Surface Representation Research Articles

Automatic segmentation and implicit surface representation of dynamic cardiac data

Segmentation of anatomical structures on 2D images of cardiac exams is necessary for performing 3D volumetric analysis, enabling the computation of parameters for diagnosing cardiovascular disease. In this work, we present robust algorithms to automatically segment cardiac imaging data and generate a volumetric anatomical reconstruction of a patient-specific heart model by propagating active contour output within a patient stack through a self-supervised learning model. Contour initializations are automatically generated, then output segmentations on sparse image slices are transferred and merged across a stack of images within the same heart data set during the segmentation process. We demonstrate whole-heart segmentation and compare the results with ground truth manual annotations. Additionally, we provide a framework to represent segmented heart data in the form of implicit surfaces, allowing interpolation operations to generate intermediary models of heart sections and volumes throughout the cardiac cycle and to estimate ejection fraction.

A Molecular Dynamics Perspective on the Impacts of Random Rough Surface, Film Thickness, and Substrate Temperature on the Adsorbed Film’s Liquid–Vapor Phase Transition Regime

While recent studies have proven an unexpected liquid–vapor phase transition of adsorbed liquid films, a comprehensive description of the mechanisms of different types of phase change regimes over realistic representations of random rough surfaces is absent in the literature. The current comprehensive study investigates the effects of a gold random rough surface, liquid film thickness, and substrate temperature on the liquid–vapor phase change regime of an adsorbed sodium liquid film, considering the evaporator section of a wicked heat pipe (WHP) using a molecular dynamics (MD) simulation. At first, to generate a realistic random rough surface, a new and promising method is proposed that is entirely based on MD simulations. Then, to simulate the evaporator section of a WHP, a unique configuration for eliminating the vapor domain is developed. The simulation results reveal that three distinct regimes, namely, normal evaporation, cluster boiling, and film boiling, could be identified, which are presented on two-dimensional diagrams with the substrate temperature and liquid film thickness as coordinates for the ideally smooth and random rough surfaces. The results also manifest that even though using the random rough surface could lead to different phase transition regimes, the type of regime depends mainly on the substrate temperature and liquid film thickness. Furthermore, this study displays two different modes for normal evaporation. Also, it is shown that the impacts of the liquid film thickness and substrate temperature on the mode of normal evaporation are much more significant than the surface roughness.

Correction for geometric distortion in the flattened representation of pipeline external surface

Conventional cameras often produce external pipeline surface images with significant perspective-projection distortions, making determining the type and size of defects on the pipeline surface difficult. To address this issue, we present a novel approach for correcting the geometric distortion of a constant diameter pipeline (CDP) external surface image based on apparent contour pairs (ACPs). First, the camera is calibrated and the real projection position of ACPs accurately extracted. Second, a single-view perspective projection model of the CDP is adopted to realize a three-dimensional reconstruction of the pipeline. Subsequently, the flattened image of the CDP’s outer surface is obtained by performing equidistant sampling of cross sections, determining the visibility of discrete points, and mapping projection points onto a flat surface. Simulations and real experiments demonstrated the high accurate method in the correction of CDP images. Experiments conducted under different outdoor scenarios confirmed the robustness of the proposed method.

Solving inverse obstacle scattering problem with latent surface representations

We propose a novel iterative numerical method to solve the three-dimensional inverse obstacle scattering problem of recovering the shape of an obstacle from far-field measurements. To address the inherent ill-posed nature of the inverse problem, we advocate the use of a trained latent representation of surfaces as the generative prior. This prior enjoys excellent expressivity within the given class of shapes, and meanwhile, the latent dimensionality is low, which greatly facilitates the computation. Thus, the admissible manifold of surfaces is realistic and the resulting optimization problem is less ill-posed. We employ the shape derivative to evolve the latent surface representation, by minimizing the loss, and we provide a local convergence analysis of a gradient descent type algorithm to a stationary point of the loss. We present several numerical examples, including also backscattered and phaseless data, to showcase the effectiveness of the proposed algorithm.

