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arXiv 2024年

作者： Mody, Prerak Chaves-De-Plaza, Nicolas F. Rao, Chinmay Astrenidou, Eleftheria de Ridder, Mischa Hoekstra, Nienke Hildebrandt, Klaus Staring, Marius Department of Radiology Leiden University Medical Center Leiden Netherlands HollandPTC consortium Erasmus Medical Center Rotterdam Holland Proton Therapy Centre Delft Leiden University Medical Center Leiden and TU Delft Delft Netherlands Computer Graphics and Visualization Group EEMCS TU Delft Delft Netherlands Department of Radiation Oncology Leiden University Medical Center Leiden Netherlands Department of Radiation Oncology University Medical Center Utrecht Netherlands

Increased usage of automated tools like deep learning in medical image segmentation has alleviated the bottleneck of manual contouring. This has shifted manual labour to quality assessment (QA) of automated contours which involves detecting errors and correcting them. A potential solution to semi-automated QA is to use deep Bayesian uncertainty to recommend potentially erroneous regions, thus reducing time spent on error detection. Previous work has investigated the correspondence between uncertainty and error, however, no work has been done on improving the "utility" of Bayesian uncertainty maps such that it is only present in inaccurate regions and not in the accurate ones. Our work trains the FlipOut model with the Accuracy-vs-Uncertainty (AvU) loss which promotes uncertainty to be present only in inaccurate regions. We apply this method on datasets of two radiotherapy body sites, c.f. head-and-neck CT and prostate MR scans. Uncertainty heatmaps (i.e. predictive entropy) are evaluated against voxel inaccuracies using Receiver Operating Characteristic (ROC) and Precision-Recall (PR) curves. Numerical results show that when compared to the Bayesian baseline the proposed method successfully suppresses uncertainty for accurate voxels, with similar presence of uncertainty for inaccurate voxels. Code to reproduce experiments is available at https://***/prerakmody/bayesuncertainty-error-correspondence. © 2024, CC BY.

关键词： Image segmentation

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Continuous global optimization in surface reconstruction from an oriented point cloud

arXiv

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arXiv 2017年

作者： Pan, Rongjiang Skala, Vaclav School of Computer Science and Technology Shandong University Jinan China Centre of Computer Graphics and Data Visualization Department of Computer Science and Engineering University of West Bohemia Plzen Czech Republic

We introduce a continuous global optimization method to the field of surface reconstruction from discrete noisy cloud of points with weak information on orientation. The proposed method uses an energy functional combining flux-based data-fit measures and a regularization term. A continuous convex relaxation scheme assures the global minima of the geometric surface functional. The reconstructed surface is implicitly represented by the binary segmentation of vertices of a 3D uniform grid and a triangulated surface can be obtained by extracting an appropriate isosurface. Unlike the discrete graph-cut solution, the continuous global optimization entails advantages like memory requirements, reduction of metrication errors for geometric quantities, allowing globally optimal surface reconstruction at higher grid resolutions. We demonstrate the performance of the proposed method on several oriented point clouds captured by laser scanners. Experimental results confirm that our approach is robust to noise, large holes and non-uniform sampling density under the condition of very coarse orientation information. Copyright © 2017, The Authors. All rights reserved.

关键词： Global optimization

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Surface reconstruction with higher-order smoothness

arXiv

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arXiv 2017年

作者： Pan, Rongjiang Skala, Vaclav School of Computer Science and Technology Shandong University Jinan250100 China Centre of Computer Graphics and Data Visualization Department of Computer Science and Engineering University of West Bohemia Plzen Czech Republic

This work proposes a method to reconstruct surfaces with higher-order smoothness from noisy 3D measurements. The reconstructed surface is implicitly represented by the zero level-set of a continuous valued embedding function. The key idea is to find a function whose higher-order derivatives are regularized and whose gradient is best aligned with a vector field defined by the input point set. In contrast to methods based on the first-order variation of the function that are biased towards the constant functions and treat the extraction of the isosurface without aliasing artifacts as an afterthought, we impose higher-order smoothness directly on the embedding function. After solving a convex optimization problem with a multi-scale iterative scheme, a triangulated surface can be extracted using the marching cubes algorithm. We demonstrated the proposed method on several data sets obtained from raw laser-scanners and multi-view stereo approaches. Experimental results confirm that our approach allows us to reconstruct smooth surfaces from points in the presence of noise, outliers, large missing parts and very coarse orientation information. Copyright © 2017, The Authors. All rights reserved.

