Displaying publications 21 - 40 of 90 in total

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  1. Localization of burn mark under an abnormal topography on MOSFET chip surface using liquid crystal and emission microscopy tools
    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.
  2. Image noise cross-correlation for signal-to-noise ratio estimation in scanning electron microscope images
    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.
  3. Autoregressive Wiener filtering in a scanning electron microscopy imaging system
    Sim KS, Kamel NS, Chuah HT
    Scanning, 2005 6 7;27(3):147-53.
    PMID: 15934507
    In this paper, we propose to use the autoregressive (AR)-based interpolator with Wiener filter and apply the idea to scanning electron microscope (SEM) images. The concept for combining the AR-based interpolator with Wiener filtering comes from the essential requirement of Wiener filtering for accurate and consistent estimation of the power of the noise in images prior to filter implementation. The resultant filter is called AR-Wiener filter. The proposed filter is embedded onto the frame grabber card of the scanning electron microscope (SEM) for real-time image processing. Different images are captured using SEM and used to compare the performances of the conventional Wiener and the proposed AR-Wiener technique.
  4. Robust image signal-to-noise ratio estimation using mixed Lagrange time delay estimation autoregressive model
    Sim KS, Cheng Z, Chuah HT
    Scanning, 2004 12 23;26(6):287-95.
    PMID: 15612206
    A new technique based on the statistical autoregressive (AR) model has recently been developed as a solution to signal-to-noise (SNR) estimation in scanning electron microscope (SEM) images. In the present study, we propose to cascade the Lagrange time delay (LTD) estimator with the AR model. We call this technique the mixed Lagrange time delay estimation autoregressive (MLTDEAR) model. In a few test cases involving different images, this model is found to present an optimum solution for SNR estimation problems under different noise environments. In addition, it requires only a small filter order and has no noticeable estimation bias. The performance of the proposed estimator is compared with three existing methods: simple method, first-order linear interpolator, and AR-based estimator over several images. The efficiency of the MLTDEAR estimator, being more robust with noise, is significantly greater than that of the other three methods.
  5. Brain early infarct detection using gamma correction extreme-level eliminating with weighting distribution
    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.
  6. Adaptive noise Wiener filter for scanning electron microscope imaging system
    Sim KS, Teh V, Nia ME
    Scanning, 2016 Mar;38(2):148-63.
    PMID: 26235517 DOI: 10.1002/sca.21250
    Noise on scanning electron microscope (SEM) images is studied. Gaussian noise is the most common type of noise in SEM image. We developed a new noise reduction filter based on the Wiener filter. We compared the performance of this new filter namely adaptive noise Wiener (ANW) filter, with four common existing filters as well as average filter, median filter, Gaussian smoothing filter and the Wiener filter. Based on the experiments results the proposed new filter has better performance on different noise variance comparing to the other existing noise removal filters in the experiments. SCANNING 38:148-163, 2016. © 2015 Wiley Periodicals, Inc.
  7. Signal-to-noise ratio estimation using adaptive tuning on the piecewise cubic Hermite interpolation model for images
    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.
  8. Signal-to-noise ratio enhancement on SEM images using a cubic spline interpolation with Savitzky-Golay filters and weighted least squares error
    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.
  9. Fulltext Cytotoxic effect of Alpinia scabra (Blume) Náves extracts on human breast and ovarian cancer cells
    Reddy AS, Abd Malek SN, Ibrahim H, Sim KS
    BMC Complement Altern Med, 2013 Nov 12;13:314.
    PMID: 24215354 DOI: 10.1186/1472-6882-13-314
    BACKGROUND: Alpinia scabra, locally known as 'Lengkuas raya', is an aromatic, perennial and rhizomatous herb from the family Zingiberaceae. It is a wild species which grows largely on mountains at moderate elevations in Peninsular Malaysia, but it can also survive in the lowlands like in the states of Terengganu and Northern Johor. The present study reports the cytotoxic potential of A. scabra extracts from different parts of the plant.

    METHODS: The experimental approach in the present study was based on a bioassay-guided fractionation. The crude methanol and fractionated extracts (hexane, chloroform and water) from different parts of A. scabra (leaves, rhizomes, roots and pseudo stems) were prepared prior to the cytotoxicity evaluation against human ovarian (SKOV-3) and hormone-dependent breast (MCF7) carcinoma cells. The identified cytotoxic extracts were then subjected to chemical investigations in order to identify the active ingredients. A normal human lung fibroblast cell line (MRC-5) was used to determine the specificity for cancerous cells. The cytotoxic extracts and fractions were also subjected to morphological assessment, DNA fragmentation analysis and DAPI nuclear staining.