Spatial circulatory networks based on the peripheral medial axis transform

This article presents a method for constructing circulatory networks that intrinsically combine geometric, topological, and semantic spatial attributes. The objective of this work is to generate concise graph representations extracted from spatial geometry that may be used for wayfinding and code compliance analyses to inform architectural design and urban planning. Our approach is based on shape analysis using the Medial Axis Transform skeletonization method. We present a process for the semantic classification of its nodes and edges by constructing an analytical rational piece-wise 3D surface representation. This overcomes the problem of identifying salient or otherwise graph features. Furthermore, we augment the networks with peripheral pathways. This addresses the fundamental limitation of skeletal graphs forcing paths exclusively through the middle of space and thus producing unreasonable detours. We demonstrate that our approach encompasses subtle circulatory features and generates concise graphs for open and free-form spaces that do not exhibit corridor-like structures.

Real-time volume rendering with octree-based implicit surface representation

Recent breakthroughs in neural radiance fields have significantly advanced the field of novel view synthesis and 3D reconstruction from multi-view images. However, the prevalent neural volume rendering techniques often suffer from long rendering time and require extensive network training. To address these limitations, recent initiatives have explored explicit voxel representations of scenes to expedite training. Yet, they often fall short in delivering accurate geometric reconstructions due to a lack of effective 3D representation. In this paper, we propose an octree-based approach for the reconstruction of implicit surfaces from multi-view images. Leveraging an explicit, network-free data structure, our method substantially increases rendering speed, achieving real-time performance. Moreover, our reconstruction technique yields surfaces with quality comparable to state-of-the-art network-based learning methods. The source code and data can be downloaded from https://github.com/LaoChui999/Octree-VolSDF.

Differentiable design of a double-freeform lens with multi-level radial basis functions for extended source irradiance tailoring

Freeform optics are key for generating prescribed illumination patterns from given sources, which are crucial for solid-state lighting and machine vision illumination. There is an increasing demand for compact freeform optics, which presents a substantial challenge for current design methods since the source dimensions must be considered. Most current extended-source design methods, although requiring profound knowledge of optics and mathematics, focus on the modest goal of obtaining uniform irradiance distributions. We address a more challenging design problem of generating an irradiance distribution of arbitrary shape through a double-freeform lens that can fully encompass the extended source. We propose a differentiable design method whose uniqueness lies in the representation of the double-freeform surfaces using multi-level spherical radial basis functions, which has a natural link to a multi-scale optimization technique. In addition, we employ a sequential unconstrained minimization technology complemented with Lagrange multipliers that add key feasibility constraints on lens shape and size. The proposed method is flexible, general, and efficient in designing highly compact freeform lenses for generating both simple and complex irradiance distributions, as demonstrated through the design examples. This could enable a universal solution to the extended-source design problem.

Motor function in multiple sclerosis assessed by navigated transcranial magnetic stimulation mapping.

Impaired motor function is a major cause of disability in multiple sclerosis (MS), involving various neuroplasticity processes typically assessed by neuroimaging. This study aimed to determine whether navigated transcranial magnetic stimulation (nTMS) could also provide biomarkers of motor cortex plasticity in patients with MS (pwMS). nTMS motor mapping was performed for hand and leg muscles bilaterally. nTMS variables included the amplitude and latency of motor evoked potentials (MEPs), corticospinal excitability measures, and the size of cortical motor maps (CMMs). Clinical assessment included disability (Expanded Disability Status Scale, EDSS), strength (MRC scale, pinch and grip), and dexterity (9-hole Pegboard Test). nTMS motor mapping was performed in 68 pwMS. PwMS with high disability (EDSS ≥ 3) had enlarged CMMs with less dense distribution of MEPs and various MEP parameter changes compared to pwMS with low disability (EDSS < 3). Patients with progressive MS had also various MEP parameter changes compared to pwMS with relapsing remitting form. MRC score correlated positively with MEP amplitude and negatively with MEP latency, pinch strength correlated negatively with CMM volume and dexterity with MEP latency. This is the first study to perform 4-limb cortical motor mapping in pwMS using a dedicated nTMS procedure. By quantifying the cortical surface representation of a given muscle and the variability of MEP within this representation, nTMS can provide new biomarkers of motor function impairment in pwMS. Our study opens perspectives for the use of nTMS as an objective method for assessing pwMS disability in clinical practice.

