Umar Alqasemi

University of Connecticut, Storrs, Connecticut, United States

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Publications (26)33.47 Total impact

  • Hai Li, Patrick Kumavor, Umar Salman Alqasemi, Quing Zhu
    Journal of Biomedical Optics 01/2015; 20(1):16002. DOI:10.1117/1.JBO.20.1.016002 · 2.75 Impact Factor
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    ABSTRACT: Laser diodes are widely used in diffuse optical tomography (DOT) systems but are typically expensive and fragile, while light-emitting diodes (LEDs) are cheaper and are also available in the near-infrared (NIR) range with adequate output power for imaging deeply seated targets. In this study, we introduce a new low-cost DOT system using LEDs of four wavelengths in the NIR spectrum as light sources. The LEDs were modulated at 20 kHz to avoid ambient light. The LEDs were distributed on a hand-held probe and a printed circuit board was mounted at the back of the probe to separately provide switching and driving current to each LED. Ten optical fibers were used to couple the reflected light to 10 parallel photomultiplier tube detectors. A commercial ultrasound system provided simultaneous images of target location and size to guide the image reconstruction. A frequency-domain (FD) laser-diode-based system with ultrasound guidance was also used to compare the results obtained from those of the LED-based system. Results of absorbers embedded in intralipid and inhomogeneous tissue phantoms have demonstrated that the LED-based system provides a comparable quantification accuracy of targets to the FD system and has the potential to image deep targets such as breast lesions. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)
    Journal of Biomedical Optics 12/2014; 19(12):126003. DOI:10.1117/1.JBO.19.12.126003 · 2.75 Impact Factor
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    ABSTRACT: Coregistered ultrasound (US) and photoacoustic imaging are emerging techniques for mapping the echogenic anatomical structure of tissue and its corresponding optical absorption. We report a 128-channel imaging system with real-time coregistration of the two modalities, which provides up to 15 coregistered frames per second limited by the laser pulse repetition rate. In addition, the system integrates a compact transvaginal imaging probe with a custom-designed fiber optic assembly for in vivo detection and characterization of human ovarian tissue. We present the coregistered US and photoacoustic imaging system structure, the optimal design of the PC interfacing software, and the reconfigurable field programmable gate array operation and optimization. Phantom experiments of system lateral resolution and axial sensitivity evaluation, examples of the real-time scanning of a tumor-bearing mouse, and ex vivo human ovaries studies are demonstrated. (C) 2014 Society of Photo-Optical Instrumentation Engineers (SPIE)
    Journal of Biomedical Optics 07/2014; 19(7):76020. DOI:10.1117/1.JBO.19.7.076020 · 2.75 Impact Factor
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    ABSTRACT: Human ovarian tissue features extracted from photoacoustic spectra data, beam envelopes and co-registered ultrasound and photoacoustic images are used to characterize cancerous vs. normal processes using a support vector machine (SVM) classifier. The centers of suspicious tumor areas are estimated from the Gaussian fitting of the mean Radon transforms of the photoacoustic image along 0 and 90 degrees. Normalized power spectra are calculated using the Fourier transform of the photoacoustic beamformed data across these suspicious areas, where the spectral slope and 0-MHz intercepts are extracted. Image statistics, envelope histogram fitting and maximum output of 6 composite filters of cancerous or normal patterns along with other previously used features are calculated to compose a total of 17 features. These features are extracted from 169 datasets of 19 ex vivo ovaries. Half of the cancerous and normal datasets are randomly chosen to train a SVM classifier with polynomial kernel and the remainder is used for testing. With 50 times data resampling, the SVM classifier, for the training group, gives 100% sensitivity and 100% specificity. For the testing group, it gives 89.68± 6.37% sensitivity and 93.16± 3.70% specificity. These results are superior to those obtained earlier by our group using features extracted from photoacoustic raw data or image statistics only.
    SPIE Photonics West, Photons Plus Ultrasound: Imaging and Sensing, San Francisco, USA; 03/2014
