Siping Chen

Zhejiang University, Hang-hsien, Zhejiang Sheng, China

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Publications (61)53.8 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Acquisition of the standard plane is crucial for medical ultrasound diagnosis. However, this process requires substantial experience and a thorough knowledge of human anatomy. Therefore it is very challenging for novices and even time consuming for experienced examiners. We proposed a hierarchical, supervised learning framework for automatically detecting the standard plane from consecutive 2-D ultrasound images. We tested this technique by developing a system that localizes the fetal abdominal standard plane from ultrasound video by detecting three key anatomical structures: the stomach bubble, umbilical vein and spine. We first proposed a novel radial component-based model to describe the geometric constraints of these key anatomical structures. We then introduced a novel selective search method which exploits the vessel probability algorithm to produce probable locations for the spine and umbilical vein. Next, using component classifiers trained by random forests, we detected the key anatomical structures at their probable locations within the regions constrained by the radial component-based model. Finally, a second-level classifier combined the results from the component detection to identify an ultrasound image as either a "fetal abdominal standard plane" or a "non- fetal abdominal standard plane." Experimental results on 223 fetal abdomen videos showed that the detection accuracy of our method was as high as 85.6% and significantly outperformed both the full abdomen and the separate anatomy detection methods without geometric constraints. The experimental results demonstrated that our system shows great promise for application to clinical practice.
    Ultrasound in medicine & biology. 09/2014;
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    ABSTRACT: Research on how lexical tone is neuroanatomically represented in the human brain is central to our understanding of cortical regions subserving language. Past studies have exclusively focused on tone perception of the spoken language, and little is known as to the lexical tone processing in reading visual words and its associated brain mechanisms. In this study, we performed two experiments to identify neural substrates in Chinese tone reading. First, we used a tone judgment paradigm to investigate tone processing of visually presented Chinese characters. We found that, relative to baseline, tone perception of printed Chinese characters were mediated by strong brain activation in bilateral frontal regions, left inferior parietal lobule, left posterior middle/medial temporal gyrus, left inferior temporal region, bilateral visual systems, and cerebellum. Surprisingly, no activation was found in superior temporal regions, brain sites well known for speech tone processing. In activation likelihood estimation (ALE) meta-analysis to combine results of relevant published studies, we attempted to elucidate whether the left temporal cortex activities identified in Experiment one is consistent with those found in previous studies of auditory lexical tone perception. ALE results showed that only the left superior temporal gyrus and putamen were critical in auditory lexical tone processing. These findings suggest that activation in the superior temporal cortex associated with lexical tone perception is modality-dependent. Hum Brain Mapp, 2014. © 2014 Wiley Periodicals, Inc.
    Human Brain Mapping 09/2014; · 6.88 Impact Factor
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    ABSTRACT: Ultrasonic elastography, a non-invasive technique for assessing the elasticity properties of tissues, has shown promising results for disease diagnosis. However, biological soft tissues are viscoelastic in nature. Shearwave dispersion ultrasound vibrometry (SDUV) can simultaneously measure the elasticity and viscosity of tissue using shear wave propagation speeds at different frequencies. In this paper, the viscoelasticity of rat livers was measured quantitatively by SDUV for normal (stage F0) and fibrotic livers (stage F2). Meanwhile, an independent validation study was presented in which SDUV results were compared with those derived from dynamic mechanical analysis (DMA), which is the only mechanical test that simultaneously assesses the viscoelastic properties of tissue. Shear wave speeds were measured at frequencies of 100, 200, 300 and 400Hz with SDUV and the storage moduli and loss moduli were measured at the frequency range of 1-40Hz with DMA. The Voigt viscoelastic model was used in the two methods. The mean elasticity and viscosity obtained by SDUV ranged from 0.84±0.13kPa (F0) to 1.85±0.30kPa (F2) and from 1.12±0.11Pas (F0) to 1.70±0.31Pas (F2), respectively. The mean elasticity and viscosity derived from DMA ranged from 0.62±0.09kPa (F0) to 1.70±0.84kPa (F2) and from 3.38±0.32Pas (F0) to 4.63±1.30Pas (F2), respectively. Both SDUV and DMA demonstrated that the elasticity of rat livers increased from stage F0 to F2, a finding which was consistent with previous literature. However, the elasticity measurements obtained by SDUV had smaller differences than those obtained by DMA, whereas the viscosities obtained by the two methods were obviously different. We suggest that the difference could be related to factors such as tissue microstructure, the frequency range, sample size and the rheological model employed. For future work we propose some improvements in the comparative tests between SDUV and DMA, such as enlarging the harmonic frequency range of the shear wave to highlight the role of viscosity, finding an appropriate rheological model to improve the accuracy of tissue viscoelasticity estimations.