Automated Measurement and Three-Dimensional Fitting of Corneal Ulcerations and Erosions via AI-Based Image Analysis

Purpose Artificial intelligence (AI)-tools hold great potential to compensate for missing resources in health-care systems but often fail to be implemented in clinical routine. Intriguingly, no-code and low-code technologies allow clinicians to develop Artificial intelligence (AI)-tools without requiring in-depth programming knowledge. Clinician-driven projects allow to adequately identify and address real clinical needs and, therefore, hold superior potential for clinical implementation. In this light, this study aimed for the clinician-driven development of a tool capable of measuring corneal lesions relative to total corneal surface area and eliminating inaccuracies in two-dimensional measurements by three-dimensional fitting of the corneal surface. Methods Standard slit-lamp photographs using a blue-light filter after fluorescein instillation taken during clinical routine were used to train a fully convolutional network to automatically detect the corneal white-to-white distance, the total fluorescent area and the total erosive area. Based on these values, the algorithm calculates the affected area relative to total corneal surface area and fits the area on a three-dimensional representation of the corneal surface. Results The developed algorithm reached dice scores >0.9 for an automated measurement of the relative lesion size. Furthermore, only 25% of conventional manual measurements were within a ± 10% range of the ground truth. Conclusions The developed algorithm is capable of reliably providing exact values for corneal lesion sizes. Additionally, three-dimensional modeling of the corneal surface is essential for an accurate measurement of lesion sizes. Besides telemedicine applications, this approach harbors great potential for clinical trials where exact quantitative and observer-independent measurements are essential.

Identification and classification of surface defects for digital twin models of the workpiece.

Workpiece surface defect detection is an indispensable part of intelligent production. The surface information obtained by traditional 2D image detection has some limitations due to the influence of environmental light factors and part complexity. However, the digital twin model has the characteristics of high fidelity and scalability, and the digital twin surface can be obtained by a device with a scanning accuracy of 0.02mm to achieve the representation of the real surface of the workpiece. The surface defect detection system for digital twin models is proposed based on the improved YOLOv5 model in this paper. Firstly, the digital twin model of the workpiece is reconstructed by the point cloud data obtained by the scanning device, and the surface features with defects are captured. Subsequently, the training dataset is calibrated based on the defect surface, where the defect types include Inclusion, Perforation, pitting surface and Rolled-in scale. Finally, the improved YOLOv5 model with CBAM mechanism and BiFPN module was used to identify the surface defects of the digital twin model and compare it with the original YOLOv5 model and other common models. The results show that the improved YOLOv5 model can realize the identification and classification of surface defects. Compared with the original YOLOv5 model, the mAP value of the improved YOLOv5 model has increased by 0.2%, and the model has high precision. On the basis of the same data set, the improved YOLOv5 model has higher recognition accuracy than other models, improving 11.7%, 3.4%, 6.2%, 33.5%, respectively. As a result, this study provides a practical and systematic detection method for digital twin model surface during the intelligent production process, and realizes the rapid screening of the workpiece with defects.

Rovibrational calculations without model Hamiltonians: The infrared and microwave spectra of thiopropynal

AbstractRovibrational configuration interaction theory has been used to study the rotational spectrum and low lying rovibrational states of thiopropynal, a molecule, which has recently been detected in an interstellar cloud. Geometrical parameters, fundamental vibrational transitions and spectroscopic constants are also provided. All calculations rely on an ‐mode representation of the multidimensional potential energy surface, which has been obtained from explicitly correlated coupled‐cluster approaches including core correlation effects and an approximate treatment of high‐order coupled‐cluster terms. Comparison with experimental data is provided for several properties and the agreement was found to be excellent in most cases.

SRX Net: A point cloud segmentation framework based on surface representation and X-Net

We propose a novel unified point cloud segmentation framework called SRX Net. This framework is composed of our proposed SurRep Group module and X-Net architecture, reconstructing point cloud segmentation models from two aspects: point cloud surface representation and network architecture. The SurRep Group can model the local surface structure of the point cloud through structures such as the Ellipsoid Surface Representation and Umbrella Surface Representation, providing rich geometric information to the network. The XNet establishes an inverse encoding–decoding path to deepen the modeling of shallow semantics, solving the interference of shallow semantics on deep semantics in prediction in the U-Net architecture. It also introduces a GLFEnhancement module to enhance each point’s perception of global information. As a unified framework, SRX Net can improve the semantic segmentation effects of various existing models. Extensive experimental results show that our model produces more accurate segmentation edges and significantly reduces discrete predicted points. Based on Point Transformer, our SRX-PT Net achieves state-of-the-art performance of 72.1 mIoU on S3DIS, Scannet V2, and WCS3D datasets, respectively.

