Search results for: sequence image

Authors: Dr. H. B. Kekre, Sudeep D. Thepade

Abstract:

Panoramic view generation has always offered novel and distinct challenges in the field of image processing. Panoramic view generation is nothing but construction of bigger view mosaic image from set of partial images of the desired view. The paper presents a solution to one of the problems of image seascape formation where some of the partial images are color and others are grayscale. The simplest solution could be to convert all image parts into grayscale images and fusing them to get grayscale image panorama. But in the multihued world, obtaining the colored seascape will always be preferred. This could be achieved by picking colors from the color parts and squirting them in grayscale parts of the seascape. So firstly the grayscale image parts should be colored with help of color image parts and then these parts should be fused to construct the seascape image. The problem of coloring grayscale images has no exact solution. In the proposed technique of panoramic view generation, the job of transferring color traits from reference color image to grayscale image is done by palette based method. In this technique, the color palette is prepared using pixel windows of some degrees taken from color image parts. Then the grayscale image part is divided into pixel windows with same degrees. For every window of grayscale image part the palette is searched and equivalent color values are found, which could be used to color grayscale window. For palette preparation we have used RGB color space and Kekre-s LUV color space. Kekre-s LUV color space gives better quality of coloring. The searching time through color palette is improved over the exhaustive search using Kekre-s fast search technique. After coloring the grayscale image pieces the next job is fusion of all these pieces to obtain panoramic view. For similarity estimation between partial images correlation coefficient is used.

Keywords: Panoramic View, Similarity Estimate, Color Transfer, Color Palette, Kekre's Fast Search, Kekre's LUV

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Authors: Randa Boukhris Trabelsi, Alima Damak Masmoudi, Dorra Sellami Masmoudi

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Nowadays, hand vein recognition has attracted more attentions in identification biometrics systems. Generally, hand vein image is acquired with low contrast and irregular illumination. Accordingly, if you have a good preprocessing of hand vein image, we can easy extracted the feature extraction even with simple binarization. In this paper, a proposed approach is processed to improve the quality of hand vein image. First, a brief survey on existing methods of enhancement is investigated. Then a Radon Like features method is applied to preprocessing hand vein image. Finally, experiments results show that the proposed method give the better effective and reliable in improving hand vein images.

Keywords: Hand Vein, Enhancement, Contrast, RLF, SDME

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Authors: Michele Sinico

Abstract:

The psychological present has an actual extension. When a sequence of instantaneous stimuli falls in this short interval of time, observers perceive a compresence of events in succession and the temporal order depends on the qualitative relationships between the perceptual properties of the events. Two experiments were carried out to study the influence of perceptual grouping, with and without temporal displacement, on the duration of auditory sequences. The psychophysical method of adjustment was adopted. The first experiment investigated the effect of temporal displacement of a white noise on sequence duration. The second experiment investigated the effect of temporal displacement, along the pitch dimension, on temporal shortening of sequence. The results suggest that the temporal order of sounds, in the case of temporal displacement, is organized along the pitch dimension.

Keywords: Time perception, perceptual present, temporal displacement, gestalt laws of perceptual organization

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Authors: Vipin Saxena, Deepa Raj

Abstract:

Unified Modeling language (UML) is one of the important modeling languages used for the visual representation of the research problem. In the present paper, UML model is designed for the Instruction pipeline which is used for the evaluation of the instructions of software programs. The class and sequence diagrams are designed & performance is evaluated for instructions of a sample program through a case study.

Keywords: UML, Instruction Pipeline, Class Diagram &Sequence Diagram.

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Authors: Amnach Khawne, Kazuhiko Hamamoto, Orachat Chitsobhuk

Abstract:

Most of the image watermarking methods, using the properties of the human visual system (HVS), have been proposed in literature. The component of the visual threshold is usually related to either the spatial contrast sensitivity function (CSF) or the visual masking. Especially on the contrast masking, most methods have not mention to the effect near to the edge region. Since the HVS is sensitive what happens on the edge area. This paper proposes ultrasound image watermarking using the visual threshold corresponding to the HVS in which the coefficients in a DCT-block have been classified based on the texture, edge, and plain area. This classification method enables not only useful for imperceptibility when the watermark is insert into an image but also achievable a robustness of watermark detection. A comparison of the proposed method with other methods has been carried out which shown that the proposed method robusts to blockwise memoryless manipulations, and also robust against noise addition.

