Rapid model-guided design of organ-scale synthetic vasculature for biomanufacturing

Our ability to produce human-scale bio-manufactured organs is critically limited by the need for vascularization and perfusion. For tissues of variable size and shape, including arbitrarily complex geometries, designing and printing vasculature capable of adequate perfusion has posed a major hurdle. Here, we introduce a model-driven design pipeline combining accelerated optimization methods for fast synthetic vascular tree generation and computational hemodynamics models. We demonstrate rapid generation, simulation, and 3D printing of synthetic vasculature in complex geometries, from small tissue constructs to organ scale networks. We introduce key algorithmic advances that all together accelerate synthetic vascular generation by more than 230-fold compared to standard methods and enable their use in arbitrarily complex shapes through localized implicit functions. Furthermore, we provide techniques for joining vascular trees into watertight networks suitable for hemodynamic CFD and 3D fabrication. We demonstrate that organ-scale vascular network models can be generated in silico within minutes and can be used to perfuse engineered and anatomic models including a bioreactor, annulus, bi-ventricular heart, and gyrus. We further show that this flexible pipeline can be applied to two common modes of bioprinting with free-form reversible embedding of suspended hydrogels and writing into soft matter. Our synthetic vascular tree generation pipeline enables rapid, scalable vascular model generation and fluid analysis for bio-manufactured tissues necessary for future scale up and production.Comment: 58 pages (19 main and 39 supplement pages), 4 main figures, 9 supplement figure

Simulation of a new respiratory phase sorting method for 4D-imaging using optical surface information towards precision radiotherapy

Background: Respiratory signal detection is critical for 4-dimensional (4D) imaging. This study proposes and evaluates a novel phase sorting method using optical surface imaging (OSI), aiming to improve the precision of radiotherapy. Method: Based on 4D Extended Cardiac-Torso (XCAT) digital phantom, OSI in point cloud format was generated from the body segmentation, and image projections were simulated using the geometries of Varian 4D kV cone-beam-CT (CBCT). Respiratory signals were extracted respectively from the segmented diaphragm image (reference method) and OSI respectively, where Gaussian Mixture Model and Principal Component Analysis (PCA) were used for image registration and dimension reduction respectively. Breathing frequencies were compared using Fast-Fourier-Transform. Consistency of 4DCBCT images reconstructed using Maximum Likelihood Expectation Maximization algorithm was also evaluated quantitatively, where high consistency can be suggested by lower Root-Mean-Square-Error (RMSE), Structural-Similarity-Index (SSIM) value closer to 1, and larger Peak-Signal-To-Noise-Ratio (PSNR) respectively. Results: High consistency of breathing frequencies was observed between the diaphragm-based (0.232 Hz) and OSI-based (0.251 Hz) signals, with a slight discrepancy of 0.019Hz. Using end of expiration (EOE) and end of inspiration (EOI) phases as examples, the mean±1SD values of the 80 transverse, 100 coronal and 120 sagittal planes were 0.967, 0,972, 0.974 (SSIM); 1.657 ± 0.368, 1.464 ± 0.104, 1.479 ± 0.297 (RMSE); and 40.501 ± 1.737, 41.532 ± 1.464, 41.553 ± 1.910 (PSNR) for the EOE; and 0.969, 0.973, 0.973 (SSIM); 1.686 ± 0.278, 1.422 ± 0.089, 1.489 ± 0.238 (RMSE); and 40.535 ± 1.539, 41.605 ± 0.534, 41.401 ± 1.496 (PSNR) for EOI respectively. Conclusions: This work proposed and evaluated a novel respiratory phase sorting approach for 4D imaging using optical surface signals, which can potentially be applied to precision radiotherapy. Its potential advantages were non-ionizing, non-invasive, non-contact, and more compatible with various anatomic regions and treatment/imaging systems

BodyNet: Volumetric Inference of 3D Human Body Shapes

Human shape estimation is an important task for video editing, animation and fashion industry. Predicting 3D human body shape from natural images, however, is highly challenging due to factors such as variation in human bodies, clothing and viewpoint. Prior methods addressing this problem typically attempt to fit parametric body models with certain priors on pose and shape. In this work we argue for an alternative representation and propose BodyNet, a neural network for direct inference of volumetric body shape from a single image. BodyNet is an end-to-end trainable network that benefits from (i) a volumetric 3D loss, (ii) a multi-view re-projection loss, and (iii) intermediate supervision of 2D pose, 2D body part segmentation, and 3D pose. Each of them results in performance improvement as demonstrated by our experiments. To evaluate the method, we fit the SMPL model to our network output and show state-of-the-art results on the SURREAL and Unite the People datasets, outperforming recent approaches. Besides achieving state-of-the-art performance, our method also enables volumetric body-part segmentation.Comment: Appears in: European Conference on Computer Vision 2018 (ECCV 2018). 27 page

Can point cloud networks learn statistical shape models of anatomies?