SurfPro-NN: A 3D point cloud neural network for the scoring of protein–protein docking models based on surfaces features and protein language models

Protein–protein interactions (PPI) play a crucial role in numerous key biological processes, and the structure of protein complexes provides valuable clues for in-depth exploration of molecular-level biological processes. Protein–protein docking technology is widely used to simulate the spatial structure of proteins. However, there are still challenges in selecting candidate decoys that closely resemble the native structure from protein–protein docking simulations. In this study, we introduce a docking evaluation method based on three-dimensional point cloud neural networks named SurfPro-NN, which represents protein structures as point clouds and learns interaction information from protein interfaces by applying a point cloud neural network. With the continuous advancement of deep learning in the field of biology, a series of knowledge-rich pre-trained models have emerged. We incorporate protein surface representation models and language models into our approach, greatly enhancing feature representation capabilities and achieving superior performance in protein docking model scoring tasks. Through comprehensive testing on public datasets, we find that our method outperforms state-of-the-art deep learning approaches in protein–protein docking model scoring. Not only does it significantly improve performance, but it also greatly accelerates training speed. This study demonstrates the potential of our approach in addressing protein interaction assessment problems, providing strong support for future research and applications in the field of biology.

NeUDF: Learning Neural Unsigned Distance Fields With Volume Rendering.

Multi-view shape reconstruction has achieved impressive progresses thanks to the latest advances in the neural implicit rendering. However, existing methods based on signed distance function (SDF) are limited to closed surfaces, failing to reconstruct a wide range of real-world objects that contain open-surface structures. In this work, we introduce a new neural rendering framework, coded NeUDF, that can reconstruct surfaces with arbitrary topologies solely from multi-view supervision. To gain the flexibility of representing arbitrary surfaces, NeUDF leverages the unsigned distance function (UDF) as surface representation. While a naive extension of SDF-based neural renderer cannot scale to UDF, we formalize the rules of neural volume rendering for open surface reconstruction (e.g., self-consistent, unbiased, occlusion-aware), and derive a dedicated rendering weight function specially tailored for UDF. Furthermore, to cope with open surface rendering, where the in/out test is no longer valid, we present a dedicated normal regularization strategy to resolve the surface orientation ambiguity. We extensively evaluate our method over a number of challenging datasets, including two typical open surface datasets MGN (Bhatnagar et al., 2019) and Deep Fashion 3D (Zhu et al., 2020). Experimental results demonstrate that NeUDF can significantly outperform the state-of-the-art methods in the task of multi-view surface reconstruction, especially for the complex shapes with open boundaries.

ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles.

The rapid growth in the number of experimental and predicted protein structures and more complicated protein structures poses a significant challenge for computational biology in leveraging structural information and accurate representation of protein surface properties. Recently, AlphaFold2 released the comprehensive proteomes of various species, and protein surface property representation plays a crucial role in protein-molecule interaction predictions, including those involving proteins, nucleic acids and compounds. Here, we proposed the first extensive database, namely ProNet DB, that integrates multiple protein surface representations and RNA-binding landscape for 326 175 protein structures. This collection encompasses the 16 model organism proteomes from the AlphaFold Protein Structure Database and experimentally validated structures from the Protein Data Bank. For each protein, ProNet DB provides access to the original protein structures along with the detailed surface property representations encompassing hydrophobicity, charge distribution and hydrogen bonding potential as well as interactive features such as the interacting face and RNA-binding sites and preferences. To facilitate an intuitive interpretation of these properties and the RNA-binding landscape, ProNet DB incorporates visualization tools like Mol* and an Online 3D Viewer, allowing for the direct observation and analysis of these representations on protein surfaces. The availability of pre-computed features enables instantaneous access for users, significantly advancing computational biology research in areas such as molecular mechanism elucidation, geometry-based drug discovery and the development of novel therapeutic approaches. Database URL: https://proj.cse.cuhk.edu.hk/aihlab/pronet/.

