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Detecting circular and rectangular particles based on geometric feature detection in electron micrographs,” (2004)

by Z Yu, C Bajaj
Venue:J. Struct. Biol.,
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CRYSTAL IMAGE ANALYSIS USING 2D SYNCHROSQUEEZED TRANSFORMS

by Haizhao Yang, Jianfeng Lu, Lexing Ying
"... 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.
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...Dr ∣∣ f̂ (ξ)∣∣ . The component task to identify the most dominant energy bump in E(r ) here belongs to a simple case of geometric object identification problems which have been extensively studied in =-=[2, 15, 16, 35]-=-. For a 1D discrete signal of length L, it has been proved that the optimal complexity to detect bumps in this signal is O(L) in [2]. Since E(r ) has only a few well-separated and sharp energy bumps w...

Structural Morphology Based Automatic Virus Particle Detection Using Robust Segmentation and Decision Tree Classification

by Saffna Shajahan
"... 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.
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...8th July -2014 Copyright to IJIRSET www.ijirset.com 161 accumulation. When the current pixel is at the center of a virus particle, the pixels covered by the mask will generate a minimum amount of entropy, compared to the situation where both functions and covered background areas with similar amounts of entropy, which will give an entropy ratio ≈1.The deepest regional minima in the entropy proportion image resulting from this process were located using h-min transform that suppresses all minima whose depth is less than x% of the deeper one, resulting in a binary image. Morphological filtering [6] based on area and eccentricity indices enabled the isolation of the smaller area corresponding to the sharp minima, the coordinates of centroid of each of these areas defined the coordinates of a candidate point. (a) (b) Fig 3:Sequence illustrating pre processing 2: (a) contrast enhnaced image followed by (b) wavelet decomposition/reconstruction with two levels of details suppressed. C. Preprocessing 2 The preprocessing is aimed to smooth the radiometric fluctuations inside the particle and to enhance the borders, in order to detect the abrupt change in particle/background with the local stan...

DOI 10.1007/s00138-006-0021-7 ORIGINAL PAPER Computer vision for nanoscale imaging

by Eraldo Ribeiro, Mubarak Shah, E. Ribeiro (b
"... 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
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...presentative Work Image enhancement and noise removal Anisotropic diffusion [8,76,77] Structured illumination for super-resolution [31,73] Particle detection Template correlation [63] Detecting edges =-=[37,92,94,95]-=- Gray level intensity statistics [79,91] Appearance-based recognition [58,96] Neural networks [65] 3D reconstruction Multiple-view geometry [12,13,42] Tomographic projection reconstruction [28,43,60,7...

Contents lists available at ScienceDirect Journal of Structural Biology

by unknown authors
"... 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
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... Ogura and Sato, 2004; Plaisier et al., 2004; Short, 2004; Volkmann, 2004). Still, some other algorithms rely on a simplified geometric description of the overall shape of the particles being sought (=-=Yu and Bajaj, 2004-=-). The algorithms based on a 3D reference volume are useful for an advanced stage of the image processing in which such a reference already exists and it is used to collect more images. However, they ...

Segmentation of Rectangular Objects Lying on an Unknown Background in a Small Preview Scan Image

by Michael Guerzhoy, Hui Zhou
"... ..."
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...ge detection [9]; Hough transform of the edge space and subsequent search for rectangle hypotheses in Hough space [6]; distance transforms may be used to detect corners and group them into rectangles =-=[11]-=-. The methods above can be directly applied to the problem of segmentation of rectangular objects in a scanned image; however, they do not make use of all of the available domain knowledge. Namely, we...

Virology Journal BioMed Central Methodology

by Martin Ryner, Jan-olov Strömberg, Cecilia Söderberg-nauclér, Mohammed Homman-loudiyi , 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
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...been devoted to exploring different methods of identification, as discussed in a recent review[5]. In cryo-micrographs, cross correlation employing multiple templates[6] and methods for edge detection=-=[7]-=- have been applied successfully. Accordingly, in the present investigation, a similar approach has been applied to the analysis of HCMV capsids in the nucleus of infected cells that are at defined sta...

Detection of incomplete enclosures of rectangular shape in remotely sensed images

by Igor Zingman, Dietmar Saupe, Karsten Lambers
"... 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.
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...es are detection of buildings in remotely sensed images [24, 19, 14, 3, 12, 15, 1, 31, 30, 23, 26], traffic signs [21, 13, 22], and particles of a rectangular shape in cryo-electron microscopy images =-=[36, 35]-=-. The methods used were based on Markov Random Fields [15, 21], Marked Point Processes [1, 26], search on a graph [14, 38], Hough Transform and other voting schemes [3, 12, 36, 13, 22], template match...

Complementary Space for Enhanced Uncertainty and Dynamics Visualization

by Rajit Bajaj, Andrew Gillette, Samrat Goswami, Bong June Kwon
"... 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
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...oint sample of the surface, as was characterized by Edelsbrunner [9] and Giesen and John [12]. The distance function has been used in a variety of applications, including image feature identification =-=[5,21]-=-, stable medial axis construction [6], object segmentation and matching [8], annotation of flat and tubular features [13], and detection of secondary structural motifs in proteins [2]. In previous wor...

Segmentation of Neuronal Structures Using SARSA (l)-Based Boundary Amendment with Reinforced Gradient-Descent Curve Shape Fitting

by Fei Zhu, Quan Liu, Yuchen Fu, Bairong Shen
"... 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
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...proach to the comprehensive anatomical reconstruction of neuronal microcircuitry based on transmission EM sections of a small brain, i.e., the early larval brain of Drosophila melanogaster. Yu et al. =-=[20]-=- proposed a method for particle picking based on shape feature detection. Jurrus et al. [21] used Kalman-snakes and optical flow computation to track axons across large distances in volumes acquired b...

machine

by C. O. S. Sorzano, E. Recarte, M. Alcorlo, J. R. Bilbao-castro, C. San-martín, J. M. Carazo
"... particle selection from electron micrographs using ..."
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particle selection from electron micrographs using
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