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CRYSTAL IMAGE ANALYSIS USING 2D SYNCHROSQUEEZED TRANSFORMS
"... ABSTRACT. We propose efficient algorithms based on a band-limited version of 2D synchrosqueezed transforms to extract mesoscopic and microscopic information from atomic crystal images. The methods analyze atomic crystal images as an assemblage of non-overlapping segments of 2D general intrinsic mode ..."
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ABSTRACT. We propose efficient algorithms based on a band-limited version of 2D synchrosqueezed transforms to extract mesoscopic and microscopic information from atomic crystal images. The methods analyze atomic crystal images as an assemblage of non-overlapping segments of 2D general intrinsic mode type functions, which are superpositions of non-linear wave-like components. In particular, crystal defects are interpreted as the irregularity of local energy; crystal rotations are described as the angle deviation of local wave vectors from their references; the gradient of a crystal elastic deformation can be obtained by a linear system generated by local wave vectors. Several numerical examples of synthetic and real crystal images are provided to illustrate the efficiency, robustness, and reliability of our methods. 1.
Structural Morphology Based Automatic Virus Particle Detection Using Robust Segmentation and Decision Tree Classification
"... ABSTRACT: Accurate and automatic approach to locate virus particles in electron microscopy is cardinal because of the large number of electron views that are needed to perform high resolution three dimensional reconstructions at the ultrastructural level. This paper describes a fully automatic appr ..."
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ABSTRACT: Accurate and automatic approach to locate virus particles in electron microscopy is cardinal because of the large number of electron views that are needed to perform high resolution three dimensional reconstructions at the ultrastructural level. This paper describes a fully automatic approach to locate adenovirus particles where low level of entropy is compared to the surrounding unorganized area. Characterization of the structural morphology of the virus particles based on area and eccentricity helps to detect the candidate points. The detected points are subjected to credibility test based on features extracted from each point from a texture image followed by decision tree classification. Final validation of approved candidate's takes place with 3D entropy proportion coordinates, computed in the original image, compensated work image1 and strongly filtered work image 2.
DOI 10.1007/s00138-006-0021-7 ORIGINAL PAPER Computer vision for nanoscale imaging
"... Abstract The main goal of Nanotechnology is to analyze and understand the properties of matter at the atomic and molecular level. Computer vision is rapidly expanding into this new and exciting field of application, and considerable research efforts are currently being spent on developing new image- ..."
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Abstract The main goal of Nanotechnology is to analyze and understand the properties of matter at the atomic and molecular level. Computer vision is rapidly expanding into this new and exciting field of application, and considerable research efforts are currently being spent on developing new image-based characterization techniques to analyze nanoscale images. Nanoscale characterization requires algorithms to perform image analysis under extremely challenging conditions such as low signal-to-noise ratio and low resolution. To achieve this, nanotechnology researchers require imaging tools that are able to enhance images, detect objects and features, reconstruct 3D geometry, and tracking. This paper reviews current advances in computer vision and related areas applied to imaging nanoscale objects. We categorize the algorithms, describe their representative methods, and conclude with several promising directions of future investigation. 1
Contents lists available at ScienceDirect Journal of Structural Biology
"... journal homepage: www.elsevier.com/locate/yjsbi Automatic particle selection from electron micrographs using machine ..."
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journal homepage: www.elsevier.com/locate/yjsbi Automatic particle selection from electron micrographs using machine
Segmentation of Rectangular Objects Lying on an Unknown Background in a Small Preview Scan Image
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Virology Journal BioMed Central Methodology
, 2006
"... Identification and classification of human cytomegalovirus capsids in textured electron micrographs using deformed template matching ..."
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Identification and classification of human cytomegalovirus capsids in textured electron micrographs using deformed template matching
Detection of incomplete enclosures of rectangular shape in remotely sensed images
"... We develop an approach for detection of ruins of live-stock enclosures in alpine areas captured by high-resolution remotely sensed images. These structures are usually of approximately rectangular shape and appear in images as faint fragmented contours in complex background. We ad-dress this problem ..."
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We develop an approach for detection of ruins of live-stock enclosures in alpine areas captured by high-resolution remotely sensed images. These structures are usually of approximately rectangular shape and appear in images as faint fragmented contours in complex background. We ad-dress this problem by introducing a new rectangularity fea-ture that quantifies the degree of alignment of an optimal subset of extracted linear segments with a contour of rect-angular shape. The rectangularity feature has high values not only for perfect enclosures, but also for broken ones with distorted angles, fragmented walls, or even a com-pletely missing wall. However, it has zero value for spu-rious structures with less than three sides of a perceivable rectangle. Performance analysis using large imagery of an alpine environment is provided. We show how the detection performance can be improved by learning from only a few representative examples and a large number of negatives. 1.
Complementary Space for Enhanced Uncertainty and Dynamics Visualization
"... Fig. 1. Visualizations of the hemoglobin molecule undergoing dynamic deformation as oxygen binds to it. (a) A primal space visualization of the first time step with the heme group identified. (b) Visualization of the complementary space of the first time step shows the geometry of the interior. The ..."
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Fig. 1. Visualizations of the hemoglobin molecule undergoing dynamic deformation as oxygen binds to it. (a) A primal space visualization of the first time step with the heme group identified. (b) Visualization of the complementary space of the first time step shows the geometry of the interior. The surface has been made transparent, revealing a large tunnel through the surface (yellow) with many mouths (red). (c) Zooming in on the heme group reveals the structure of space around it while oxygen is bound. (d-f) The corresponding images of (a-c) for the final time step. Complementary space has changed dramatically both in the interior volume and near the heme group, though this is not evident from the primal space visualizations. Comparing (c) and (f), we observe that the connectivity of the mouth of the tunnel near the heme group has changed, illustrating the time-dependency of the topological features of complementary space. We quantify and discuss this example further in Section 3.5. 1
Segmentation of Neuronal Structures Using SARSA (l)-Based Boundary Amendment with Reinforced Gradient-Descent Curve Shape Fitting
"... The segmentation of structures in electron microscopy (EM) images is very important for neurobiological research. The low resolution neuronal EM images contain noise and generally few features are available for segmentation, therefore application of the conventional approaches to identify the neuron ..."
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The segmentation of structures in electron microscopy (EM) images is very important for neurobiological research. The low resolution neuronal EM images contain noise and generally few features are available for segmentation, therefore application of the conventional approaches to identify the neuron structure from EM images is not successful. We therefore present a multi-scale fused structure boundary detection algorithm in this study. In the algorithm, we generate an EM image Gaussian pyramid first, then at each level of the pyramid, we utilize Laplacian of Gaussian function (LoG) to attain structure boundary, we finally assemble the detected boundaries by using fusion algorithm to attain a combined neuron structure image. Since the obtained neuron structures usually have gaps, we put forward a reinforcement learning-based boundary amendment method to connect the gaps in the detected boundaries. We use a SARSA (l)-based curve traveling and amendment approach derived from reinforcement learning to repair the incomplete curves. Using this algorithm, a moving point starts from one end of the incomplete curve and walks through the image where the decisions are supervised by the approximated curve model, with the aim of minimizing the connection cost until the gap is closed. Our approach provided stable and efficient structure segmentation. The test results using 30 EM images from ISBI 2012 indicated that both of our approaches, i.e., with or without boundary amendment, performed better than six conventional boundary detection approaches. In particular, after amendment, the Rand error and warping error, which are the most important performance