Weierstrass Representation of Minimal Surfaces and Related Basic Quantities

Weierstrass Representation of Minimal Surfaces and Related Basic Quantities

Analytical Review of Numerical Analysis in Hydrodynamic Performance of the Ship: Effect to Hull-Form Modifications

&lt;span lang="EN-GB"&gt;This review paper provides an overview of simulation-based hydrodynamic design optimization for ship hull forms. It also includes a numerical analysis aimed at accomplish early-stage simulation-based design in terms of hydrodynamic performance. A hydrodynamic module, a hull surface modeling module, and an optimization module are the primary components of this numerical analysis. The hydrodynamic module includes both simple design approaches and high-fidelity numeric tools; these integrated tools are used to evaluate hydrodynamic performances at different design stages. The hull surface modeling module offers a variety of techniques for ship hull surface representation and modification. It is also used to automatically create hull forms or change existing hull forms based on hydrodynamic performance and design constraints. The optimization module includes several optimization algorithms and surrogate models used to determine optimal designs in terms of hydrodynamic performance. Numerical findings indicate that the current tool is well suited for hull form design optimization at the early design stage because it can produce effective optimal designs within a short time.&lt;/span&gt;

LISR: Learning Linear 3D Implicit Surface Representation Using Compactly Supported Radial Basis Functions

Implicit 3D surface reconstruction of an object from its partial and noisy 3D point cloud scan is the classical geometry processing and 3D computer vision problem. In the literature, various 3D shape representations have been developed, differing in memory efficiency and shape retrieval effectiveness, such as volumetric, parametric, and implicit surfaces. Radial basis functions provide memory-efficient parameterization of the implicit surface. However, we show that training a neural network using the mean squared error between the ground-truth implicit surface and the linear basis-based implicit surfaces does not converge to the global solution. In this work, we propose locally supported compact radial basis functions for a linear representation of the implicit surface. This representation enables us to generate 3D shapes with arbitrary topologies at any resolution due to their continuous nature. We then propose a neural network architecture for learning the linear implicit shape representation of the 3D surface of an object. We learn linear implicit shapes within a supervised learning framework using ground truth Signed-Distance Field (SDF) data for guidance. The classical strategies face difficulties in finding linear implicit shapes from a given 3D point cloud due to numerical issues (requires solving inverse of a large matrix) in basis and query point selection. The proposed approach achieves better Chamfer distance and comparable F-score than the state-of-the-art approach on the benchmark dataset. We also show the effectiveness of the proposed approach by using it for the 3D shape completion task.

A General Implicit Framework for Fast NeRF Composition and Rendering

A variety of Neural Radiance Fields (NeRF) methods have recently achieved remarkable success in high render speed. However, current accelerating methods are specialized and incompatible with various implicit methods, preventing real-time composition over various types of NeRF works. Because NeRF relies on sampling along rays, it is possible to provide general guidance for acceleration. To that end, we propose a general implicit pipeline for composing NeRF objects quickly. Our method enables the casting of dynamic shadows within or between objects using analytical light sources while allowing multiple NeRF objects to be seamlessly placed and rendered together with any arbitrary rigid transformations. Mainly, our work introduces a new surface representation known as Neural Depth Fields (NeDF) that quickly determines the spatial relationship between objects by allowing direct intersection computation between rays and implicit surfaces. It leverages an intersection neural network to query NeRF for acceleration instead of depending on an explicit spatial structure.Our proposed method is the first to enable both the progressive and interactive composition of NeRF objects. Additionally, it also serves as a previewing plugin for a range of existing NeRF works.

HISR: Hybrid Implicit Surface Representation for Photorealistic 3D Human Reconstruction

Neural reconstruction and rendering strategies have demonstrated state-of-the-art performances due, in part, to their ability to preserve high level shape details. Existing approaches, however, either represent objects as implicit surface functions or neural volumes and still struggle to recover shapes with heterogeneous materials, in particular human skin, hair or clothes. To this aim, we present a new hybrid implicit surface representation to model human shapes. This representation is composed of two surface layers that represent opaque and translucent regions on the clothed human body. We segment different regions automatically using visual cues and learn to reconstruct two signed distance functions (SDFs). We perform surface-based rendering on opaque regions (e.g., body, face, clothes) to preserve high-fidelity surface normals and volume rendering on translucent regions (e.g., hair). Experiments demonstrate that our approach obtains state-of-the-art results on 3D human reconstructions, and also shows competitive performances on other objects.