Displaying publications 1 - 20 of 90 in total

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  1. Sim KS, Chuah HT, Zheng C
    J Microsc, 2005 Jul;219(Pt 1):1-17.
    PMID: 15998361
    A novel technique based on the statistical autoregressive (AR) model has recently been developed as a solution to estimate the signal-to-noise ratio (SNR) in scanning electron microscope (SEM) images. In another research study, the authors also developed an algorithm by cascading the AR model with the Lagrange time delay (LTD) estimator. This technique is named the mixed Lagrange time delay estimation autoregressive (MLTDEAR) model. In this paper, the fundamental performance limits for the problem of single-image SNR estimation as derived from the Cramer-Rao inequality is presented. We compared the experimental performances of several existing methods--the simple method, the first-order linear interpolator, the AR-based estimator as well as the MLTDEAR method--with respect to this performance bound. In a few test cases involving different images, the efficiency of the MLTDEAR single-image estimation technique proved to be significantly better than that of the other three methods. Study of the effect of different SEM setting conditions that affect the autocorrelation function curve is also discussed.
  2. Sim KS, Lim MS, Yeap ZX
    J Microsc, 2016 07;263(1):64-77.
    PMID: 26871742 DOI: 10.1111/jmi.12376
    A new technique to quantify signal-to-noise ratio (SNR) value of the scanning electron microscope (SEM) images is proposed. This technique is known as autocorrelation Levinson-Durbin recursion (ACLDR) model. To test the performance of this technique, the SEM image is corrupted with noise. The autocorrelation function of the original image and the noisy image are formed. The signal spectrum based on the autocorrelation function of image is formed. ACLDR is then used as an SNR estimator to quantify the signal spectrum of noisy image. The SNR values of the original image and the quantified image are calculated. The ACLDR is then compared with the three existing techniques, which are nearest neighbourhood, first-order linear interpolation and nearest neighbourhood combined with first-order linear interpolation. It is shown that ACLDR model is able to achieve higher accuracy in SNR estimation.
  3. Teh V, Sim KS, Wong EK
    Scanning, 2016 Nov;38(6):842-856.
    PMID: 27302216 DOI: 10.1002/sca.21334
    According to the statistic from World Health Organization (WHO), stroke is one of the major causes of death globally. Computed tomography (CT) scan is one of the main medical diagnosis system used for diagnosis of ischemic stroke. CT scan provides brain images in Digital Imaging and Communication in Medicine (DICOM) format. The presentation of CT brain images is mainly relied on the window setting (window center and window width), which converts an image from DICOM format into normal grayscale format. Nevertheless, the ordinary window parameter could not deliver a proper contrast on CT brain images for ischemic stroke detection. In this paper, a new proposed method namely gamma correction extreme-level eliminating with weighting distribution (GCELEWD) is implemented to improve the contrast on CT brain images. GCELEWD is capable of highlighting the hypodense region for diagnosis of ischemic stroke. The performance of this new proposed technique, GCELEWD, is compared with four of the existing contrast enhancement technique such as brightness preserving bi-histogram equalization (BBHE), dualistic sub-image histogram equalization (DSIHE), extreme-level eliminating histogram equalization (ELEHE), and adaptive gamma correction with weighting distribution (AGCWD). GCELEWD shows better visualization for ischemic stroke detection and higher values with image quality assessment (IQA) module. SCANNING 38:842-856, 2016. © 2016 Wiley Periodicals, Inc.
  4. Sim KS, White JD
    J Microsc, 2005 Mar;217(Pt 3):235-40.
    PMID: 15725127
    The quality of an image generated by a scanning electron microscope is dependent on secondary emission, which is a strong function of surface condition. Thus, empirical formulae and available databases are unable to take into account actual metrology conditions. This paper introduces a simple and reliable measurement technique to measure secondary electron yield (delta) and backscattered electron yield (eta) that is suitable for in-situ measurements on a specimen immediately prior to imaging. The reliability of this technique is validated on a number of homogenous surfaces. The measured electron yields are shown to be within the range of published data and the calculated signal-to-noise ratio compares favourably with that estimated from the image.
