combined epicardial/endocardial intramural activation time reconstruction technique.

We used 11 simulations of ventricular activation paced from sites throughout myocardial wall and extracted endocardial and epicardial activation maps at approximate clinical resolution. From these maps, we interpolated the activation times through the myocardium using thin-plate-spline radial basis functions. We evaluated activation time reconstruction accuracy using root-mean-squared error (RMSE) of activation times and the percent of nodes within 1 ms of the ground truth.

Reconstructed intramural activation times showed an RMSE and percentage of nodes within 1 ms of the ground truth simulations of 3 ms and 70%, respectively. In the worst case, the RMSE and percentage of nodes were 4 ms and 60%, respectively.
Conclusion

We showed that a simple, yet effective combination of clinical endocardial and epicardial activation maps can accurately reconstruct intramural wavefronts. Furthermore, we showed that this approach provided robust reconstructions across multiple intramural stimulation sites.

Accuracy of estimating the heart’s electrical activity with Electrocardiographic Imaging (ECGI) is challenging due to using an error-prone physics-based model (forward model). While getting better results than the traditional numerical methods following the underlying physics, modern deep learning approaches ignore the physics behind the electrical propagation in the body and do not allow the use of patientspecific geometry. We introduce a deep-learning-based ECGI framework capable of understanding the underlying physics, aware of geometry, and adjustable to patient-specific data. Using a variational autoencoder (VAE), we uncover the forward model’s parameter space, and when solving the inverse problem, these parameters will be optimized to reduce the errors in the forward model. In both simulation and real data experiments, we demonstrated the ability of the presented framework to provide accurate reconstruction of the heart’s electrical potentials and localization of the earliest activation sites.

Objective
Several severity metrics have been developed for metopic craniosynostosis, including a recent machine learning-derived algorithm. This study assessed the diagnostic concordance between machine learning and previously published severity indices.

Preoperative computed tomography (CT) scans of patients who underwent surgical correction of metopic craniosynostosis were quantitatively analyzed for severity. Each scan was manually measured to derive manual severity scores and also received a scaled metopic severity score (MSS) assigned by the machine learning algorithm. Regression analysis was used to correlate manually captured measurements to MSS. ROC analysis was performed for each severity metric and were compared to how accurately they distinguished cases of metopic synostosis from controls.
In total, 194 CT scans were analyzed, 167 with metopic synostosis and 27 controls. The mean scaled MSS for the patients with metopic was 6.18 ± 2.53 compared to 0.60 ± 1.25 for controls. Multivariable regression analyses yielded an R-square of 0.66, with significant manual measurements of endocranial bifrontal angle (EBA) (P = 0.023), posterior angle of the anterior cranial fossa (p < 0.001), temporal depression angle (P = 0.042), age (P < 0.001), biparietal distance (P < 0.001), interdacryon distance (P = 0.033), and orbital width (P < 0.001). ROC analysis demonstrated a high diagnostic value of the MSS (AUC = 0.96, P < 0.001), which was comparable to other validated indices including the adjusted EBA (AUC = 0.98), EBA (AUC = 0.97), and biparietal/bitemporal ratio (AUC = 0.95).
The machine learning algorithm offers an objective assessment of morphologic severity that provides a reliable composite impression of severity. The generated score is comparable to other severity indices in ability to distinguish cases of metopic synostosis from controls.

This study sought to evaluate atrial fibrillation (AF) ablation outcomes based on scar patterns and contiguous area available for AF wavefronts to propagate.

