Automatic Virus Identification using TEM : Image Segmentation and Texture Analysis ; Automatisk identifiering av virus med hjälp av transmissionselektronmikroskopi : bildsegmentering och texturanalys

Viruses and their morphology have been detected and studied with electron microscopy (EM) since the end of the 1930s. The technique has been vital for the discovery of new viruses and in establishi ...

[1]  J Pulokas,et al.  Leginon: an automated system for acquisition of images from vitreous ice specimens. , 2000, Journal of structural biology.

[2]  P. Roingeard.  Viral detection by electron microscopy: past, present and future , 2008, Biology of the cell.

[3]  Vinod Chandran,et al.  Identification of gastroenteric viruses by electron microscopy using higher order spectral features. , 2005, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[4]  L. Nanni,et al.  A Comparison of Multi-scale Approaches for Extracting Image Descriptors from the Co-occurrence Matrix , 2013 .

[5]  M. Teague.  Image analysis via the general theory of moments , 1980 .

[6]  Jana Reinhard,et al.  Textures A Photographic Album For Artists And Designers , 2016 .

[7]  N. Dimmock,et al.  Introduction to Modern Virology , 1974 .

[8]  Xiaoyang Tan,et al.  Enhanced Local Texture Feature Sets for Face Recognition Under Difficult Lighting Conditions , 2007, IEEE Transactions on Image Processing.

[9]  Javier González,et al.  A New Distance for Probability Measures Based on the Estimation of Level Sets , 2012, ICANN.

[10]  Bertrand Zavidovique,et al.  Median Binary Pattern for Textures Classification , 2007, ICIAR.

[11]  Marko Heikkilä,et al.  A texture-based method for modeling the background and detecting moving objects , 2006, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[12]  Maria da Conceição M. Sangreman Proenca,et al.  Automatic Virus Particle Selection—The Entropy Approach , 2013, IEEE Transactions on Image Processing.

[13]  Sriram Subramaniam,et al.  Automated image acquisition and processing using a new generation of 4K x 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies. , 2003, Journal of structural biology.

[14]  Bogdan J. Matuszewski,et al.  Hierarchical iterative Bayesian approach to automatic recognition of biological viruses in electron microscope images , 2001, Proceedings 2001 International Conference on Image Processing (Cat. No.01CH37205).

[15]  B. Matos,et al.  Applications of transmission electron microscopy to virus detection and identification , 2010 .

[16]  Sansanee Auephanwiriyakul,et al.  A Novel Fuzzy Co-occurrence Matrix for Texture Feature Extraction , 2013, ICCSA.

[17]  C O S Sorzano,et al.  Comparison of single‐particle analysis and electron tomography approaches: an overview , 2008, Journal of microscopy.

[18]  Eiko Nakazawa,et al.  Application of an automated specimen search system installed in a transmission electron microscope for the detection of caliciviruses in clinical specimens. , 2002, Journal of virological methods.

[19]  Anchi Cheng,et al.  Automated molecular microscopy: the new Leginon system. , 2005, Journal of structural biology.

[20]  H. Ruska.  Versuch zu einer Ordnung der Virusarten , 1943, Archives of Virology.

[21]  R. Fisher.  THE USE OF MULTIPLE MEASUREMENTS IN TAXONOMIC PROBLEMS , 1936 .

[22]  L. Nanni,et al.  Virus image classification using different texture descriptors , 2014 .

[23]  Mark Johnston,et al.  A One-Shot Learning Approach to Image Classification Using Genetic Programming , 2013, Australasian Conference on Artificial Intelligence.

[24]  G. Hall,et al.  A novel segmentation and classification method for identification of viruses in electron microscope images , 1997 .

[25]  Paul F. Whelan,et al.  Evaluation of robustness against rotation of LBP, CCR and ILBP features in granite texture classification , 2011, Machine Vision and Applications.

[26]  Wah Chiu,et al.  JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles. , 2009, Journal of structural biology.

[27]  Matti Pietikäinen,et al.  Multiresolution Gray-Scale and Rotation Invariant Texture Classification with Local Binary Patterns , 2002, IEEE Trans. Pattern Anal. Mach. Intell..