  5. Kiani MA, Sim KS, Nia ME, Tso CP
    J Microsc, 2015 May;258(2):140-50.
    PMID: 25676007 DOI: 10.1111/jmi.12227
    A new technique based on cubic spline interpolation with Savitzky-Golay smoothing using weighted least squares error filter is enhanced for scanning electron microscope (SEM) images. A diversity of sample images is captured and the performance is found to be better when compared with the moving average and the standard median filters, with respect to eliminating noise. This technique can be implemented efficiently on real-time SEM images, with all mandatory data for processing obtained from a single image. Noise in images, and particularly in SEM images, are undesirable. A new noise reduction technique, based on cubic spline interpolation with Savitzky-Golay and weighted least squares error method, is developed. We apply the combined technique to single image signal-to-noise ratio estimation and noise reduction for SEM imaging system. This autocorrelation-based technique requires image details to be correlated over a few pixels, whereas the noise is assumed to be uncorrelated from pixel to pixel. The noise component is derived from the difference between the image autocorrelation at zero offset, and the estimation of the corresponding original autocorrelation. In the few test cases involving different images, the efficiency of the developed noise reduction filter is proved to be significantly better than those obtained from the other methods. Noise can be reduced efficiently with appropriate choice of scan rate from real-time SEM images, without generating corruption or increasing scanning time.
  6. Sim KS, Kiani MA, Nia ME, Tso CP
    J Microsc, 2014 Jan;253(1):1-11.
    PMID: 24164248 DOI: 10.1111/jmi.12089
    A new technique based on cubic spline interpolation with Savitzky-Golay noise reduction filtering is designed to estimate signal-to-noise ratio of scanning electron microscopy (SEM) images. This approach is found to present better result when compared with two existing techniques: nearest neighbourhood and first-order interpolation. When applied to evaluate the quality of SEM images, noise can be eliminated efficiently with optimal choice of scan rate from real-time SEM images, without generating corruption or increasing scanning time.
  7. Sim KS, Ting HY, Lai MA, Tso CP
    J Microsc, 2009 Jun;234(3):243-50.
    PMID: 19493101 DOI: 10.1111/j.1365-2818.2009.03167.x
    An improvement to the previously proposed Canny optimization technique for scanning electron microscope image colorization is reported. The additional process is adaptive tuning, where colour tuning is performed adaptively, based on comparing the original luminance values with calculated luminance values. The complete adaptive Canny optimization technique gives significantly better mechanical contrast on scanning electron microscope grey-scale images than do existing methods.
  8. Sim KS, Thong LW, Ting HY, Tso CP
    J Microsc, 2010 Feb;237(2):111-8.
    PMID: 20096041 DOI: 10.1111/j.1365-2818.2009.03325.x
    Interpolation techniques that are used for image magnification to obtain more useful details of the surface such as morphology and mechanical contrast usually rely on the signal information distributed around edges and areas of sharp changes and these signal information can also be used to predict missing details from the sample image. However, many of these interpolation methods tend to smooth or blur out image details around the edges. In the present study, a Lagrange time delay estimation interpolator method is proposed and this method only requires a small filter order and has no noticeable estimation bias. Comparing results with the original scanning electron microscope magnification and results of various other interpolation methods, the Lagrange time delay estimation interpolator is found to be more efficient, more robust and easier to execute.
  9. Sim KS, Lee JK, Lai MA, Tso CP
    J Microsc, 2009 Oct;236(1):18-34.
    PMID: 19772533 DOI: 10.1111/j.1365-2818.2009.03194.x
    A new and robust parameter estimation technique, named Gaussian-Taylor interpolation, is proposed to predict the signal-to-noise ratio (SNR) of scanning electron microscope images. The results of SNR and variance estimation values are tested and compared with piecewise cubic Hermite interpolation, quadratic spline interpolation, autoregressive moving average and moving average. Overall, the proposed estimations for noise-free peak and SNR are most consistent and accurate to within a certain acceptable degree compared with the others.