Statistical Shape Modeling (SSM) is a valuable tool for investigating and quantifying anatomical variations within populations of anatomies. However, traditional correspondence-based SSM generation methods have a prohibitive inference process and require complete geometric proxies (e.g., high-resolution binary volumes or surface meshes) as input shapes to construct the SSM. Unordered 3D point cloud representations of shapes are more easily acquired from various medical imaging practices (e.g., thresholded images and surface scanning). Point cloud deep networks have recently achieved remarkable success in learning permutation-invariant features for different point cloud tasks (e.g., completion, semantic segmentation, classification). However, their application to learning SSM from point clouds is to-date unexplored. In this work, we demonstrate that existing point cloud encoder-decoder-based completion networks can provide an untapped potential for SSM, capturing population-level statistical representations of shapes while reducing the inference burden and relaxing the input requirement. We discuss the limitations of these techniques to the SSM application and suggest future improvements. Our work paves the way for further exploration of point cloud deep learning for SSM, a promising avenue for advancing shape analysis literature and broadening SSM to diverse use cases.Comment: Accepted to MICCAI 2023. 13 pages, 5 figures, appendi

Studies of the effects of gravitational and inertial forces on cardiovascular and respiratory dynamics

The current status and application are described of the biplane video roentgen densitometry, videometry and video digitization systems. These techniques were developed, and continue to be developed for studies of the effects of gravitational and inertial forces on cardiovascular and respiratory dynamics in intact animals and man. Progress is reported in the field of lung dynamics and three-dimensional reconstruction of the dynamic thoracic contents from roentgen video images. It is anticipated that these data will provide added insight into the role of shape and internal spatial relationships (which is altered particularly by acceleration and position of the body) of these organs as an indication of their functional status

A fast and robust patient specific Finite Element mesh registration technique: application to 60 clinical cases

Finite Element mesh generation remains an important issue for patient specific biomechanical modeling. While some techniques make automatic mesh generation possible, in most cases, manual mesh generation is preferred for better control over the sub-domain representation, element type, layout and refinement that it provides. Yet, this option is time consuming and not suited for intraoperative situations where model generation and computation time is critical. To overcome this problem we propose a fast and automatic mesh generation technique based on the elastic registration of a generic mesh to the specific target organ in conjunction with element regularity and quality correction. This Mesh-Match-and-Repair (MMRep) approach combines control over the mesh structure along with fast and robust meshing capabilities, even in situations where only partial organ geometry is available. The technique was successfully tested on a database of 5 pre-operatively acquired complete femora CT scans, 5 femoral heads partially digitized at intraoperative stage, and 50 CT volumes of patients' heads. The MMRep algorithm succeeded in all 60 cases, yielding for each patient a hex-dominant, Atlas based, Finite Element mesh with submillimetric surface representation accuracy, directly exploitable within a commercial FE software

Correlation Between Computed Contact Parameters and Wear Patterns on a Retrieved UHMWPE Tibial Insert

Throughout the life of a total knee arthroplasty implant repeated loading causes wear on the contact surfaces. Attempts have been made in the past to predict locations of wear through computational modeling and physical testing. This study examines a method of using computer modeling techniques to describe the kinematics of an implant, and to use kinematic data in finding areas of contact and internal shear stress that correlate to observed wear damage. A retrieved cruciate-retaining knee implant was reverse engineered and analyzed in one cycle of simulated gait using multibody dynamics and aligned according to resulting kinematic data for finite element analysis. Results showed a correlation between the predicted areas of contact and internal shear stresses and the observed wear damage

Augmenting CT cardiac roadmaps with segmented streaming ultrasound

Static X-ray computed tomography (CT) volumes are often used as anatomic roadmaps during catheter-based cardiac interventions performed under X-ray fluoroscopy guidance. These CT volumes provide a high-resolution depiction of soft-tissue structures, but at only a single point within the cardiac and respiratory cycles. Augmenting these static CT roadmaps with segmented myocardial borders extracted from live ultrasound (US) provides intra-operative access to real-time dynamic information about the cardiac anatomy. In this work, using a customized segmentation method based on a 3D active mesh, endocardial borders of the left ventricle were extracted from US image streams (4D data sets) at a frame rate of approximately 5 frames per second. The coordinate systems for CT and US modalities were registered using rigid body registration based on manually selected landmarks, and the segmented endocardial surfaces were overlaid onto the CT volume. The root-mean squared fiducial registration error was 3.80 mm. The accuracy of the segmentation was quantitatively evaluated in phantom and human volunteer studies via comparison with manual tracings on 9 randomly selected frames using a finite-element model (the US image resolutions of the phantom and volunteer data were 1.3 x 1.1 x 1.3 mm and 0.70 x 0.82 x 0.77 mm, respectively). This comparison yielded 3.70±2.5 mm (approximately 3 pixels) root-mean squared error (RMSE) in a phantom study and 2.58±1.58 mm (approximately 3 pixels) RMSE in a clinical study. The combination of static anatomical roadmap volumes and dynamic intra-operative anatomic information will enable better guidance and feedback for image-guided minimally invasive cardiac interventions