[28]  Robert M. Haralick,et al.  Textural Features for Image Classification , 1973, IEEE Trans. Syst. Man Cybern..

[29]  Francesco Bianconi,et al.  Evaluation of the effects of Gabor filter parameters on texture classification , 2007, Pattern Recognit..

[30]  Michael Gadermayr,et al.  Scale-Adaptive Texture Classification , 2014, 2014 22nd International Conference on Pattern Recognition.

[31]  D. Marinescu,et al.  Automatic Identification of Icosahedral Virus Particles in Electron Micrographs , 1996 .

[32]  G. Rake,et al.  The Use of the Electron Microscope in Diagnosis of Variola, Vaccinia, and Varicella , 1948, Journal of bacteriology.

[33]  Matti Pietikäinen,et al.  Computer Vision Using Local Binary Patterns , 2011, Computational Imaging and Vision.

[34]  John M. Walker,et al.  Principles and Techniques of Biochemistry and Molecular Biology: Plate sections , 2005 .

[35]  Matti Pietikäinen,et al.  Outex - new framework for empirical evaluation of texture analysis algorithms , 2002, Object recognition supported by user interaction for service robots.

[36]  F. Cobo,et al.  Application of Molecular Diagnostic Techniques for Viral Testing , 2012, The open virology journal.

[37]  Andrew Zisserman,et al.  Classifying Images of Materials: Achieving Viewpoint and Illumination Independence , 2002, ECCV.

[38]  Loris Nanni,et al.  A local approach based on a Local Binary Patterns variant texture descriptor for classifying pain states , 2010, Expert Syst. Appl..

[39]  S Subramaniam,et al.  Automated data collection with a Tecnai 12 electron microscope: applications for molecular imaging by cryomicroscopy. , 2001, Journal of structural biology.

[40]  Matti Pietikäinen,et al.  A comparative study of texture measures with classification based on featured distributions , 1996, Pattern Recognit..

[41]  Andrew R. Webb,et al.  Statistical Pattern Recognition , 1999 .

[42]  H. Gelderblom,et al.  Electron microscopy for rapid diagnosis of infectious agents in emergent situations. , 2003, Emerging infectious diseases.

[43]  Christian Suloway,et al.  Fully automated, sequential tilt-series acquisition with Leginon. , 2009, Journal of structural biology.

[44]  Topi Mäenpää,et al.  The local binary pattern approach to texture analysis - extensions and applications , 2003 .

[45]  Paul Smith,et al.  Robotic grid loading system for a transmission electron microscope. , 2004, Journal of structural biology.

[46]  D A Agard,et al.  Automated microscopy for electron tomography. , 1992, Ultramicroscopy.

[47]  Arivazhagan Selvaraj,et al.  Texture classification using Gabor wavelets based rotation invariant features , 2006, Pattern Recognit. Lett..

[48]  David N Mastronarde,et al.  Automated electron microscope tomography using robust prediction of specimen movements. , 2005, Journal of structural biology.

[49]  Joachim Frank,et al.  Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope. , 2005, Journal of structural biology.

[50]  D. Kriegman,et al.  Automatic particle selection: results of a comparative study. , 2004, Journal of structural biology.

[51]  J. Maniloff,et al.  Virus taxonomy : eighth report of the International Committee on Taxonomy of Viruses , 2005 .

[52]  M. C. Proenca,et al.  Texture Indicators for Segmentation of Polyomavirus Particles in Transmission Electron Microscopy Images , 2013, Microscopy and Microanalysis.

[53]  J. Flusser,et al.  Moments and Moment Invariants in Pattern Recognition , 2009 .

[54]  C. R. Rao,et al.  The Utilization of Multiple Measurements in Problems of Biological Classification , 1948 .

[55]  Sriram Subramaniam,et al.  Automated 100-position specimen loader and image acquisition system for transmission electron microscopy. , 2007, Journal of structural biology.

[56]  Andreas Uhl,et al.  A scale-adaptive extension to methods based on LBP using scale-normalized Laplacian of Gaussian extrema in scale-space , 2014, 2014 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[57]  Cordelia Schmid,et al.  A sparse texture representation using local affine regions , 2005, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[58]  Antonio Fernández,et al.  ASSESSMENT OF ROTATION-INVARIANT TEXTURE CLASSIFICATION THROUGH GABOR FILTERS AND DISCRETE FOURIER TRANSFORM , 2008 .