  10. Sim KS, Law KK, Tso CP
    Microsc Res Tech, 2007 Nov;70(11):919-27.
    PMID: 17661362
    A new filter is developed for the enhancement of scanning electron microscope (SEM) images. A mixed Lagrange time delay estimation auto-regression (MLTDEAR)-based interpolator is used to provide an estimate of noise variance to a standard Wiener filter. A variety of images are captured and the performance of the filter is shown to surpass the conventional noise filters. As all the information required for processing is extracted from a single image, this method is not constrained by image registration requirements and thus can be applied in real-time in cases where specimen drift is presented in the SEM image.
  11. Yeap ZX, Sim KS, Tso CP
    Microsc Res Tech, 2019 Apr;82(4):402-414.
    PMID: 30575192 DOI: 10.1002/jemt.23181
    Image processing is introduced to remove or reduce the noise and unwanted signal that deteriorate the quality of an image. Here, a single level two-dimensional wavelet transform is applied to the image in order to obtain the wavelet transform sub-band signal of an image. An estimation technique to predict the noise variance in an image is proposed, which is then fed into a Wiener filter to filter away the noise from the sub-band of the image. The proposed filter is called adaptive tuning piecewise cubic Hermite interpolation with Wiener filter in the wavelet domain. The performance of this filter is compared with four existing filters: median filter, Gaussian smoothing filter, two level wavelet transform with Wiener filter and adaptive noise Wiener filter. Based on the results, the adaptive tuning piecewise cubic Hermite interpolation with Wiener filter in wavelet domain has better performance than the other four methods.
  12. Sim KS, Nia ME, Tso CP
    Scanning, 2013 May-Jun;35(3):205-12.
    PMID: 22961698 DOI: 10.1002/sca.21055
    A number of techniques have been proposed during the last three decades for noise variance and signal-to-noise ratio (SNR) estimation in digital images. While some methods have shown reliability and accuracy in SNR and noise variance estimations, other methods are dependent on the nature of the images and perform well on a limited number of image types. In this article, we prove the accuracy and the efficiency of the image noise cross-correlation estimation model, vs. other existing estimators, when applied to different types of scanning electron microscope images.
  13. Lau CK, Sim KS, Tso CP
    Scanning, 2011 Jan-Feb;33(1):13-20.
    PMID: 21462221 DOI: 10.1002/sca.20216
    This article focuses on the localization of burn mark in MOSFET and the scanning electron microscope (SEM) inspection on the defect location. When a suspect abnormal topography is shown on the die surface, further methods to pin-point the defect location is necessary. Fault localization analysis becomes important because an abnormal spot on the chip surface may and may not have a defect underneath it. The chip surface topography can change due to the catastrophic damage occurred at layers under the chip surface, but it could also be due to inconsistency during metal deposition in the wafer fabrication process. Two localization techniques, liquid crystal thermography and emission microscopy, were performed to confirm that the abnormal topography spot is the actual defect location. The tiny burn mark was surfaced by performing a surface decoration at the defect location using hot hydrochloric acid. SEM imaging, which has the high magnification and three-dimensional capabilities, was used to capture the images of the burn mark.
  14. Sim KS, Nia ME, Tso CP
    Scanning, 2011 Mar-Apr;33(2):82-93.
    PMID: 21381045 DOI: 10.1002/sca.20223
    A new and robust parameter estimation technique, named image noise cross-correlation, is proposed to predict the signal-to-noise ratio (SNR) of scanning electron microscope images. The results of SNR and variance estimation values are tested and compared with nearest neighborhood and first-order interpolation. Overall, the proposed method is best as its estimations for the noise-free peak and SNR are most consistent and accurate to within a certain acceptable degree, compared with the others.
  15. Sim KS, Yeap ZX, Tso CP
    Scanning, 2016 Nov;38(6):502-514.