    RESULTS: The leaf (hexane and chloroform) and rhizome (chloroform) extracts showed high inhibitory effect against the tested cells. Ten fractions (LC1-LC10) were yielded after purification of the leaf chloroform extract. Fraction LC4 which showed excellent cytotoxic activity was further purified and resulted in 17 sub-fractions (VLC1-VLC17). Sub-fraction VLC9 showed excellent cytotoxicity against MCF7 and SKOV-3 cells but not toxic against normal MRC-5 cells. Meanwhile, eighteen fractions (RC1-RC18) were obtained after purification of the rhizome chloroform extract, of which fraction RC5 showed cytotoxicity against SKOV-3 cells with high selectivity index. There were marked morphological changes when observed using phase-contrast inverted microscope, DAPI nuclear staining and also DNA fragmentations in MCF7 and SKOV-3 cells after treatment with the cytotoxic extracts and fractions which were indicative of cell apoptosis. Methyl palmitate and methyl stearate were identified in the hexane leaf extract by GC-MS analysis.

    CONCLUSIONS: The data obtained from the current study demonstrated that the cell death induced by cytotoxic extracts and fractions of A. scabra may be due to apoptosis induction which was characterized by apoptotic morphological changes and DNA fragmentation. The active ingredients in the leaf sub-fraction VLC9 and rhizome fraction RC5 may lead to valuable compounds that have the ability to kill cancer cells but not normal cells.