    Medical engineering & physics. 05/2014;
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    ABSTRACT: Compared to 1D phased array probes with a fixed focus in elevation, multi-row arrays can significantly improved the slice thickness throughout image by expanding aperture and dynamic focusing in elevation. This paper describes the design and measurement of a 64 × 5 element 1.5D ultrasonic transducer that enables dynamic focusing and apodization in the elevation direction. We manufactured a transducer with an aperture size of 24 mm × 16 mm using a widely-used piezoelectric ceramic (PZT-5H) as the piezoelectric vibrator. The measured center frequency and -6 dB fractional bandwidth of the 1.5D transducer were 3 MHz and 79%, respectively. A two-way insertion loss of -58 dB was obtained at the average center frequency. We carried out a sound field simulation and measured the actual transmitting (one-way) sound field data by using a hydrophone. In this way the sound beam profile in elevation direction was obtained, showing the -6 dB slice thickness measured was about 2 mm throughout the whole range of interest (from near to far field). This provided a much greater focal depth and much better imaging resolution in the elevation direction than can be achieved by using 1D probe.
    Sensors and Actuators A Physical 01/2014; · 1.84 Impact Factor
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    ABSTRACT: Blood-Brain Barrier (BBB) can be opened locally, noninvasively and reversibly by low frequency focused ultra-sound (FUS) in the presence of microbubbles. In this study, Evans blue (EB) dye extravasation across BBB was enhanced by 1 MHz FUS at acoustic pressure of 0.35MPa in the presence of microbubbles at clinically comparable dosage. The spatial distribution of EB extravasation was visualized using fluorescence imaging method. The center region of BBB disruption area showed more enhanced fluorescence signal than the surrounding region in general. However, EB dye deposition was heterogeneous in the center region. The findings in this study indicated potential use of fluorescence imaging to evaluate large molecules delivery across BBB.
    Bio-medical materials and engineering 01/2014; 24(6):2831-8. · 1.09 Impact Factor
  • Haoming Lin, Tianfu Wang, Siping Chen
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    ABSTRACT: This paper describes a new method for shear wave velocity estimation that is capable of extruding outliers automatically without preset threshold. The proposed method is an adaptive random sample consensus (ARANDSAC) and the metric used here is finding the certain percentage of inliers according to the closest distance criterion. To evaluate the method, the simulation and phantom experiment results were compared using linear regression with all points (LRWAP) and radon sum transform (RS) method. The assessment reveals that the relative biases of mean estimation are 20.00%, 4.67% and 5.33% for LRWAP, ARANDSAC and RS respectively for simulation, 23.53%, 4.08% and 1.08% for phantom experiment. The results suggested that the proposed ARANDSAC algorithm is accurate in shear wave speed estimation.