Keywords: Medical image watermarking, Human Visual System, Image Adaptive Watermark

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Authors: Abdelouahab Moussaoui, Nabila Ferahta, Victor Chen

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The development of aid's systems for the medical diagnosis is not easy thing because of presence of inhomogeneities in the MRI, the variability of the data from a sequence to the other as well as of other different source distortions that accentuate this difficulty. A new automatic, contextual, adaptive and robust segmentation procedure by MRI brain tissue classification is described in this article. A first phase consists in estimating the density of probability of the data by the Parzen-Rozenblatt method. The classification procedure is completely automatic and doesn't make any assumptions nor on the clusters number nor on the prototypes of these clusters since these last are detected in an automatic manner by an operator of mathematical morphology called skeleton by influence zones detection (SKIZ). The problem of initialization of the prototypes as well as their number is transformed in an optimization problem; in more the procedure is adaptive since it takes in consideration the contextual information presents in every voxel by an adaptive and robust non parametric model by the Markov fields (MF). The number of bad classifications is reduced by the use of the criteria of MPM minimization (Maximum Posterior Marginal).

Keywords: Clustering, Automatic Classification, SKIZ, MarkovFields, Image segmentation, Maximum Posterior Marginal (MPM).

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Authors: Yayun Hsu, Henry Horng-Shing Lu

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This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate crosstalk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds, since biological information is inherently included inside the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.

Keywords: Brainbow, 3D imaging, image segmentation, neuron morphology, biological data mining, non-parametric learning.

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Authors: Ahmet Çay, Savvas Vassiliadis, Maria Rangoussi, Işık Tarakçıoğlu

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This paper presents a novel approach to assessing textile porosity by the application of the image analysis techniques. The images of different types of sample fabrics, taken through a microscope when the fabric is placed over a constant light source,transfer the problem into the image analysis domain. Indeed, porosity can thus be expressed in terms of a brightness percentage index calculated on the digital microscope image. Furthermore, it is meaningful to compare the brightness percentage index with the air permeability and the tightness indices of each fabric type. We have experimentally shown that there exists an approximately linear relation between brightness percentage and air permeability indices.

Keywords: Textile fabrics, porosity, air permeability, image analysis, light transmission.

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Authors: Imran Usman, Asifullah Khan, Rafiullah Chamlawi, Abdul Majid

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Information hiding for authenticating and verifying the content integrity of the multimedia has been exploited extensively in the last decade. We propose the idea of using genetic algorithm and non-deterministic dependence by involving the un-watermarkable coefficients for digital image authentication. Genetic algorithm is used to intelligently select coefficients for watermarking in a DCT based image authentication scheme, which implicitly watermark all the un-watermarkable coefficients also, in order to thwart different attacks. Experimental results show that such intelligent selection results in improvement of imperceptibility of the watermarked image, and implicit watermarking of all the coefficients improves security against attacks such as cover-up, vector quantization and transplantation.

Keywords: Digital watermarking, fragile watermarking, geneticalgorithm, Image authentication.

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Authors: Lisa M. Weltzer-Ward, Abbie Brown

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The sequence Analyze, Design, Develop, Implement, and Evaluate (ADDIE) provides a powerful methodology for designing computer-based educational materials. Helping students to understand this design process sequence may be achieved by providing them with direct, guided experience. This article examines such help and guidance and the overall learning process from a student-s personal experience.

Keywords: ADDIE, education, instructional design, web design.