[59]  Hannah Ong.  Virus recognition in electron microscope images using higher order spectral features , 2006 .

[60]  Gunilla Borgefors,et al.  A refined circular template matching method for classification of human cytomegalovirus capsids in TEM images , 2004, Comput. Methods Programs Biomed..

[61]  Rafael C. González,et al.  Digital image processing, 3rd Edition , 2008 .

[62]  Ying Zhang,et al.  Electron microscopy: essentials for viral structure, morphogenesis and rapid diagnosis , 2013, Science China Life Sciences.

[63]  Sara E. Miller,et al.  Modern Uses of Electron Microscopy for Detection of Viruses , 2009, Clinical Microbiology Reviews.

[64]  C. Söderberg-Nauclér,et al.  Identification and classification of human cytomegalovirus capsids in textured electron micrographs using deformed template matching , 2006, Virology Journal.

[65]  Alan Curry,et al.  Application of transmission electron microscopy to the clinical study of viral and bacterial infections: Present and future , 2005, Micron.

[66]  Mark Johnston,et al.  Binary image classification using genetic programming based on local binary patterns , 2013, 2013 28th International Conference on Image and Vision Computing New Zealand (IVCNZ 2013).

[67]  Friedrich Förster,et al.  TOM software toolbox: acquisition and analysis for electron tomography. , 2005, Journal of structural biology.

[68]  Gustaf Kylberg,et al.  Kylberg Texture Dataset v. 1.0 , 2011 .

[69]  E. Ruska,et al.  Die Bedeutung der Übermikroskopie für die Virusforschung , 1939, Archiv für die gesamte Virusforschung.

[70]  Anil K. Jain,et al.  Learning Texture Discrimination Masks , 1996, IEEE Trans. Pattern Anal. Mach. Intell..

[71]  DH Kruger,et al.  Helmut Ruska and the visualisation of viruses , 2000, The Lancet.

[72]  Javier González,et al.  On the Generalization of the Mahalanobis Distance , 2013, CIARP.

[73]  Loris Nanni,et al.  Local binary patterns variants as texture descriptors for medical image analysis , 2010, Artif. Intell. Medicine.

[74]  Hanqing Lu,et al.  Face detection using improved LBP under Bayesian framework , 2004, Third International Conference on Image and Graphics (ICIG'04).

[75]  Seiichi Serikawa,et al.  Texture databases - A comprehensive survey , 2013, Pattern Recognit. Lett..

[76]  Gilles Hermann,et al.  ANIMATED-TEM: a toolbox for electron microscope automation based on image analysis , 2011, Machine Vision and Applications.

[77]  J. Schramlová,et al.  The role of electron microscopy in the rapid diagnosis of viral infections — review , 2010, Folia Microbiologica.

[78]  Matti Pietikäinen,et al.  Rotation-Invariant Image and Video Description With Local Binary Pattern Features , 2012, IEEE Transactions on Image Processing.

[79]  Emanuele Menegatti,et al.  Different Approaches for Extracting Information from the Co-Occurrence Matrix , 2013, PloS one.

[80]  T S Baker,et al.  Identification of spherical virus particles in digitized images of entire electron micrographs. , 1997, Journal of structural biology.

[81]  M. Pietikäinen,et al.  SOFT HISTOGRAMS FOR LOCAL BINARY PATTERNS , 2007 .

[82]  Dimitrios K. Iakovidis,et al.  Fuzzy Local Binary Patterns for Ultrasound Texture Characterization , 2008, ICIAR.

[83]  J. A. Comer,et al.  Cell Culture and Electron Microscopy for Identifying Viruses in Diseases of Unknown Cause , 2013, Emerging infectious diseases.

[84]  Anchi Cheng,et al.  Automated electron microscopy for evaluating two-dimensional crystallization of membrane proteins. , 2010, Journal of structural biology.

[85]  H. Nyquist,et al.  Certain Topics in Telegraph Transmission Theory , 1928, Transactions of the American Institute of Electrical Engineers.