    PMID: 26618491 DOI: 10.1002/sca.21286
    An improvement to the existing technique of quantifying signal-to-noise ratio (SNR) of scanning electron microscope (SEM) images using piecewise cubic Hermite interpolation (PCHIP) technique is proposed. The new technique uses an adaptive tuning onto the PCHIP, and is thus named as ATPCHIP. To test its accuracy, 70 images are corrupted with noise and their autocorrelation functions are then plotted. The ATPCHIP technique is applied to estimate the uncorrupted noise-free zero offset point from a corrupted image. Three existing methods, the nearest neighborhood, first order interpolation and original PCHIP, are used to compare with the performance of the proposed ATPCHIP method, with respect to their calculated SNR values. Results show that ATPCHIP is an accurate and reliable method to estimate SNR values from SEM images. SCANNING 38:502-514, 2016. © 2015 Wiley Periodicals, Inc.
  16. Ranjit S, Sim K, Besar R, Tso C
    Biomed Imaging Interv J, 2009 Jul;5(3):e32.
    PMID: 21611059 MyJurnal DOI: 10.2349/biij.5.3.e32
    By applying a hexagon-diamond search (HDS) method to an ultrasound image, the path of an object is able to be monitored by extracting images into macro-blocks, thereby achieving image redundancy is reduced from one frame to another, and also ascertaining the motion vector within the parameters searched. The HDS algorithm uses six search points to form the six sides of the hexagon pattern, a centre point, and a further four search points to create diamond pattern within the hexagon that clarifies the focus of the subject area.
  17. Sim KS, Tso CP, Ting HY
    J Microsc, 2008 Nov;232(2):313-34.
    PMID: 19017231 DOI: 10.1111/j.1365-2818.2008.02103.x
    Images of scanning electron microscope are usually in the monochrome mode. A simple and user-friendly approach is proposed to improve the mechanical contrast of the scanning electron microscope grey images. Also, most colourization techniques involve image segmentation or region tracking, which tend to degrade the image with fuzzy or complex region boundaries. A technique is proposed, which is a hybrid between the Canny edge detection technique and the optimization technique. Compared with existing methods, the new Canny optimization technique gives satisfactory results for scanning electron microscope images.
  18. Sim KS, Kho YY, Tso CP, Nia ME, Ting HY
    Scanning, 2013 Mar-Apr;35(2):75-87.
    PMID: 22777599 DOI: 10.1002/sca.21037
    Detection of cracks from stainless steel pipe images is done using contrast stretching technique. The technique is based on an image filter technique through mathematical morphology that can expose the cracks. The cracks are highlighted and noise removal is done efficiently while still retaining the edges. An automated crack detection system with a camera platform has been successfully implemented. We compare crack extraction in terms of quality measures with those of Otsu's threshold technique and the another technique (Iyer and Sinha, 2005). The algorithm shown is able to achieve good results and perform better than these other techniques.
  19. Wan Ismail WZ, Sim KS, Tso CP, Ting HY
    Scanning, 2011 Jul-Aug;33(4):233-51.
    PMID: 21611953 DOI: 10.1002/sca.20237
    To reduce undesirable charging effects in scanning electron microscope images, Rayleigh contrast stretching is developed and employed. First, re-scaling is performed on the input image histograms with Rayleigh algorithm. Then, contrast stretching or contrast adjustment is implemented to improve the images while reducing the contrast charging artifacts. This technique has been compared to some existing histogram equalization (HE) extension techniques: recursive sub-image HE, contrast stretching dynamic HE, multipeak HE and recursive mean separate HE. Other post processing methods, such as wavelet approach, spatial filtering, and exponential contrast stretching, are compared as well. Overall, the proposed method produces better image compensation in reducing charging artifacts.
  20. Wong LP, Ong RT, Poh WT, Liu X, Chen P, Li R, et al.
    Am J Hum Genet, 2013 Jan 10;92(1):52-66.
    PMID: 23290073 DOI: 10.1016/j.ajhg.2012.12.005
    Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (<5%) markers, a larger number of individuals might have to be whole-genome sequenced so that the accuracy currently afforded by the 1KGP can be achieved. The SSMP data are expected to be the benchmark for evaluating the value of deep population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.
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