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Authors: H. B. Kekre, Sudeep D. Thepade

Abstract:

The automatic construction of large, high-resolution image vistas (mosaics) is an active area of research in the fields of photogrammetry [1,2], computer vision [1,4], medical image processing [4], computer graphics [3] and biometrics [8]. Image stitching is one of the possible options to get image mosaics. Vista Creation in image processing is used to construct an image with a large field of view than that could be obtained with a single photograph. It refers to transforming and stitching multiple images into a new aggregate image without any visible seam or distortion in the overlapping areas. Vista creation process aligns two partial images over each other and blends them together. Image mosaics allow one to compensate for differences in viewing geometry. Thus they can be used to simplify tasks by simulating the condition in which the scene is viewed from a fixed position with single camera. While obtaining partial images the geometric anomalies like rotation, scaling are bound to happen. To nullify effect of rotation of partial images on process of vista creation, we are proposing rotation invariant vista creation algorithm in this paper. Rotation of partial image parts in the proposed method of vista creation may introduce some missing region in the vista. To correct this error, that is to fill the missing region further we have used image inpainting method on the created vista. This missing view regeneration method also overcomes the problem of missing view [31] in vista due to cropping, irregular boundaries of partial image parts and errors in digitization [35]. The method of missing view regeneration generates the missing view of vista using the information present in vista itself.

Keywords: Vista, Overlap Estimation, Rotation Invariance, Missing View Regeneration.

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Authors: Yiming Nie, Tao Wu, Xiangjing An, Hangen He

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Fast depth estimation from binocular vision is often desired for autonomous vehicles, but, most algorithms could not easily be put into practice because of the much time cost. We present an image-processing technique that can fast estimate depth image from binocular vision images. By finding out the lines which present the best matched area in the disparity space image, the depth can be estimated. When detecting these lines, an edge-emphasizing filter is used. The final depth estimation will be presented after the smooth filter. Our method is a compromise between local methods and global optimization.

Keywords: Depth estimation, image filters, stereo match.

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Authors: G. Balakrishnan, G. Sainarayanan, R. Nagarajan, Sazali Yaacob

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This paper presents a review on vision aided systems and proposes an approach for visual rehabilitation using stereo vision technology. The proposed system utilizes stereo vision, image processing methodology and a sonification procedure to support blind navigation. The developed system includes a wearable computer, stereo cameras as vision sensor and stereo earphones, all moulded in a helmet. The image of the scene infront of visually handicapped is captured by the vision sensors. The captured images are processed to enhance the important features in the scene in front, for navigation assistance. The image processing is designed as model of human vision by identifying the obstacles and their depth information. The processed image is mapped on to musical stereo sound for the blind-s understanding of the scene infront. The developed method has been tested in the indoor and outdoor environments and the proposed image processing methodology is found to be effective for object identification.

Keywords: Blind navigation, stereo vision, image processing, object preference, music tones.

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Authors: A. K. Bhandari, A. Kumar, P. K. Padhy

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In this paper, a novel contrast enhancement technique for contrast enhancement of a low-contrast satellite image has been proposed based on the singular value decomposition (SVD) and discrete cosine transform (DCT). The singular value matrix represents the intensity information of the given image and any change on the singular values change the intensity of the input image. The proposed technique converts the image into the SVD-DCT domain and after normalizing the singular value matrix; the enhanced image is reconstructed by using inverse DCT. The visual and quantitative results suggest that the proposed SVD-DCT method clearly shows the increased efficiency and flexibility of the proposed method over the exiting methods such as Linear Contrast Stretching technique, GHE technique, DWT-SVD technique, DWT technique, Decorrelation Stretching technique, Gamma Correction method based techniques.

Keywords: Singular Value Decomposition (SVD), discretecosine transforms (DCT), image equalization and satellite imagecontrast enhancement.