    Bio-medical materials and engineering 01/2014; 24(1):467-74. · 1.09 Impact Factor
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    ABSTRACT: Automation-assisted reading (AAR) techniques have the potential to reduce errors and increase productivity in cervical cancer screening. The sensitivity of AAR relies heavily on automated segmentation of abnormal cervical cells, which is handled poorly by current segmentation algorithms. In this paper, a global and local scheme based on graph cut approach is proposed to segment cervical cells in images with a mix of healthy and abnormal cells. For cytoplasm segmentation, the multi-way graph cut is performed globally on the a* channel enhanced image, which can be effective when the image histogram presents a non-bimodal distribution. For segmentation of nuclei, especially when they are abnormal, we propose to use graph cut adaptively and locally, which allows the combination of intensity, texture, boundary and region information. Two concave points-based approaches are integrated to split the touching-nuclei. As part of an ongoing clinical trial, preliminary validation results obtained from 21 cervical cell images with non-ideal imaging condition and pathology show that our segmentation method achieved 93% accuracy for cytoplasm, and 88.4% F-measure for abnormal nuclei, outperforming state of the art methods in terms of accuracy. Our method has the potential to improve the sensitivity of AAR in screening for cervical cancer.
    Computerized medical imaging and graphics: the official journal of the Computerized Medical Imaging Society 01/2014; · 1.04 Impact Factor
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    ABSTRACT: Currently, placental maturity staging is mainly based on subjective observation of the physician. To address this issue, a new method is proposed for automatic staging of placental maturity based on B-mode ultrasound images. Due to small variations in the placental images, dense descriptor is utilized in place of the sparse descriptor to boost performance. Dense sampled DAISY descriptor is investigated for the demonstrated scale and translation invariant properties. Moreover, the extracted dense features are encoded by vector locally aggregated descriptor (VLAD) for performance boosting. The experimental results demonstrate an accuracy of 0.874, a sensitivity of 0.996 and a specificity of 0.874 for placental maturity staging. The experimental results also show that the dense features outperform the sparse features.
    Bio-medical materials and engineering 01/2014; 24(6):2821-9. · 1.09 Impact Factor
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    ABSTRACT: Current automation-assisted technologies for screening cervical cancer mainly rely on automated liquid-based cytology slides with proprietary stain. This is not a cost-efficient approach to be utilized in developing countries. In this article, we propose the first automation-assisted system to screen cervical cancer in manual liquid-based cytology (MLBC) slides with hematoxylin and eosin (H&E) stain, which is inexpensive and more applicable in developing countries. This system consists of three main modules: image acquisition, cell segmentation, and cell classification. First, an autofocusing scheme is proposed to find the global maximum of the focus curve by iteratively comparing image qualities of specific locations. On the autofocused images, the multiway graph cut (GC) is performed globally on the a* channel enhanced image to obtain cytoplasm segmentation. The nuclei, especially abnormal nuclei, are robustly segmented by using GC adaptively and locally. Two concave-based approaches are integrated to split the touching nuclei. To classify the segmented cells, features are selected and preprocessed to improve the sensitivity, and contextual and cytoplasm information are introduced to improve the specificity. Experiments on 26 consecutive image stacks demonstrated that the dynamic autofocusing accuracy was 2.06 μm. On 21 cervical cell images with nonideal imaging condition and pathology, our segmentation method achieved a 93% accuracy for cytoplasm, and a 87.3% F-measure for nuclei, both outperformed state of the art works in terms of accuracy. Additional clinical trials showed that both the sensitivity (88.1%) and the specificity (100%) of our system are satisfyingly high. These results proved the feasibility of automation-assisted cervical cancer screening in MLBC slides with H&E stain, which is highly desirable in community health centers and small hospitals. © 2013 International Society for Advancement of Cytometry.