Electrocardiographic imaging is an imaging modality that has been introduced recently to help in visualizing the electrical activity of the heart and consequently guide the ablation therapy for ventricular arrhythmias. One of the main challenges of this modality is that the electrocardiographic signals recorded at the torso surface are contaminated with noise from different sources. Low amplitude leads are more affected by noise due to their low peak-to-peak amplitude. In this paper, we have studied 6 datasets from two torso tank experiments (Bordeaux and Utah experiments) to investigate the impact of removing or interpolating these low amplitude leads on the inverse reconstruction of cardiac electrical activity. Body surface potential maps used were calculated by using the full set of recorded leads, removing 1, 6, 11, 16, or 21 low amplitude leads, or interpolating 1, 6, 11, 16, or 21 low amplitude leads using one of the three interpolation methods – Laplacian interpolation, hybrid interpolation, or the inverse-forward interpolation. The epicardial potential maps and activation time maps were computed from these body surface potential maps and compared with those recorded directly from the heart surface in the torso tank experiments. There was no significant change in the potential maps and activation time maps after the removal of up to 11 low amplitude leads. Laplacian interpolation and hybrid interpolation improved the inverse reconstruction in some datasets and worsened it in the rest. The inverse forward interpolation of low amplitude leads improved it in two out of 6 datasets and at least remained the same in the other datasets. It was noticed that after doing the inverse-forward interpolation, the selected lambda value was closer to the optimum lambda value that gives the inverse solution best correlated with the recorded one.

Salinet et al. Electrocardiographic Imaging for Atrial Fibrillation treatment guidance (for example, localization of AF triggers and sustaining mechanisms), and we discuss the technological requirements and validation. We address experimental and clinical results, limitations, and future challenges for fruitful application of ECGI for AF understanding and management. We pay attention to existing techniques and clinical application, to computer models and (animal or human) experiments, to challenges of methodological and clinical validation. The overall objective of the study is to provide a consensus on valuable directions that ECGI research may take to provide future improvements in AF characterization and treatment guidance.

In situ computation of Lagrangian flow maps to enable post hoc time-varying vector field analysis has recently become an active area of research. However, the current literature is largely limited to theoretical settings and lacks a solution to address scalability of the technique in distributed memory. To improve scalability, we propose and evaluate the benefits and limitations of a simple, yet novel, performance optimization. Our proposed optimization is a communication-free model resulting in local Lagrangian flow maps, requiring no message passing or synchronization between processes, intrinsically improving scalability, and thereby reducing overall execution time and alleviating the encumbrance placed on simulation codes from communication overheads. To evaluate our approach, we computed Lagrangian flow maps for four time-varying simulation vector fields and investigated how execution time and reconstruction accuracy are impacted by the number of GPUs per compute node, the total number of compute nodes, particles per rank, and storage intervals. Our study consisted of experiments computing Lagrangian flow maps with up to 67M particle trajectories over 500 cycles and used as many as 2048 GPUs across 512 compute nodes. In all, our study contributes an evaluation of a communication-free model as well as a scalability study of computing distributed Lagrangian flow maps at scale using in situ infrastructure on a modern supercomputer.

Despite advances in many of the techniques used in Electrocardiographic Imaging (ECGI), uncertainty remains insufficiently quantified for many aspects of the pipeline. The effect of geometric uncertainty, particularly due to segmentation variability, may be the least explored to date. We use statistical shape modeling and uncertainty quantification (UQ) to compute the effect of segmentation variability on ECGI solutions. The shape model was made with Shapeworks from nine segmentations of the same patient and incorporated into an ECGI pipeline. We computed uncertainty of the pericardial potentials and local activation times (LATs) using polynomial chaos expansion (PCE) implemented in UncertainSCI. Uncertainty in pericardial potentials from segmentation variation mirrored areas of high variability in the shape model, near the base of the heart and the right ventricular outflow tract, and that ECGI was less sensitive to uncertainty in the posterior region of the heart. Subsequently LAT calculations could vary dramatically due to segmentation variability, with a standard deviation as high as 126ms, yet mainly in regions with low conduction velocity. Our shape modeling and UQ pipeline presented possible uncertainty in ECGI due to segmentation variability and can be used by researchers to reduce said uncertainty or mitigate its effects. The demonstrated use of statistical shape modeling and UQ can also be extended to other types of modeling pipelines.