3D SEM Surface Reconstruction: An Optimized, Adaptive, and Intelligent Approach

Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, including biological, mechanical, and material sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution greater than one nanometer. Whereas SEM micrographs still remain two-dimensional (2D), many research and educational questions truly require knowledge and information about their three-dimensional (3D) surface structures. Having 3D surfaces from SEM images would provide true anatomic shapes of micro samples which would allow for quantitative measurements and informative visualization of the systems being investigated. In this research project, we novel design and develop an optimized, adaptive, and intelligent multi-view approach named 3DSEM++ for 3D surface reconstruction of SEM images, making a 3D SEM dataset publicly and freely available to the research community. The work is expected to stimulate more interest and draw attention from the computer vision and multimedia communities to the fast-growing SEM application area

3D SEM Surface Reconstruction from Multi-View Images

The scanning electron microscope (SEM), a promising imaging equipment has been used to determine the surface properties such as compositions or geometries of specimens by achieving increased magnification, contrast, and resolution. SEM micro-graphs, however, remain two-dimensional (2D). The knowledge and information about their three-dimensional (3D) surface structures are critical in many real-world applications. Having 3D surfaces from SEM images provides true anatomic shapes of micro-scale samples which allow for quantitative measurements and informative visualization of the systems being investigated. A novel multi-view approach for reconstruction of SEM images is demonstrated in this research project. This thesis focuses on the 3D SEM surface reconstruction from multi-view images. We investigate an approach to reconstruction of 3D surfaces from stereo SEM image pairs and then discuss how 3D point clouds may be registered to generate more complete 3D shapes from multi-views of the microscopic specimen. Then we introduce a method that uses an algorithm called KAZE, which reconstructs 3D surfaces from multiple views of objects. Then Numerous results are presented to show the effectiveness of the presented approaches

Study of Computational Image Matching Techniques: Improving Our View of Biomedical Image Data

Image matching techniques are proven to be necessary in various fields of science and engineering, with many new methods and applications introduced over the years. In this PhD thesis, several computational image matching methods are introduced and investigated for improving the analysis of various biomedical image data. These improvements include the use of matching techniques for enhancing visualization of cross-sectional imaging modalities such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), denoising of retinal Optical Coherence Tomography (OCT), and high quality 3D reconstruction of surfaces from Scanning Electron Microscope (SEM) images. This work greatly improves the process of data interpretation of image data with far reaching consequences for basic sciences research. The thesis starts with a general notion of the problem of image matching followed by an overview of the topics covered in the thesis. This is followed by introduction and investigation of several applications of image matching/registration in biomdecial image processing: a) registration-based slice interpolation, b) fast mesh-based deformable image registration and c) use of simultaneous rigid registration and Robust Principal Component Analysis (RPCA) for speckle noise reduction of retinal OCT images. Moving towards a different notion of image matching/correspondence, the problem of view synthesis and 3D reconstruction, with a focus on 3D reconstruction of microscopic samples from 2D images captured by SEM, is considered next. Starting from sparse feature-based matching techniques, an extensive analysis is provided for using several well-known feature detector/descriptor techniques, namely ORB, BRIEF, SURF and SIFT, for the problem of multi-view 3D reconstruction. This chapter contains qualitative and quantitative comparisons in order to reveal the shortcomings of the sparse feature-based techniques. This is followed by introduction of a novel framework using sparse-dense matching/correspondence for high quality 3D reconstruction of SEM images. As will be shown, the proposed framework results in better reconstructions when compared with state-of-the-art sparse-feature based techniques. Even though the proposed framework produces satisfactory results, there is room for improvements. These improvements become more necessary when dealing with higher complexity microscopic samples imaged by SEM as well as in cases with large displacements between corresponding points in micrographs. Therefore, based on the proposed framework, a new approach is proposed for high quality 3D reconstruction of microscopic samples. While in case of having simpler microscopic samples the performance of the two proposed techniques are comparable, the new technique results in more truthful reconstruction of highly complex samples. The thesis is concluded with an overview of the thesis and also pointers regarding future directions of the research using both multi-view and photometric techniques for 3D reconstruction of SEM images

Taking aim at moving targets in computational cell migration

Cell migration is central to the development and maintenance of multicellular organisms. Fundamental understanding of cell migration can, for example, direct novel therapeutic strategies to control invasive tumor cells. However, the study of cell migration yields an overabundance of experimental data that require demanding processing and analysis for results extraction. Computational methods and tools have therefore become essential in the quantification and modeling of cell migration data. We review computational approaches for the key tasks in the quantification of in vitro cell migration: image pre-processing, motion estimation and feature extraction. Moreover, we summarize the current state-of-the-art for in silico modeling of cell migration. Finally, we provide a list of available software tools for cell migration to assist researchers in choosing the most appropriate solution for their needs

Modeling and Simulation in Engineering

This book provides an open platform to establish and share knowledge developed by scholars, scientists, and engineers from all over the world, about various applications of the modeling and simulation in the design process of products, in various engineering fields. The book consists of 12 chapters arranged in two sections (3D Modeling and Virtual Prototyping), reflecting the multidimensionality of applications related to modeling and simulation. Some of the most recent modeling and simulation techniques, as well as some of the most accurate and sophisticated software in treating complex systems, are applied. All the original contributions in this book are jointed by the basic principle of a successful modeling and simulation process: as complex as necessary, and as simple as possible. The idea is to manipulate the simplifying assumptions in a way that reduces the complexity of the model (in order to make a real-time simulation), but without altering the precision of the results