    Cytometry Part A 12/2013; · 3.71 Impact Factor
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    ABSTRACT: Experimental MS(n) mass spectral libraries currently do not adequately cover chemical space. This limits the robust annotation of metabolites in metabolomics studies of complex biological samples. In-silico fragmentation libraries would improve the identification of compounds from experimental multi-stage fragmentation data when experimental reference data is unavailable. Here we present a freely-available software package to automatically control Mass Frontier software to construct in-silico mass spectral libraries, and to perform spectral matching. Based on two case studies we have demonstrated that HAMMER allows researchers to generate in-silico mass spectral libraries in an automated and high-throughput fashion with little or no human intervention required. Documentation, examples, results and source code are available at http://www.biosciences-labs.bham.ac.uk/viant/hammer/ CONTACT: m.viant@bham.ac.uk.
    Bioinformatics 12/2013; · 5.47 Impact Factor
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    ABSTRACT: Currently, most medical images are stored and exchanged with little or no security; hence it is important to provide protection for the intellectual property of these images in a secured environment. In this paper, a new and reversible watermarking method is proposed to address this security issue. Specifically, signature information and textual data are inserted into the original medical images based on recursive dither modulation (RDM) algorithm after wavelet transform and singular value decomposition (SVD). In addition, differential evolution (DE) is applied to design the quantization steps (QSs) optimally for controlling the strength of the watermark. Using these specially designed hybrid techniques, the proposed watermarking technique obtains good imperceptibility and high robustness. Experimental results indicate that the proposed method is not only highly competitive, but also outperforms the existing methods.
    Expert Systems with Applications 11/2013; · 1.85 Impact Factor
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    ABSTRACT: T-rays is sensitive to covalently cross-linked proteins and can be used to probe unique dynamic properties of water surrounding a protein. In this paper, we demonstrate the unique absorption properties of the dynamic hydration shells determined by hemagglutinin (HA) protein in terahertz frequency. We study the changes arising from different concentrations in detail and show that nonlinear absorption coefficient is induced by the dynamic hydration water. The binary and ternary component model were used to interpret the nonlinearity absorption behaviors and predict the thickness of the hydration shells around the HA protein in aqueous phase.
    Journal of Innovative Optical Health Sciences 10/2013; 06(04). · 0.63 Impact Factor
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    ABSTRACT: Developing an acoustic radiation force excitation module including 64 channels based in FPGA for ultrasound elastography. The circuit of the module was drived in bipolar, and the parameters such as excitation frequency, pulse repetition frequency, pulse number, element number and focus depth were ajustable. The acoustic field for special parameter was experimented with OptiSon laser acoustic field system with a result which reflects the width of focal spot is about 3 mm. The acoustic power was experimented with RFB2000 radiation force balance with a result which reflects acoustic power is increasing linearly with the number of pulses and the number of elements, and is increasing squarely with the peak-to-peak value of excitation voltage. The module is promising in factual application which can be triggered externally in synchronously, and can be combined with B-mode ultrasound system for ultrasound elastograpy.
    Chinese journal of Medical Instrumentation. 09/2013; 37(5):322-6.
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    ABSTRACT: Ultrasound elastography, based on shear wave propagation, enables the quantitative and non-invasive assessment of liver mechanical properties such as stiffness and has been found to be feasible for and useful in the diagnosis of hepatic fibrosis. Most ultrasound elastographic methods use a purely elastic model to describe liver mechanical properties. However, to describe tissue that is dispersive and to obtain an accurate measure of tissue elasticity, the viscoelasticity of the tissue should be examined. The objective of this study was to investigate the shear viscoelastic characteristics, as measured by ultrasound elastography, of liver fibrosis in a rat model and to evaluate the diagnostic accuracy of viscoelasticity for staging liver fibrosis. Liver fibrosis was induced in 37 rats using carbon tetrachloride (CCl4); 6 rats served as controls. Liver viscoelasticity was measured in vitro using shear waves induced by acoustic radiation force. The measured mean values of liver elasticity and viscosity ranged from 0.84 to 3.45 kPa and from 1.12 to 2.06 Pa·s for fibrosis stages F0-F4, respectively. Spearman correlation coefficients indicated that stage of fibrosis was well correlated with elasticity (0.88) and moderately correlated with viscosity (0.66). The areas under receiver operating characteristic curves were 0.97 (≥F2), 0.91 (≥F3) and 1.00 (F4) for elasticity and 0.91 (≥F2), 0.79 (≥F3) and 0.74 (F4) for viscosity, respectively. The results confirmed that shear wave velocity was dispersive in frequency, suggesting a viscoelastic model to describe liver fibrosis. The study finds that although viscosity is not as good as elasticity for staging fibrosis, it is important to consider viscosity to make an accurate estimation of elasticity; it may also provide other mechanical insights into liver tissues.