  10. Signal-to-noise ratio estimation on SEM images using cubic spline interpolation with Savitzky-Golay smoothing
    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.
  11. Fulltext Performance of new signal-to-noise ratio estimation for SEM images based on single image noise cross-correlation
    Sim KS, Nia ME, Tso CP, Lim WK
    J Microsc, 2012 Nov;248(2):120-8.
    PMID: 22900970 DOI: 10.1111/j.1365-2818.2012.03657.x
    A new technique for estimation of signal-to-noise ratio in scanning electron microscope images is reported. The method is based on the image noise cross-correlation estimation model recently developed. We derive the basic performance limits on a single image signal-to-noise ratio estimation using the Cramer-Rao inequality. The results are compared with those from existing estimation methods including the nearest neighbourhood (the simple method), the first order linear interpolator, and the autoregressive based estimator. The comparisons were made using several tests involving different images within the performance bounds. From the results obtained, the efficiency and accuracy of image noise cross-correlation estimation technique is considerably better than the other three methods.
  12. A study on discrete wavelet-based noise removal from EEG signals
    Asaduzzaman K, Reaz MB, Mohd-Yasin F, Sim KS, Hussain MS
    Adv Exp Med Biol, 2010;680:593-9.
    PMID: 20865544 DOI: 10.1007/978-1-4419-5913-3_65
    Electroencephalogram (EEG) serves as an extremely valuable tool for clinicians and researchers to study the activity of the brain in a non-invasive manner. It has long been used for the diagnosis of various central nervous system disorders like seizures, epilepsy, and brain damage and for categorizing sleep stages in patients. The artifacts caused by various factors such as Electrooculogram (EOG), eye blink, and Electromyogram (EMG) in EEG signal increases the difficulty in analyzing them. Discrete wavelet transform has been applied in this research for removing noise from the EEG signal. The effectiveness of the noise removal is quantitatively measured using Root Mean Square (RMS) Difference. This paper reports on the effectiveness of wavelet transform applied to the EEG signal as a means of removing noise to retrieve important information related to both healthy and epileptic patients. Wavelet-based noise removal on the EEG signal of both healthy and epileptic subjects was performed using four discrete wavelet functions. With the appropriate choice of the wavelet function (WF), it is possible to remove noise effectively to analyze EEG significantly. Result of this study shows that WF Daubechies 8 (db8) provides the best noise removal from the raw EEG signal of healthy patients, while WF orthogonal Meyer does the same for epileptic patients. This algorithm is intended for FPGA implementation of portable biomedical equipments to detect different brain state in different circumstances.
  13. Fulltext Phenolic content and antioxidant activity of Pereskia grandifolia Haw. (Cactaceae) extracts
    Sim KS, Nurestri AM, Norhanom AW
    Pharmacogn Mag, 2010 Jul;6(23):248-54.
    PMID: 20931088 DOI: 10.4103/0973-1296.66945
    The leaves of Pereskia grandifolia Haw. (Cactaceae), commonly known as "Jarum Tujuh Bilah" in Malaysia, have been traditionally used as natural remedy in folk medicine by the locals. In the present study, the antioxidant potential of P. grandifolia crude methanol and its fractionated extracts (hexane, ethyl acetate and water) have been investigated, employing three different established testing systems, such as scavenging activity on 1,1-diphenyl-2-picrylhydrazyl (DPPH) radicals, reducing power assay and β-carotene method. The total phenolic content of the P. grandifolia extracts was also assessed by the Folin-Ciocalteau's method. The ethyl acetate extract showed significantly the highest total phenolic content, DPPH scavenging ability and antioxidant activity in β-carotene bleaching assay while the hexane extract possessed significantly strongest reducing power. The data obtained in these testing systems clearly establish the antioxidant potency of P. grandifolia. As such, this is the first report on the antioxidant activities of P. grandifolia.
  14. Single image signal-to-noise ratio estimation for magnetic resonance images
    Sim KS, Lai MA, Tso CP, Teo CC
    J Med Syst, 2011 Feb;35(1):39-48.
    PMID: 20703587 DOI: 10.1007/s10916-009-9339-9
    A novel technique to quantify the signal-to-noise ratio (SNR) of magnetic resonance images is developed. The image SNR is quantified by estimating the amplitude of the signal spectrum using the autocorrelation function of just one single magnetic resonance image. To test the performance of the quantification, SNR measurement data are fitted to theoretically expected curves. It is shown that the technique can be implemented in a highly efficient way for the magnetic resonance imaging system.
  15. Fulltext Improvement to the scanning electron microscope image colorization by adaptive tuning
    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.
  16. Fulltext Lagrange time delay estimation for scanning electron microscope image magnification
    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.
  17. Fulltext Gaussian-Taylor signal-to-noise ratio estimation for scanning electron microscope images
    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.
  18. Real-time image quality assessment with mixed Lagrange time delay estimation autoregressive (MLTDEAR) model
    Sim KS, Tso CP, Tan YY, Lim WK
    J Microsc, 2007 Jun;226(Pt 3):230-43.
    PMID: 17535262
    A proposal to assess the quality of scanning electron microscope images using mixed Lagrange time delay estimation technique is presented. With optimal scanning electron microscope scan rate information, online images can be quantified and improved. The online quality assessment technique is embedded onto a scanning electron microscope frame grabber card for real-time image processing. Different images are captured using scanning electron microscope and a database is built to optimally choose filter parameters. An optimum choice of filter parameters is obtained. With the optimum choice of scan rate, noise can be removed from real-time scanning electron microscope images without causing any sample contamination or increasing scanning time.
  19. Fulltext Genome Sequence of Salmonella enterica subsp. enterica Serovar Typhi Isolate PM016/13 from Untreated Well Water Associated with a Typhoid Outbreak in Pasir Mas, Kelantan, Malaysia
    Muhamad Harish S, Sim KS, Najimudin N, Aziah I
    Genome Announc, 2015;3(6).
    PMID: 26564032 DOI: 10.1128/genomeA.01261-15
    Salmonella enterica subsp. enterica serovar Typhi is a human-restricted pathogen that causes typhoid fever. Even though it is a human-restricted pathogen, the bacterium is also isolated from environments such as groundwater and pond water. Here, we describe the genome sequence of the Salmonella enterica subsp. enterica serovar Typhi PM016/13 which was isolated from well water during a typhoid outbreak in Kelantan, Malaysia, in 2013.
  20. Fulltext Leptospermum flavescens Constituent-LF1 Causes Cell Death through the Induction of Cell Cycle Arrest and Apoptosis in Human Lung Carcinoma Cells
    Navanesan S, Abdul Wahab N, Manickam S, Sim KS
    PLoS One, 2015;10(8):e0135995.
    PMID: 26287817 DOI: 10.1371/journal.pone.0135995
    Leptospermum flavescens Sm. (Myrtaceae), locally known as 'Senna makki' is a smallish tree that is widespread and recorded to naturally occur in the montane regions above 900 m a.s.l from Burma to Australia. Although the species is recorded to be used traditionally to treat various ailments, there is limited data on biological and chemical investigations of L. flavescens. The aim of the present study was to investigate and understand the ability of L. flavescens in inducing cell death in lung cancer cells. The cytotoxic potentials of the extraction yields (methanol, hexane, ethyl acetate and water extracts as wells as a semi pure fraction, LF1) were evaluated against two human non-small cell lung carcinoma cell lines (A549 and NCI-H1299) using the MTT assay. LF1 showed the greatest cytotoxic effect against both cell lines with IC50 values of 7.12 ± 0.07 and 9.62 ± 0.50 μg/ml respectively. LF1 treated cells showed a sub-G1 region in the cell cycle analysis and also caused the presence of apoptotic morphologies in cells stained with acridine orange and ethidium bromide. Treatment with LF1 manifested an apoptotic population in cells that were evaluated using the Annexin V/ propidium iodide assay. Increasing dosage of LF1 caused a rise in the presence of activated caspase-3 enzymes in treated cells. Blockage of cell cycle progression was also observed in LF1-treated cells. These findings suggest that LF1 induces apoptosis and cell cycle arrest in treated lung cancer cells. Further studies are being conducted to isolate and identify the active compound as well to better understand the mechanism involved in inducing cell death.
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