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Authors: Wan-Hyun Cho, In-Seop Na, Seong-ChaeSeo, Sang-Kyoon Kim, Soon-Young Park

Abstract:

In this paper, we propose the variational approach to solve single image defogging problem. In the inference process of the atmospheric veil, we defined new functional for atmospheric veil that satisfy edge-preserving regularization property. By using the fundamental lemma of calculus of variations, we derive the Euler-Lagrange equation foratmospheric veil that can find the maxima of a given functional. This equation can be solved by using a gradient decent method and time parameter. Then, we can have obtained the estimated atmospheric veil, and then have conducted the image restoration by using inferred atmospheric veil. Finally we have improved the contrast of restoration image by various histogram equalization methods. The experimental results show that the proposed method achieves rather good defogging results.

Keywords: Image defogging, Image restoration, Atmospheric veil, Transmission, Variational approach, Euler-Lagrange equation, Image enhancement.

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Authors: Mirzaee Mahmoodabadi Reza, Afghah Massih, Saeedi Somaye

Abstract:

Pabdeh shaly formation (Paleocene-Oligomiocene) has been expanded in Fars, Khozestan and Lorestan. The lower lithostratigraphic limit of this formation in Shiraz area is distinguished from Gurpi formation by purple shale. Its upper limit is gradational and conformable with Asmari formation. In order to study sequence stratigraphy and microfacies of Pabdeh formation in Shiraz area, one stratigraphic section have been chosen (Zanjiran section). Petrographic studies resulted in the identification of 9 pelagic and calciturbidite microfacies. The calciturbidite microfacies have been formed when the sea level was high, the rate of carbonate deposition was high and it slumped into the deep marine. Sequence stratigraphy studies show that Pabdeh formation in the studied zone consists of two depositional sequences (DS) that the lower contact is erosional (purple shale - type one, SBI or type two, SB2) and the upper contact is correlative conformity (type two, SB2).

Keywords: Pabdeh formation, Shiraz, Microfacies, Purple Shale, Zanjiran Section, Sequence Stratigraphy

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Authors: Sang-Wan Kim, Hoon Lee, Kyung-Ho Choi, Soon-Young Park

Abstract:

A talking head system (THS) is presented to animate the face of a speaking 3D avatar in such a way that it realistically pronounces the given Korean text. The proposed system consists of SAPI compliant text-to-speech (TTS) engine and MPEG-4 compliant face animation generator. The input to the THS is a unicode text that is to be spoken with synchronized lip shape. The TTS engine generates a phoneme sequence with their duration and audio data. The TTS applies the coarticulation rules to the phoneme sequence and sends a mouth animation sequence to the face modeler. The proposed THS can make more natural lip sync and facial expression by using the face animation generator than those using the conventional visemes only. The experimental results show that our system has great potential for the implementation of talking head for Korean text.

Keywords: Talking head, Lip sync, TTS, MPEG4.

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Authors: Seiichi Gohshi, Hiroyuki Sekiguchi, Yoshiyasu Shimizu, Takeshi Ikenaga

Abstract:

Super resolution (SR) technologies are now being applied to video to improve resolution. Some TV sets are now equipped with SR functions. However, it is not known if super resolution image reconstruction (SRR) for TV really works or not. Super resolution with non-linear signal processing (SRNL) has recently been proposed. SRR and SRNL are the only methods for processing video signals in real time. The results from subjective assessments of SSR and SRNL are described in this paper. SRR video was produced in simulations with quarter precision motion vectors and 100 iterations. These are ideal conditions for SRR. We found that the image quality of SRNL is better than that of SRR even though SRR was processed under ideal conditions.

Keywords: Super Resolution Image Reconstruction, Super Resolution with Non-Linear Signal Processing, Subjective Assessment, Image Quality

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Authors: C. Deepika, J. Nithya

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Segmentation is one of the essential tasks in image processing. Thresholding is one of the simplest techniques for performing image segmentation. Multilevel thresholding is a simple and effective technique. The primary objective of bi-level or multilevel thresholding for image segmentation is to determine a best thresholding value. To achieve multilevel thresholding various techniques has been proposed. A study of some nature inspired metaheuristic algorithms for multilevel thresholding for image segmentation is conducted. Here, we study about Particle swarm optimization (PSO) algorithm, artificial bee colony optimization (ABC), Ant colony optimization (ACO) algorithm and Cuckoo search (CS) algorithm.

