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  • 1. Ibrahim, Muhammad Talal
    et al.
    Khan, M. Aurangzeb
    Alimgeer, Khurram Saleem
    Niazi, M Khalid Khan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
    Taj, Imtiaz A.
    Guan, Ling
    Velocity and pressure-based partitions of horizontal and vertical trajectories for on-line signature verification2010In: Pattern Recognition, ISSN 0031-3203, E-ISSN 1873-5142, Vol. 43, no 8, p. 2817-2832Article in journal (Refereed)
    Abstract [en]

    In general, shape of an on-line signature is used as a single discriminating feature. Sometimes shape of signature is used alone for verification purposes and sometimes it is used in combination with some other dynamic features such as velocity, pressure and acceleration. The shape of an on-line signature is basically formed due to the wrist and fingers movements where the wrist movement is represented by the horizontal trajectory and the movement of the fingers is represented by vertical trajectory. As the on-line signature is formed due to the combination of two movements that are essentially independent of each other, it will be more effective to use them as two separate discriminating features. Based on this observation, we propose to use these trajectories in isolation by first decomposing the pressure and velocity profiles into two partitions and then extracting the underlying horizontal and vertical trajectories. So the overall process can be thought as the process which exploits the inter-feature dependencies by decomposing signature trajectories depending upon pressure and velocity information and performs verification on each partition separately. As a result, we are able to extract eight discriminating features and among them the most stable discriminating feature is used in verification process. Further Principal Component Analysis (PCA) has been proposed to make the signatures rotation invariant. Experimental results demonstrate superiority of our approach in on-line signature verification in comparison with other techniques.

  • 2. Ibrahim, Muhammad Talal
    et al.
    Niazi, M. Khalid Khan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Guan, Ling
    Horizontal features based illumination normalization method for face recognition2011Conference paper (Refereed)
  • 3. Khan, Mohammad A. U.
    et al.
    Niazi, M. Khalid Khan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
    Khan, M. Aurangzeb
    Ibrahim, M. Talal
    Endothelial Cell Image Enhancement using Non-subsampled Image Pyramid2007In: Information Technology Journal, ISSN 1812-5638, E-ISSN 1812-5646, Vol. 6, no 7, p. 1057-1062Article in journal (Refereed)
    Abstract [en]

    A corneal endothelial cell image provides vast amount of information about a human eye. The cell density and cell shape parameters of a given endothelial cell image help opthamologists in making many vital clinical decisions. The acquired endothelial image is poor in contrast where cell boundaries are masked in the background. Previously, most of the work was based on morphological operations in spatial domain. However, if we think of cell structure as texture hidden in noisy background, we can get help from texture segmentation, a well studied area. In this work, we propose a non-subsampled Gaussian pyramid decomposition of lowpass region. At certain level of the pyramid, we start observing cleaner cell boundary structure which greatly facilitates its segmentation. Once segmented automatic cell counting can be used and simulation results have shown improvement in cell density count.

  • 4.
    Niazi, M. Khalid Khan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Image Filtering Methods for Biomedical Applications2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Filtering is a key step in digital image processing and analysis. It is mainly used for amplification or attenuation of some frequencies depending on the nature of the application. Filtering can either be performed in the spatial domain or in a transformed domain. The selection of the filtering method, filtering domain, and the filter parameters are often driven by the properties of the underlying image. This thesis presents three different kinds of biomedical image filtering applications, where the filter parameters are automatically determined from the underlying images.

    Filtering can be used for image enhancement. We present a robust image dependent filtering method for intensity inhomogeneity correction of biomedical images. In the presented filtering method, the filter parameters are automatically determined from the grey-weighted distance transform of the magnitude spectrum. An evaluation shows that the filter provides an accurate estimate of intensity inhomogeneity.

    Filtering can also be used for analysis. The thesis presents a filtering method for heart localization and robust signal detection from video recordings of rat embryos. It presents a strategy to decouple motion artifacts produced by the non-rigid embryonic boundary from the heart. The method also filters out noise and the trend term with the help of empirical mode decomposition. Again, all the filter parameters are determined automatically based on the underlying signal.

    Transforming the geometry of one image to fit that of another one, so called image registration, can be seen as a filtering operation of the image geometry. To assess the progression of eye disorder, registration between temporal images is often required to determine the movement and development of the blood vessels in the eye. We present a robust method for retinal image registration. The method is based on particle swarm optimization, where the swarm searches for optimal registration parameters based on the direction of its cognitive and social components. An evaluation of the proposed method shows that the method is less susceptible to becoming trapped in local minima than previous methods.

    With these thesis contributions, we have augmented the filter toolbox for image analysis with methods that adjust to the data at hand.