关键词： Convex optimization

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3rd International Workshop on visualization in Medicine and Life Sciences, VMLS 2013

作者： Fangerau, Jens Höckendorf, Burkhard Rieck, Bastian Heine, Christian Wittbrodt, Joachim Leitte, Heike Computer Graphics and Visualization Heidelberg University Heidelberg Germany Centre for Organismal Studies Heidelberg University Heidelberg Germany Scientific Visualization Group ETH Zürich Zürich Switzerland

ISBN: (纸本)9783319245218

Automatic feature tracking is widely used for the analysis of timedependent data. If the features exhibit splitting behavior, it is best characterized by tree-like tracks. For a large number of time steps, each with numerous features, these data become increasingly difficult to analyze. In this paper, we focus on the problem of comparing and contrasting hundreds to thousands of trees to support developmental biologists in their study of cell division patterns in embryos. To this end, we propose a new visual analytics method called structure map. This two-dimensional, color-coded map arranges trees into tiles along a Hilbert curve, preserving a tree similarity measure, which we define via graph Laplacians. The structure map supports both global and local analysis based on user-selected tree descriptors. It helps analysts identify similar trees, observe clustering and sizes of clusters within the forest, and detect outliers in a compact and uniform representation. We apply the structure map for analyzing 3D cell tracking from two periods of zebrafish embryogenesis: blastulation to early epiboly and tailbud extension. In both cases, we show how the structure map supported biologists to find systematic differences in the data set as well as detect erroneous cell behaviors. © Springer International Publishing Switzerland 2016.

关键词： Cell proliferation

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Opacity volume based halo generation and depth-dependent halos

Opacity volume based halo generation and depth-dependent hal...

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作者： Tao, Yubo Wang, Chao Lin, Hai Dong, Feng Clapworthy, Gordon State Key Lab of CAD and CG Zhejiang University Hangzhou China University of Wollongong Wollongong Australia Centre for Computer Graphics and Visualization University of Bedfordshire Luton United Kingdom

Halos are generally used to enhance depth perception and display spatial relationships in illustrative visualization. In this paper, we present a simple and effective method to create volumetric halo illustration. At the preprocessing stage, we generate, on graphics hardware, a view-independent halo intensity volume, which contains all of the potential halos around the boundaries of features, based on the opacity volume. During halo rendering, the halo intensity volume is used to extract halos only around the contours of structures for the current viewpoint. The performance of our approach is significantly faster than previous halo illustration methods, which perform both halo generation and rendering during direct volume rendering. We further propose depth-dependent halo effects, including depth color fading and depth width fading. These halo effects adaptively modulate the visual properties of halos to provide more perceptual cues for depth interpretation. Experimental results demonstrate the efficiency of our proposed approach and the effectiveness of depth-dependent halos. © 2012 Springer-Verlag Berlin Heidelberg.

关键词： Volume rendering

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Volume Upscaling Using Local Self-Examples for High Quality Volume visualization

Volume Upscaling Using Local Self-Examples for High Quality ...

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IEEE International Conference on computer-Aided Design and computer graphics

作者： Qirui Wang Yubo Tao Chao Wang Feng Dong Hai Lin Gordon Clapworthy State Key Lab of CAD&CG Zhejiang University Zhejiang China Centre for Computer Graphics & Visualization University of Bedfordshire Luton UK

Volume up scaling enlarges the size of a volume to make feature analysis more accurate and efficient. Linear interpolation, widely used in volume up scaling, result in jagged artifacts around features and losses of high-frequency components. Based on the example-based up scaling framework, this paper presents a new high-quality volume up scaling technique, predicting the high-frequency components by searching for the best matched patch in the input volume. As each slice can be taken as an image, the existing image up scaling technique based on the local self-similarity assumption can be directly applied to achieve slice up scaling. We further validate that the local self-similarity assumption is still valid for 3D volumes, and we extend this technique to 3D volume up scaling, i.e., isotropic volume up scaling. We compare our volume up scaling technique with traditional linear and cubic spline interpolations, and demonstrate that our method can generate a higher quality volume with better shape and details preserved. The proposed volume up scaling technique is well suitable for legacy low-resolution volumes to improve their visual qualities in visualization and analysis.

关键词： Interpolation Rendering (computer graphics) Image resolution Three-dimensional displays Biomedical imaging visualization Image reconstruction

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IEEE Symposium on Biological Data visualization (BioVis)

作者： Jens Fangerau Burkhard Höckendorf Joachim Wittbrodt Heike Leitte Computer Graphics and Visualization Heidelberg University Germany Centre for Organismal Studies (COS) Heidelberg University Germany

Modern 3D+T video microscopy techniques enable biologists to acquire data of living organisms with unprecedented resolution in time and space. These datasets contain a wealth of biologically relevant and quantifiable information, e.g. the movements of all individual cells in a complex organism. However, extraction, validation, and analysis of this information are both challenging and time-consuming. In this paper, we present a computational technique that classifies and validates similar patterns of cell movements and cell divisions in organisms that consist of up to thousands of cells. Our algorithm determines tracking paths of traced cells that exhibit similar features and shape structures. These similarity values are assigned to our cluster algorithm that clusters paths into groups of coherent behavior. The data can be interactively explored in 2D projections and a 3D cell movement representation. For the first time, this visualization allows biologists to exhaustively assess similarities and differences in division patterns and cell migration on the scale of an entire organism. For validation, we applied our method on a synthetic dataset and two real datasets including zebrafish periods from blastula stage to early epiboly and growing zebrafish tail. We show that our method succeeds in detecting similarities based on shape and cell-movement based features.

关键词： Trajectory Data visualization Shape Vectors Embryo Couplings

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Implicit surface modeling suitable for inside/outside tests with radial basis functions

Implicit surface modeling suitable for inside/outside tests ...

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2007 10th IEEE International Conference on computer Aided Design and computer graphics, CAD/graphics 2007

作者： Pan, Rongjiang Skala, Vaclav School of Computer Science and Technology Shandong University Jinan 250100 China Centre of Computer Graphics and Data Visualization Department of Computer Science and Engineering University of West Bohemia Plzen 306 14 Czech Republic

ISBN: (纸本)9781424415793

We describe a method for computing an implicit function that represents a surface by its zero level set, given a set of points scattered over the surface and associated with surface normal vectors. This implicit function is defined as a linear combination of compactly supported radial basis functions. Our method is suitable for testing whether a given point is interior or exterior to the surface, previously only associated with globally supported or globally regularized radial basis functions. We use a two-level interpolation approach. In the coarse scale interpolation, we set basis function centers by a grid that covers the enlarged bounding box of the given point set and compute their signed distances to the underlying surface using local quadratic approximations of the nearest surface points. Then a fitting to the residual errors on the surface points and additional off-surface points is performed with fine scale basis functions. The final function is the sum of the two intermediate functions and is a good approximation of the signed distance field to the surface in the bounding box. Examples of surface reconstruction and set operations between shapes are provided. © 2007 IEEE.

关键词： Interpolation

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Implicit Surface Modeling Suitable for Inside/Outside Tests with Radial Basis Functions

Implicit Surface Modeling Suitable for Inside/Outside Tests ...

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2007 10th IEEE International Conferences on computer Aided Design and computer graphics(CAD/graphics 2007)

作者： Vaclav Skala Centre of Computer Graphics and Data Visualization Department of Computer Science and EngineeringUniversity of West BohemiaPlzenCzech Republic30614

We describe a method for computing an implicit function that represents a surface by its zero level set,given a set of points scattered over the surface and associated with surface normal *** implicit function is defined as a linear combination of compactly supported radial basis *** method is suitable for testing whether a given point is interior or exterior to the surface,previously only associated with globally supported or globally regularized radial basis *** use a two-level interpolation *** the coarse scale interpolation,we set basis function centers by a grid that covers the enlarged bounding box of the given point set and compute their signed distances to the underlying surface using local quadratic approximations of the nearest surface *** a fitting to the residual errors on the surface points and additional off-surface points is performed with fine scale basis *** final function is the sum of the two intermediate functions and is a good approximation of the signed distance field to the surface in the bounding *** of surface reconstruction and set operations between shapes are provided.

关键词： Implicit Surface Modeling Suitable for Inside/Outside Tests with Radial Basis Functions

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Implicit Surface Modeling Suitable for Inside/Outside Tests with Radial Basis Functions

Implicit Surface Modeling Suitable for Inside/Outside Tests ...

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IEEE International Conference on computer-Aided Design and computer graphics

作者： Rongjiang Pan Vaclav Skala School of Computer Science and Technology Shandong University Jinan China Centre of Computer Graphics and Data Visualization Department of Computer Science and Engineering University of West Bohemia Plzen Czech Republic

关键词： Testing Surface fitting Surface reconstruction computer science Interpolation computer graphics Data visualization Data engineering Level set Scattering

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