Keywords: Ant colony optimization, Artificial bee colony optimization, Cuckoo search algorithm, Image segmentation, Multilevel thresholding, Particle swarm optimization.

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Authors: Abigail Qian Zhou

Abstract:

Since China has entered an era of mass tourism, there has been a fundamental change in the way Chinese people approach and perceive the image of other countries. With the advent of the new media era, social networking sites such as Sina Weibo have become a tool for many foreign governmental organizations to spread and promote their national image. Among them, the Japan National Tourism Organization (JNTO) was one of the first foreign official tourism agencies to register with Sina Weibo and actively implement communication activities. Due to historical and political reasons, cognition of Japan's national image by the Chinese has always been complicated and contradictory. However, since 2015, China has become the largest source of tourists visiting Japan. This clearly indicates that the broadening of Japan's national image in China has been effective and has value worthy of reference in promoting a positive Chinese perception of Japan and encouraging Japanese tourism. Within this context and using the method of content analysis in media studies through content mining software, this study analyzed how JNTO’s Sina Weibo accounts have constructed and spread Japan's national image. This study also summarized the characteristics of its content and form, and finally revealed the strategy of JNTO in building its international image. The findings of this study not only add a tourism-based perspective to traditional national image communications research, but also provide some reference for the effective international dissemination of national image in the future.

Keywords: National image, tourism, international communication, Japan, China.

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Authors: V. Masilamani, D.K. Sheena Christy, D.G. Thomas

Abstract:

Image synthesis is an important area in image processing. To synthesize images various systems are proposed in the literature. In this paper, we propose a bio-inspired system to synthesize image and to study the generating power of the system, we define the class of languages generated by our system. We call image as array in this paper. We use a primitive called iso-array to synthesize image/array. The operation is double splicing on iso-arrays. The double splicing operation is used in DNA computing and we use this to synthesize image. A comparison of the family of languages generated by the proposed self restricted double splicing systems on iso-arrays with the existing family of local iso-picture languages is made. Certain closure properties such as union, concatenation and rotation are studied for the family of languages generated by the proposed model.

Keywords: DNA computing, splicing system, iso-picture languages, iso-array double splicing system, iso-array self splicing.

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Authors: N. Shanmugapriya, R. Nallusamy

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Content-based image retrieval (CBIR) uses the contents of images to characterize and contact the images. This paper focus on retrieving the image by separating images into its three color mechanism R, G and B and for that Discrete Wavelet Transformation is applied. Then Wavelet based Generalized Gaussian Density (GGD) is practical which is used for modeling the coefficients from the wavelet transforms. After that it is agreed to Histogram of Oriented Gradient (HOG) for extracting its characteristic vectors with Relevant Feedback technique is used. The performance of this approach is calculated by exactness and it confirms that this method is wellorganized for image retrieval.

Keywords: Content-Based Image Retrieval (CBIR), Relevant Feedback, Histogram of Oriented Gradient (HOG), Generalized Gaussian Density (GGD).

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Authors: N.Subramanian, C.Murugesan

Abstract:

This paper is devoted to the study of the general properties of Orlicz space of entire sequence of fuzzy numbers by using infinite matrices.

Keywords: Fuzzy numbers, infinite matrix, Orlicz space, entiresequence.

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Authors: David Libouga Li Gwet, Marius Otesteanu, Ideal Oscar Libouga, Laurent Bitjoka, Gheorghe D. Popa

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Image segmentation is a method to extract regions of interest from an image. It remains a fundamental problem in computer vision. The increasing diversity and the complexity of segmentation algorithms have led us firstly, to make a review and classify segmentation techniques, secondly to identify the most used measures of segmentation performance and thirdly, discuss deeply on segmentation philosophy in order to help the choice of adequate segmentation techniques for some applications. To justify the relevance of our analysis, recent algorithms of segmentation are presented through the proposed classification.

Keywords: Classification, image segmentation, measures of performance.