     

    List of papers
    1. An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
    Open this publication in new window or tab >>An Iterative Method for Intensity Inhomogeneity Correction based on the Grey-weighted distance transform of the magnitude spectrum
    (English)Manuscript (preprint) (Other academic)
    National Category
    Signal Processing Medical Image Processing
    Research subject
    Computerized Image Processing; Computerized Image Analysis
    Identifiers
    urn:nbn:se:uu:diva-158673 (URN)
    Available from: 2011-09-13 Created: 2011-09-13 Last updated: 2011-10-04
    2. Bias field correction using grey-weighted distance transform applied on MR volumes
    Open this publication in new window or tab >>Bias field correction using grey-weighted distance transform applied on MR volumes
    2011 (English)In: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, p. 357-360Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE conference proceedings, 2011
    National Category
    Medical Image Processing
    Research subject
    Computerized Image Analysis
    Identifiers
    urn:nbn:se:uu:diva-144827 (URN)10.1109/ISBI.2011.5872423 (DOI)000298849400082 ()978-1-4244-4127-3 (ISBN)
    Conference
    8th IEEE International Symposium on Biomedical Imaging (ISBI)
    Available from: 2011-06-09 Created: 2011-02-02 Last updated: 2012-06-09Bibliographically approved
    3. Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
    Open this publication in new window or tab >>Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition
    Show others...
    2011 (English)In: Computer analysis of images and patterns: 14th International Conference, CAIP 2011, pt 2, Springer-Verlag , 2011, p. 523-530Conference paper, Published paper (Refereed)
    Abstract [en]

    To develop an accurate and suitable method for measuring the embryonic heart rate in vitro, a system combining Laplacian eigenmaps and empirical mode decomposition has been proposed. The proposed method assess the heart activity in two steps; signal generation and heart signal analysis. Signal generation is achieved by Laplacian eigenmaps (LEM) in conjunction with correlation co-efficient, while the signal analysis of the heart motion has been performed by the modified empirical mode decomposition (EMD). LEM helps to find the template for the atrium and the ventricle respectively, whereas EMD helps to find the non-linear trend term without defining any regression model. The proposed method also removes the motion artifacts produced due to the the non-rigid deformation in the shape of the embryo, the noise induced during the data acquisition, and the higher order harmonics. To check the authenticity of the proposed method, 151 videos have been investigated. Experimental results demonstrate the superiority of the proposed method in comparison to three recent methods.

    Place, publisher, year, edition, pages
    Springer-Verlag, 2011
    Series
    Lecture Notes in Computer Science, ISSN 0302-9743 ; 6855
    National Category
    Computer Vision and Robotics (Autonomous Systems)
    Identifiers
    urn:nbn:se:uu:diva-155123 (URN)000300567300062 ()978-3-642-23677-8 (ISBN)
    Conference
    14th International Conference on Computer Analysis of Images and Patterns (CAIP) AUG 29-31, 2011 Seville, SPAIN
    Available from: 2011-06-16 Created: 2011-06-16 Last updated: 2018-01-12Bibliographically approved
    4. Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
    Open this publication in new window or tab >>Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos
    2009 (English)In: Transactions on Mass-Data Analysis of Images and Signals, ISSN 1868-6451, Vol. 1, no 2, p. 132-146Article in journal (Refereed) Published
    Abstract [en]

    Embryo cultures of rodents is an established technique for monitoring adverse effects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of rat embryos. First it detects the heart location by using decimation free directional filter bank along with first absolute moment, and then it counts the number of heart beats for a predetermined period of time. Using this automated method many more embryos can be evaluated at reasonable cost.

    Place, publisher, year, edition, pages
    Leipzig, Germany: IBAI Publishing, 2009
    Keywords
    heart detection, absolute central moments, embryo culture, directional analysis, edge delineation
    National Category
    Computer Vision and Robotics (Autonomous Systems)
    Research subject
    Signal Processing
    Identifiers
    urn:nbn:se:uu:diva-111495 (URN)
    Available from: 2009-12-15 Created: 2009-12-15 Last updated: 2018-01-12Bibliographically approved
    5. Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
    Open this publication in new window or tab >>Improved methodology for identifying the teratogenic potential in early drug development of hERG channel blocking drugs
    Show others...
    2010 (English)In: Reproductive Toxicology, ISSN 0890-6238, E-ISSN 1873-1708, Vol. 29, no 2, p. 156-163Article in journal (Refereed) Published
    Abstract [en]

    Drugs blocking the potassium current IKr of the heart (via hERG channel-inhibition) have the potential to cause hypoxia-related teratogenic effects. However, this activity may be missed in conventional teratology studies because repeat dosing may cause resorptions. The aim of the present study was to investigate an alternative protocol to reveal the teratogenic potential of IKr-blocking drugs. The IKr blocker astemizole, given as a single dose (80mg/kg) on gestation day (GD) 13 to pregnant rats caused digital defects. In whole rat embryo culture (2h) on GD 13, astemizole caused a decrease in embryonic heart rate at 20nM, and arrhythmias at 200-400nM. Cetirizine, without IKr-blocking properties, did not affect the rat embryonic heart in vitro. The present study shows that single dose testing on sensitive days of development, together with whole embryo culture, can be a useful methodology to better characterize the teratogenic potential of IKr-blocking drugs.