    Ultrasound in medicine & biology 08/2013; · 2.46 Impact Factor
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    ABSTRACT: Muscle thickness is one of the most widely used parameters for quantifying muscle function. Ultrasonography is frequently used to estimate changes in muscle thickness in both static and dynamic contractions. Conventionally, most such measurements are conducted by manual analysis of ultrasound images. This manual approach is time consuming, subjective, susceptible to error and not suitable for measuring dynamic change. In this study, we developed an automated tracking method based on an optical flow algorithm using an affine motion model. The goal of the study was to evaluate the performance of the proposed method by comparing it with the manual approach and by determining its repeatability. Real-time B-mode ultrasound was used to examine the rectus femoris during voluntary contraction. The coefficient of multiple correlation (CMC) was used to quantify the level of agreement between the two methods and the repeatability of the proposed method. The two methods were also compared by linear regression and Bland-Altman analysis. The findings indicated that the results obtained using the proposed method were in good agreement with those obtained using the manual approach (CMC = 0.97 ± 0.02, difference = -0.06 ± 0.22 mm) and were highly repeatable (CMC = 0.91 ± 0.07). In conclusion, the automated method proposed here provides an accurate, highly repeatable and efficient approach to the estimation of muscle thickness during muscle contraction.
    Ultrasound in medicine & biology 08/2013; · 2.46 Impact Factor
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    ABSTRACT: Muscle aspect ratio of cross-sectional area (CSA) is one of the most widely used parameters for quantifying muscle function in both diagnosis and rehabilitation assessment. Ultrasound imaging has been frequently used to non-invasively study the characteristics of human muscles as a reliable method. However, the aspect ratio measurement is traditionally conducted by manual digitization of reference points, thus it is subjective, time-consuming and prone to errors. In this paper, a novel method is proposed to continuously detect the muscle aspect ratio. Two keypoint pairs are manually digitized on the lateral and longitudinal borders at the first frame, and automatically tracked by optical flow technique at the subsequent frames. The muscle aspect ratio is thereby obtained based on the estimated muscle width and thickness. Six ultrasound sequences from different subjects are used to evaluate this method, and the overall coefficient of multiple correlation (CMC) of the results between manual and proposed method is 0.97±0.02. The linear regression show that a good linear correlation between the results of the two methods is obtained (R2 = 0.974), with difference -0.01±0.16. The method proposed here provides an accurate, high repeatable and efficient approach for estimating muscle aspect ratio during human motion, thus justifying its application in biological sciences.
    IEEE transactions on bio-medical engineering 04/2013; · 2.15 Impact Factor
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    ABSTRACT: This paper proposes a method to segment the cytoplasm in cervical cell images using graph cut-based algorithm. First, the A* channel in CIE LAB color space is extracted for contrast enhancement. Then, in order to effectively extract cytoplasm boundaries when image histograms present non-bimodal distribution, Otsu multiple thresholding is performed on the contrast enhanced image to generate initial segments, based on which the segments are refined by the multi-way graph cut method. We use 21 cervical cell images with non-ideal imaging condition to evaluate cytoplasm segmentation performance. The proposed method achieved a 93% accuracy which outperformed state-of-the-art works.