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Authors: Mohammad R. M. Abdelaal, Reeman M. R. Hussein

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With the beginning of the new century, man still faces many challenges in how to form and develop his urban environment. To meet these challenges, many cities have tried to develop its visual image. This is by transforming their urban environment into a branded visual image; this is at the level of squares, the main roads, the borders, and the landmarks. In this realm, the paper aims at activating the role of branded urban spaces as an approach for the development of visual image of cities, especially in Egypt. It concludes the need to recognize the importance of developing the visual image in Egypt, through directing the urban planners to the important role of such spaces in achieving sustainability.

Keywords: Urban branded spaces, brand image, sustainable development, Cairo.

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Authors: Vijaya Prakash.A.M, K.S.Gurumurthy

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In Image processing the Image compression can improve the performance of the digital systems by reducing the cost and time in image storage and transmission without significant reduction of the Image quality. This paper describes hardware architecture of low complexity Discrete Cosine Transform (DCT) architecture for image compression[6]. In this DCT architecture, common computations are identified and shared to remove redundant computations in DCT matrix operation. Vector processing is a method used for implementation of DCT. This reduction in computational complexity of 2D DCT reduces power consumption. The 2D DCT is performed on 8x8 matrix using two 1-Dimensional Discrete cosine transform blocks and a transposition memory [7]. Inverse discrete cosine transform (IDCT) is performed to obtain the image matrix and reconstruct the original image. The proposed image compression algorithm is comprehended using MATLAB code. The VLSI design of the architecture is implemented Using Verilog HDL. The proposed hardware architecture for image compression employing DCT was synthesized using RTL complier and it was mapped using 180nm standard cells. . The Simulation is done using Modelsim. The simulation results from MATLAB and Verilog HDL are compared. Detailed analysis for power and area was done using RTL compiler from CADENCE. Power consumption of DCT core is reduced to 1.027mW with minimum area[1].

Keywords: Discrete Cosine Transform (DCT), Inverse DiscreteCosine Transform (IDCT), Joint Photographic Expert Group (JPEG), Low Power Design, Very Large Scale Integration (VLSI) .

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

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Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: Shaoyan Sun, Liwei Zhang, Chonghui Guo

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As the use of registration packages spreads, the number of the aligned image pairs in image databases (either by manual or automatic methods) increases dramatically. These image pairs can serve as a set of training data. Correspondingly, the images that are to be registered serve as testing data. In this paper, a novel medical image registration method is proposed which is based on the a priori knowledge of the expected joint intensity distribution estimated from pre-aligned training images. The goal of the registration is to find the optimal transformation such that the distance between the observed joint intensity distribution obtained from the testing image pair and the expected joint intensity distribution obtained from the corresponding training image pair is minimized. The distance is measured using the divergence measure based on Tsallis entropy. Experimental results show that, compared with the widely-used Shannon mutual information as well as Tsallis mutual information, the proposed method is computationally more efficient without sacrificing registration accuracy.

Keywords: Multimodality images, image registration, Shannonentropy, Tsallis entropy, mutual information, Powell optimization.

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Authors: Hamed Qazanfari, Hamid Hassanpour, Kazem Qazanfari

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In this paper, a method is provided for content-based image retrieval. Content-based image retrieval system searches query an image based on its visual content in an image database to retrieve similar images. In this paper, with the aim of simulating the human visual system sensitivity to image's edges and color features, the concept of color difference histogram (CDH) is used. CDH includes the perceptually color difference between two neighboring pixels with regard to colors and edge orientations. Since the HSV color space is close to the human visual system, the CDH is calculated in this color space. In addition, to improve the color features, the color histogram in HSV color space is also used as a feature. Among the extracted features, efficient features are selected using entropy and correlation criteria. The final features extract the content of images most efficiently. The proposed method has been evaluated on three standard databases Corel 5k, Corel 10k and UKBench. Experimental results show that the accuracy of the proposed image retrieval method is significantly improved compared to the recently developed methods.

Keywords: Content-based image retrieval, color difference histogram, efficient features selection, entropy, correlation.

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Authors: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

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A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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