CAD-Based Porous Scaffold Design of Intervertebral Discs in Tissue Engineering

With the development and maturity of three-dimensional (3D) printing technology over the past decade, 3D printing has been widely investigated and applied in the field of tissue engineering to repair damaged tissues or organs, such as muscles, skin, and bones, Although a number of automated fabrication methods have been developed to create superior bio-scaffolds with specific surface properties and porosity, the major challenges still focus on how to fabricate 3D natural biodegradable scaffolds that have tailor properties such as intricate architecture, porosity, and interconnectivity in order to provide the needed structural integrity, strength, transport, and ideal microenvironment for cell- and tissue-growth. In this dissertation, a robust pipeline of fabricating bio-functional porous scaffolds of intervertebral discs based on different innovative porous design methodologies is illustrated. Firstly, a triply periodic minimal surface (TPMS) based parameterization method, which has overcome the integrity problem of traditional TPMS method, is presented in Chapter 3. Then, an implicit surface modeling (ISM) approach using tetrahedral implicit surface (TIS) is demonstrated and compared with the TPMS method in Chapter 4. In Chapter 5, we present an advanced porous design method with higher flexibility using anisotropic radial basis function (ARBF) and volumetric meshes. Based on all these advanced porous design methods, the 3D model of a bio-functional porous intervertebral disc scaffold can be easily designed and its physical model can also be manufactured through 3D printing. However, due to the unique shape of each intervertebral disc and the intricate topological relationship between the intervertebral discs and the spine, the accurate localization and segmentation of dysfunctional discs are regarded as another obstacle to fabricating porous 3D disc models. To that end, we discuss in Chapter 6 a segmentation technique of intervertebral discs from CT-scanned medical images by using deep convolutional neural networks. Additionally, some examples of applying different porous designs on the segmented intervertebral disc models are demonstrated in Chapter 6

Interpolatory Catmull-Clark volumetric subdivision over unstructured hexahedral meshes for modeling and simulation applications

International audienceVolumetric modeling is an important topic for material modeling and isogeometric simulation. In this paper, two kinds of interpolatory Catmull-Clark volumetric subdivision approaches over unstructured hexahedral meshes are proposed based on the limit point formula of Catmull-Clark subdivision volume. The basic idea of the first method is to construct a new control lattice, whose limit volume by the CatmullClark subdivision scheme interpolates vertices of the original hexahedral mesh. The new control lattice is derived by the local push-back operation from one CatmullClark subdivision step with modified geometric rules. This interpolating method is simple and efficient, and several shape parameters are involved in adjusting the shape of the limit volume. The second method is based on progressive-iterative approximation using limit point formula. At each iteration step, we progressively modify vertices of an original hexahedral mesh to generate a new control lattice whose limit volume interpolates all vertices in the original hexahedral mesh. The convergence proof of the iterative process is also given. The interpolatory subdivision volume has C 2-smoothness at the regular region except around extraordinary vertices and edges. Furthermore, the proposed interpolatory volumetric subdivision methods can be used not only for geometry interpolation, but also for material attribute interpolation in the field of volumetric material modeling. The application of the proposed volumetric subdivision approaches on isogeometric analysis is also given with several examples

Quicksilver: Fast Predictive Image Registration - a Deep Learning Approach

This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni- / multi- modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software.Comment: Add new discussion

Multi-scale active shape description in medical imaging

Shape description in medical imaging has become an increasingly important research field in recent years. Fast and high-resolution image acquisition methods like Magnetic Resonance (MR) imaging produce very detailed cross-sectional images of the human body - shape description is then a post-processing operation which abstracts quantitative descriptions of anatomically relevant object shapes. This task is usually performed by clinicians and other experts by first segmenting the shapes of interest, and then making volumetric and other quantitative measurements. High demand on expert time and inter- and intra-observer variability impose a clinical need of automating this process. Furthermore, recent studies in clinical neurology on the correspondence between disease status and degree of shape deformations necessitate the use of more sophisticated, higher-level shape description techniques. In this work a new hierarchical tool for shape description has been developed, combining two recently developed and powerful techniques in image processing: differential invariants in scale-space, and active contour models. This tool enables quantitative and qualitative shape studies at multiple levels of image detail, exploring the extra image scale degree of freedom. Using scale-space continuity, the global object shape can be detected at a coarse level of image detail, and finer shape characteristics can be found at higher levels of detail or scales. New methods for active shape evolution and focusing have been developed for the extraction of shapes at a large set of scales using an active contour model whose energy function is regularized with respect to scale and geometric differential image invariants. The resulting set of shapes is formulated as a multiscale shape stack which is analysed and described for each scale level with a large set of shape descriptors to obtain and analyse shape changes across scales. This shape stack leads naturally to several questions in regard to variable sampling and appropriate levels of detail to investigate an image. The relationship between active contour sampling precision and scale-space is addressed. After a thorough review of modem shape description, multi-scale image processing and active contour model techniques, the novel framework for multi-scale active shape description is presented and tested on synthetic images and medical images. An interesting result is the recovery of the fractal dimension of a known fractal boundary using this framework. Medical applications addressed are grey-matter deformations occurring for patients with epilepsy, spinal cord atrophy for patients with Multiple Sclerosis, and cortical impairment for neonates. Extensions to non-linear scale-spaces, comparisons to binary curve and curvature evolution schemes as well as other hierarchical shape descriptors are discussed