    Place, publisher, year, edition, pages
    Elsevier, 2010
    Keywords
    Astemizole, hERG channel, IKr, Teratogenicity, Hypoxia, Embryonic cardiac adverse effects, Embryotoxicity, Toxicology
    National Category
    Pharmaceutical Sciences Computer Vision and Robotics (Autonomous Systems)
    Research subject
    Toxicology; Computerized Image Processing
    Identifiers
    urn:nbn:se:uu:diva-118335 (URN)10.1016/j.reprotox.2010.01.014 (DOI)000276326900004 ()20144703 (PubMedID)
    Available from: 2010-02-23 Created: 2010-02-23 Last updated: 2018-01-12Bibliographically approved
    6. A Modified Particle Swarm Optimization Applied in Image Registration
    Open this publication in new window or tab >>A Modified Particle Swarm Optimization Applied in Image Registration
    2010 (English)In: Proceedings of 20th International Conference on Pattern Recognition, IEEE computer society , 2010, p. 2302-2305Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    IEEE computer society, 2010
    National Category
    Computer Vision and Robotics (Autonomous Systems)
    Research subject
    Computerized Image Analysis
    Identifiers
    urn:nbn:se:uu:diva-141213 (URN)
    Conference
    20th International Conference on Pattern Recognition (ICPR 2010)
    Available from: 2011-01-11 Created: 2011-01-11 Last updated: 2018-01-12Bibliographically approved
  • 5.
    Niazi, M. Khalid Khan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Ibrahim, Muhammad Talal
    Nilsson, Mats F.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Sköld, Anna-Carin
    Guan, Ling
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Robust Signal Generation and Analysis of Rat Embryonic Heart Rate In Vitro using Laplacian Eigenmaps and Empirical Mode Decomposition2011In: Computer analysis of images and patterns: 14th International Conference, CAIP 2011, pt 2, Springer-Verlag , 2011, p. 523-530Conference paper (Refereed)
    Abstract [en]

    To develop an accurate and suitable method for measuring the embryonic heart rate in vitro, a system combining Laplacian eigenmaps and empirical mode decomposition has been proposed. The proposed method assess the heart activity in two steps; signal generation and heart signal analysis. Signal generation is achieved by Laplacian eigenmaps (LEM) in conjunction with correlation co-efficient, while the signal analysis of the heart motion has been performed by the modified empirical mode decomposition (EMD). LEM helps to find the template for the atrium and the ventricle respectively, whereas EMD helps to find the non-linear trend term without defining any regression model. The proposed method also removes the motion artifacts produced due to the the non-rigid deformation in the shape of the embryo, the noise induced during the data acquisition, and the higher order harmonics. To check the authenticity of the proposed method, 151 videos have been investigated. Experimental results demonstrate the superiority of the proposed method in comparison to three recent methods.

  • 6.
    Niazi, M. Khalid Khan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nyström, Ingela
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Ibrahim, Muhammad Talal
    Guan, Ling
    Bias field correction using grey-weighted distance transform applied on MR volumes2011In: Proc. 8th International Symposium on Biomedical Imaging, Piscataway, NJ: IEEE conference proceedings, 2011, p. 357-360Conference paper (Refereed)
  • 7.
    Niazi, Muhammad Khalid Khan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Measuring Heart Rate from Rat Embryo Videos2008In: Swedish Symposium on Image Analysis, Lund, Sweden: Swedish Society for Automated Image Analysis , 2008, p. 35-38Conference paper (Other academic)
    Abstract [en]

     

    Embryo cultures of rodents is an established technique for monitoring adverse e®ects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of mouse or rat embryos. First it detects the heart location, and then it counts the number of heart beats for a predetermined period of time.

     

  • 8.
    Niazi, Muhammad Khalid Khan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Danielsson, Bengt R.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
    Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos2009In: Transactions on Mass-Data Analysis of Images and Signals, ISSN 1868-6451, Vol. 1, no 2, p. 132-146Article in journal (Refereed)
    Abstract [en]

    Embryo cultures of rodents is an established technique for monitoring adverse effects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of rat embryos. First it detects the heart location by using decimation free directional filter bank along with first absolute moment, and then it counts the number of heart beats for a predetermined period of time. Using this automated method many more embryos can be evaluated at reasonable cost.

  • 9.
    Niazi, Muhammad Khalid Khan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis.
    Nilsson, Mats F.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Danielsson, Bengt R.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Bengtsson, Ewert
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Centre for Image Analysis.
    Fully Automatic Heart Beat Rate Determination in Digital Video Recordings of Rat Embryos2008In: ADVANCES IN MASS DATA ANALYSIS OF IMAGES AND SIGNALS IN MEDICINE, BIOTECHNOLOGY, CHEMISTRY AND FOOD INDUSTRY, PRCEEDINGS / [ed] Perner P, Salvetti O, 2008, p. 27-37Conference paper (Refereed)
    Abstract [en]

    Embryo cultures of rodents is an established technique for monitoring adverse effects of chemicals on embryonic development. The assessment involves determination of the heart rate of the embryo which is usually done visually, a technique which is tedious and error prone. We present a new method for fully automatic heart detection in digital videos of rat embryos. First it detects the heart location, and then it counts the number of heart beats for a predetermined period of time. Using this automated method many more embryos can be evaluated at reasonable cost.

1 - 9 of 9
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