    Bio-medical materials and engineering 01/2013; 23:S1177-S1183. · 1.09 Impact Factor
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    ABSTRACT: The purpose of ultrasound elastography is to identify lesions by reconstructing the hardness characteristics of tissue reconstructed from ultrasound data. Conventional quasi-static ultrasound elastography is easily applied to obtain axial strain components along the compression direction, with the results inverted to represent the distribution of tissue hardness under the assumption of constant internal stresses. However, previous works of quasi-static ultrasound elastography have found it difficult to obtain the lateral and shear strain components, due to the poor lateral resolution of conventional ultrasound probes. The physical nature of the strain field is a continuous vector field, which should be fully described by the axial, lateral, and shear strain components, and the clinical value of lateral and shear strain components of deformed tissue is gradually being recognized by both engineers and clinicians. Therefore, a biomechanical-model-constrained filtering framework is proposed here for recovering a full displacement field at a high spatial resolution from the noisy ultrasound data. In our implementation, after the biomechanical model constraint is integrated into the state-space equation, both the axial and lateral displacement components can be recovered at a high spatial resolution from the noisy displacement measurements using a robust [Formula: see text] filter, which only requires knowledge of the worst-case noise levels in the measurements. All of the strain components can then be calculated by applying a gradient operator to the recovered displacement field. Numerical experiments on synthetic data demonstrated the robustness and effectiveness of our approach, and experiments on phantom data and in-vivo clinical data also produced satisfying results.
    PLoS ONE 01/2013; 8(9):e73093. · 3.53 Impact Factor
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    ABSTRACT: Muscle thickness is one of the most widely used parameters for quantifying muscle function in both diagnosis and rehabilitation assessment. Ultrasound imaging has been frequently used to non-invasively study the thickness of human muscles as a reliable method. However, the measurement is traditionally conducted by manual digitization of reference points at the superior and inferior muscle fascias, thus it is subjective and time-consuming. In this paper, a novel method is proposed to detect the muscle thickness automatically. The superficial and deep fascias of a muscle are detected by line detection algorithm at the first ultrasound frame, and the image regions of interest (ROI) for the fascias are subsequently located and tracked by optical flow technique. The muscle thickness is geometrically obtained based on the location of the fascias for each frame. Six ultrasound sequences (250 frames in each sequence) are used to evaluate this method. The correlation coefficient of the detection results between the proposed method and manual method is 0.95 ± 0.01, and the difference is −0.05 ± 0.22 mm. The linear regression of the total 1500 detections show that a good linear correlation between the results of the two methods is obtained (R2 = 0.981). The automated method proposed here provides an accurate, high repeatable and efficient approach for estimating fascicle thickness during human motion, thus justifying its application in biological sciences.
    Biomedical Signal Processing and Control 01/2013; 8(6):792–798. · 1.07 Impact Factor
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    ABSTRACT: Multi-beam imaging is a technique which creates several scan lines of images in one transmit beam. Generally, multiple receive beams are formed by multiple beam-formers operating in parallel. However, because of the large amount of circuitry required for each beam-former, this approach is very expensive and impractical. In this paper, time multiplexing method is used to save the hardware resources of multi-beam processing. The experimental results show that the time multiplexing method can save about 40% of the hardware resources compared with the parallel processing method. In particular, the hardware resources being saved can reach up to 50% for DSP48A multipliers when two receive beams are generated simultaneously. This shows that time multiplexing method can be used to alleviate the problem of insufficient hardware resources.
    Bio-medical materials and engineering 01/2013; 23:S791-S796. · 1.09 Impact Factor

Publication Stats

13 Citations
53.80 Total Impact Points

Institutions

  • 2014
    • Zhejiang University
      • Department of Biomedical Engineering
      Hang-hsien, Zhejiang Sheng, China
  • 2011–2014
    • Shenzhen University
      Bao'an, Guangdong, China
  • 2009
    • Institute of Electrical and Electronics Engineers
      Washington, Washington, D.C., United States