An exploration of the IGA method for efficient reservoir simulation

Novel numerical methods present exciting opportunities to improve the efficiency of reservoir simulators. Because potentially significant gains to computational speed and accuracy may be obtained, it is worthwhile explore alternative computational algorithms for both general and case-by-case application to the discretization of the equations of porous media flow, fluid-structure interaction, and/or production. In the present work, the fairly new concept of isogeometric analysis (IGA) is evaluated for its suitability to reservoir simulation via direct comparison with the industry standard finite difference (FD) method and 1st order standard finite element method (SFEM). To this end, two main studies are carried out to observe IGA’s performance with regards to geometrical modeling and ability to capture steep saturation fronts. The first study explores IGA’s ability to model complex reservoir geometries, observing L2 error convergence rates under a variety of refinement schemes. The numerical experimental setup includes an 'S' shaped line sink of varying curvature from which water is produced in a 2D homogenous domain. The accompanying study simplifies the domain to 1D, but adds in multiphase physics that traditionally introduce difficulties associated with modeling of a moving saturation front. Results overall demonstrate promise for the IGA method to be a particularly effective tool in handling geometrically difficult features while also managing typically challenging numerical phenomena.Petroleum and Geosystems Engineerin

Computational Light Routing: 3D Printed Optical Fibers for Sensing and Display

Despite recent interest in digital fabrication, there are still few algorithms that provide control over how light propagates inside a solid object. Existing methods either work only on the surface or restrict themselves to light diffusion in volumes. We use multi-material 3D printing to fabricate objects with embedded optical fibers, exploiting total internal reflection to guide light inside an object. We introduce automatic fiber design algorithms together with new manufacturing techniques to route light between two arbitrary surfaces. Our implicit algorithm optimizes light transmission by minimizing fiber curvature and maximizing fiber separation while respecting constraints such as fiber arrival angle. We also discuss the influence of different printable materials and fiber geometry on light propagation in the volume and the light angular distribution when exiting the fiber. Our methods enable new applications such as surface displays of arbitrary shape, touch-based painting of surfaces, and sensing a hemispherical light distribution in a single shot.National Science Foundation (U.S.) (Grant CCF-1012147)National Science Foundation (U.S.) (Grant IIS-1116296)United States. Defense Advanced Research Projects Agency (Grant N66001-12-1-4242)Intel Corporation (Science and Technology Center for Visual Computing)Alfred P. Sloan Foundation (Sloan Research Fellowship

Diffusion is All You Need for Learning on Surfaces

We introduce a new approach to deep learning on 3D surfaces such as meshes or point clouds. Our key insight is that a simple learned diffusion layer can spatially share data in a principled manner, replacing operations like convolution and pooling which are complicated and expensive on surfaces. The only other ingredients in our network are a spatial gradient operation, which uses dot-products of derivatives to encode tangent-invariant filters, and a multi-layer perceptron applied independently at each point. The resulting architecture, which we call DiffusionNet, is remarkably simple, efficient, and scalable. Continuously optimizing for spatial support avoids the need to pick neighborhood sizes or filter widths a priori, or worry about their impact on network size/training time. Furthermore, the principled, geometric nature of these networks makes them agnostic to the underlying representation and insensitive to discretization. In practice, this means significant robustness to mesh sampling, and even the ability to train on a mesh and evaluate on a point cloud. Our experiments demonstrate that these networks achieve state-of-the-art results for a variety of tasks on both meshes and point clouds, including surface classification, segmentation, and non-rigid correspondence

Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus