Search results for: Zeyun Yu

Items from 1 to 20 out of 59 results

article

Slanted support window-based stereo matching for surface reconstruction of microscopic samples

Ahmadreza Baghaie, Chi Zhang, Ali Bakhshinejad, Heather A. Owen, more

Micron > 2017 > 103 > C > 12-21

This work is to address the limitations of 2D Scanning Electron Microscopy (SEM) micrographs in providing 3D topographical information necessary for various types of analysis in biological and biomedical sciences as well as mechanical and material engineering by investigating modern stereo vision methodologies for 3D surface reconstruction of microscopic samples. To achieve this, micrograph pairs...

article

SD-SEM: sparse-dense correspondence for 3D reconstruction of microscopic samples

Ahmadreza Baghaie, Ahmad P. Tafti, Heather A. Owen, Roshan M. D'Souza, more

Micron > 2017 > 97 > C > 41-55

Scanning electron microscopy (SEM) imaging has been a principal component of many studies in biomedical, mechanical, and materials sciences since its emergence. Despite the high resolution of captured images, they remain two-dimensional (2D). In this work, a novel framework using sparse-dense correspondence is introduced and investigated for 3D reconstruction of stereo SEM images. SEM micrographs...

article

Involuntary eye motion correction in retinal optical coherence tomography: Hardware or software solution?

Ahmadreza Baghaie, Zeyun Yu, Roshan M. D’Souza

Medical Image Analysis > 2017 > 37 > C > 129-145

In this paper, we review state-of-the-art techniques to correct eye motion artifacts in Optical Coherence Tomography (OCT) imaging. The methods for eye motion artifact reduction can be categorized into two major classes: (1) hardware-based techniques and (2) software-based techniques. In the first class, additional hardware is mounted onto the OCT scanner to gather information about the eye motion...

article

Tribological study in microscale using 3D SEM surface reconstruction

Emad Omrani, Ahmad P. Tafti, Mojtaba F. Fathi, Afsaneh Dorri Moghadam, more

Tribology International > 2016 > 103 > C > 309-315

Tribology as a branch of materials and mechanical engineering sciences incorporates concepts of friction, wear, and lubrication to discover knowledge and facts about different surfaces. The scanning electron microscope (SEM) and the optical microscope (OM) are two common imaging equipment that have been used in tribological research to visualize and characterize worn surfaces. SEMs are more practical...

chapter

3D image segmentation based on feature-sensitive and adaptive tetrahedral meshes

Ming Xu, Zeyun Yu

2016 IEEE International Conference on Image Processing (ICIP) > 854 - 858

2016 IEEE International Conference on Image Processing (ICIP)

In this paper, a tetrahedral mesh-based approach is investigated for 3D image segmentation on a given image volume. We present a series of algorithms to generate high quality, feature-sensitive, and adaptive meshes to partition a 3D volume, where the 3D Canny edge detector is utilized to preserve important feature boundaries in the generated tetrahedral mesh. Each cluster of voxels within a tetrahedron...

article

Application of Independent Component Analysis techniques in speckle noise reduction of retinal OCT images

Ahmadreza Baghaie, Roshan M. D'Souza, Zeyun Yu

Optik - International Journal for Light and Electron Optics > 2016 > 127 > 15 > 5783-5791

Optical Coherence Tomography (OCT) is an emerging technique in the field of biomedical imaging, with applications in ophthalmology, dermatology, coronary imaging, etc. OCT images usually suffer from a granular pattern, called speckle noise, which restricts the process of interpretation. Therefore the need for speckle noise reduction techniques is of high importance. To the best of our knowledge, use...

article

3DSEM++: Adaptive and intelligent 3D SEM surface reconstruction

Ahmad P. Tafti, Jessica D. Holz, Ahmadreza Baghaie, Heather A. Owen, more

Micron > 2016 > 87 > C > 33-45

Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, such as biological, mechanical, and materials sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around for decades to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution...

chapter

A Morse-Theory Based Method for Segmentation of Triangulated Freeform Surfaces

Jun Wang, Zeyun Yu

Lecture Notes in Computer Science > Advances in Visual Computing > Poster Session > 939-948

This paper presents a new algorithm for segmentation of triangulated freeform surfaces using geometric quantities and Morse theory. The method consists of two steps: initial segmentation and refinement. First, the differential geometry quantities are estimated on triangular meshes, with which the meshes are classified into different surface types. The initial segmentation is obtained by grouping the...

chapter

Normalized Gradient Vector Diffusion and Image Segmentation

Zeyun Yu, Chandrajit Bajaj

Lecture Notes in Computer Science > Computer Vision — ECCV 2002 > Texture Shading and Colour / Grouping and Segmentation / Object Recognition > 517-530

In this paper, we present an approach for image segmentation, based on the existing Active Snake Model and Watershed-based Region Merging. Our algorithm includes initial segmentation using Normalized Gradient Vector Diffusion (NGVD) and region merging based on Region Adjacency Graph (RAG). We use a set of heat diffusion equations to generate a vector field over the image domain, which provides us...

chapter

Medical Image Segmentation Based on Novel Local Order Energy

LingFeng Wang, Zeyun Yu, ChunHong Pan

Lecture Notes in Computer Science > Computer Vision – ACCV 2010 > Posters on Day 1 of ACCV 2010 > 148-159

Image segmentation plays an important role in many medical imaging systems, yet in complex circumstances it is still a challenging problem. Among many difficulties, problem caused by the image intensity inhomogeneity is the key aspect. In this work, we develop a novel local-homogeneous region-based level set segmentation method to tackle this problem. First, we propose a novel local order energy,...

article

3DSEM: A 3D microscopy dataset

Ahmad P. Tafti, Andrew B. Kirkpatrick, Jessica D. Holz, Heather A. Owen, more

Data in Brief > 2016 > 6 > C > 112-116

The Scanning Electron Microscope (SEM) as a 2D imaging instrument has been widely used in many scientific disciplines including biological, mechanical, and materials sciences to determine the surface attributes of microscopic objects. However the SEM micrographs still remain 2D images. To effectively measure and visualize the surface properties, we need to truly restore the 3D shape model from 2D...

chapter

A Novel Method for Surface Mesh Smoothing: Applications in Biomedical Modeling

Jun Wang, Zeyun Yu

Proceedings of the 18th International Meshing Roundtable > Session 2A: Optimization > 195-210

In this paper, we present a surface-fitting based smoothing algorithm for discrete, general-purpose mesh models. The surface patch around a mesh vertex is defined in a local coordinate system and fitted with a quadratic polynomial function. An initial mesh smoothing is achieved by projecting each vertex onto the fitted surface. At each vertex of the initial mesh, the curvature is estimated and used...

article

Mesh Generation and Flexible Shape Comparisons for Bio-Molecules

Zhanheng Gao, Reihaneh Rostami, Xiaoli Pang, Zhicheng Fu, more

Molecular Based Mathematical Biology > 2016 > 4 > 1

Novel approaches for generating and comparing flexible (non-rigid) molecular surface meshes are developed. The mesh-generating method is fast and memory-efficient. The resulting meshes are smooth and accurate, and possess high mesh quality. An isometric-invariant shape descriptor based on the Laplace- Beltrami operator is then explored for mesh comparing. The new shape descriptor is more powerful...

article

A Cylindrical Basis Function for Solving Partial Differential Equations on Manifolds

E.O. Asante-Asamani, Lei Wang, Zeyun Yu

Procedia Computer Science > 2016 > 80 > C > 233-244

Numerical solution of partial differential equations (PDEs) on manifolds continues to generate a lot of interest among scientists in the natural and applied sciences. On the other hand, recent developments of 3D scanning and computer vision technologies have produced a large number of 3D surface models represented as point clouds. Herein, we develop a simple and efficient method for solving PDEs on...

article

Recent advances in 3D SEM surface reconstruction

Ahmad P. Tafti, Andrew B. Kirkpatrick, Zahrasadat Alavi, Heather A. Owen, more

Micron > 2015 > 78 > C > 54-66

The scanning electron microscope (SEM), as one of the most commonly used instruments in biology and material sciences, employs electrons instead of light to determine the surface properties of specimens. However, the SEM micrographs still remain 2D images. To effectively measure and visualize the surface attributes, we need to restore the 3D shape model from the SEM images. 3D surface reconstruction...

chapter

Sparse and low rank decomposition based batch image alignment for speckle reduction of retinal OCT images

Ahmadreza Baghaie, Roshan M. D'souza, Zeyun Yu

2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI) > 226 - 230

2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI 2015)

Optical Coherence Tomography (OCT) is an emerging technique in the field of biomedical imaging, with applications in ophthalmology, dermatology, coronary imaging etc. Due to the underlying physics, OCT images usually suffer from a granular pattern, called speckle noise, which restricts the process of interpretation. Here, a sparse and low rank decomposition based method is used for speckle reduction...

article

SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

Yi Jiang, Yang Xie, Jinyong Ying, Dexuan Xie, more

Molecular Based Mathematical Biology > 2015 > 3 > 1

The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present...

article

Skeleton-enhanced line drawings for 3D models

Zhong Li, Shengwei Qin, Xiaogang Jin, Zeyun Yu, more

Graphical Models > 2014 > 76 > 6 > 620-632

We present a novel line drawing approach for 3D models by introducing their skeleton information into the rendering process. Based on the silhouettes of the input 3D models, we first extract feature lines in geometric regions by utilizing their curvature, torsion and view-dependent information. Then, the skeletons of the models are extracted by our newly developed skeleton extraction algorithm. After...

article

Skeleton-based shape analysis of protein models

Zhong Li, Shengwei Qin, Zeyun Yu, Yao Jin

Journal of Molecular Graphics and Modelling > 2014 > 53 > C > 72-81

In order to compare the similarity between two protein models, a shape analysis algorithm based on skeleton extraction is presented in this paper. It firstly extracts the skeleton of a given protein surface by an improved Multi-resolution Reeb Graph (MRG) method. A number of points on the model surface are then collected to compute the local diameter (LD) according to the skeleton. Finally the LD...

article

A compact shape descriptor for triangular surface meshes

Zhanheng Gao, Zeyun Yu, Xiaoli Pang

Computer-Aided Design > 2014 > 53 > Complete > 62-69

Three-dimensional shape-based descriptors have been widely used in object recognition and database retrieval. In the current work, we present a novel method called compact Shape-DNA (cShape-DNA) to describe the shape of a triangular surface mesh. While the original Shape-DNA technique provides an effective and isometric-invariant descriptor for surface shapes, the number of eigenvalues used is typically...

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INFONA - science communication portal

Search results for: Zeyun Yu

Slanted support window-based stereo matching for surface reconstruction of microscopic samples

SD-SEM: sparse-dense correspondence for 3D reconstruction of microscopic samples

Involuntary eye motion correction in retinal optical coherence tomography: Hardware or software solution?

Tribological study in microscale using 3D SEM surface reconstruction

3D image segmentation based on feature-sensitive and adaptive tetrahedral meshes

Application of Independent Component Analysis techniques in speckle noise reduction of retinal OCT images

3DSEM++: Adaptive and intelligent 3D SEM surface reconstruction

A Morse-Theory Based Method for Segmentation of Triangulated Freeform Surfaces

Normalized Gradient Vector Diffusion and Image Segmentation

Medical Image Segmentation Based on Novel Local Order Energy

3DSEM: A 3D microscopy dataset

A Novel Method for Surface Mesh Smoothing: Applications in Biomedical Modeling

Mesh Generation and Flexible Shape Comparisons for Bio-Molecules

A Cylindrical Basis Function for Solving Partial Differential Equations on Manifolds

Recent advances in 3D SEM surface reconstruction

Sparse and low rank decomposition based batch image alignment for speckle reduction of retinal OCT images

SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

Skeleton-enhanced line drawings for 3D models

Skeleton-based shape analysis of protein models

A compact shape descriptor for triangular surface meshes

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