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    ABSTRACT: A high-throughput ultrasound/photoacoustic probe for delivering high contrast and signal-to-noise ratio images was designed, constructed, and tested. The probe consists of a transvaginal ultrasound array integrated with four 1mm-core optical fibers and a sheath. The sheath encases transducer and is lined with highly reflecting aluminum for high intensity light output and uniformity while at the same time remaining below the maximum permissible exposure (MPE) recommended by the American National Standards Institute (ANSI). The probe design was optimized by simulating the light fluence distribution in Zemax. The performance of the probe was evaluated by experimental measurements of the fluence and real-time imaging of polyethylene-tubing filled with blood. These results suggest that our probe has great potential for in vivo imaging and characterization of ovarian cancer.
    SPIE Photonics West, Photons Plus Ultrasound: Imaging and Sensing, San Francisco, USA; 03/2014
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    ABSTRACT: In this paper, human ovarian tissues with malignant and benign features were imaged ex vivo by using an opticalresolution photoacoustic microscopy (OR-PAM) system. Several features were quantitatively extracted from PAM images to describe photoacoustic signal distributions and fluctuations. 106 PAM images from 18 human ovaries were classified by applying those extracted features to a logistic prediction model. 57 images from 9 ovaries were used as a training set to train the logistic model, and 49 images from another 9 ovaries were used to test our prediction model. We assumed that if one image from one malignant ovary was classified as malignant, it is sufficient to classify this ovary as malignant. For the training set, we achieved 100% sensitivity and 83.3% specificity; for testing set, we achieved 100% sensitivity and 66.7% specificity. These preliminary results demonstrate that PAM could be extremely valuable in assisting and guiding surgeons for in vivo evaluation of ovarian tissue.
    SPIE Photonics West , Photons Plus Ultrasound: Imaging and Sensing, San Francisco; 03/2014
  • Guangqian Yuan, Umar Alqasemi, Yi Yang, Quing Zhu
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    ABSTRACT: LEDs are also available in near infrared. In this study, we introduce a continuous-wave diffuse optical tomography system using 8 groups of LEDs of four wavelengths. Phantom experiments showed its potential to image deep targets.
    Biomedical Optics; 01/2014
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    ABSTRACT: To overcome the intensive light scattering in biological tissue, diffuse optical tomography (DOT) in the near-infrared range for breast lesion detection is usually combined with other imaging modalities, such as ultrasound, x-ray, and magnetic resonance imaging, to provide guidance. However, these guiding imaging modalities may depend on different contrast mechanisms compared to the optical contrast in the DOT. As a result, they cannot provide reliable guidance for DOT because some lesions may not be detectable by a nonoptical modality but may have a high optical contrast. An imaging modality that relies on optical contrast to provide guidance is desirable for DOT. We present a system that combines a frequency-domain DOT and real-time photoacoustic tomography (PAT) systems to detect and characterize deeply seated targets embedded in a turbid medium. To further improve the contrast, the exogenous contrast agent, indocyanine green (ICG), is used. Our experimental results show that the combined system can detect a tumor-mimicking phantom, which is immersed in intralipid solution with the concentrations ranging from 100 to 10 μM and with the dimensions of 0.8 cm×0.8 cm×0.6 cm, up to 2.5 cm in depth. Mice experiments also confirmed that the combined system can detect tumors and monitor the ICG uptake and washout in the tumor region. This method can potentially improve the accuracy to detect small breast lesions as well as lesions that are sensitive to background tissue changes, such as the lesions located just above the chest wall.
    Journal of Biomedical Optics 12/2013; 18(12):126006. DOI:10.1117/1.JBO.18.12.126006 · 2.75 Impact Factor
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    ABSTRACT: A photoacoustic contrast agent that is based on bis-carboxylic acid derivative of indocyanine green (ICG) covalently conjugated to single-wall carbon nanotubes (ICG/SWCNT) is presented. Covalently attaching ICG to the functionalized SWCNT provides a more robust system that delivers much more ICG to the tumor site. The detection sensitivity of the new contrast agent in a mouse tumor model is demonstrated in vivo by our custom-built photoacoustic imaging system. The summation of the photoacoustic tomography (PAT) beam envelope, referred to as the "PAT summation," is used to demonstrate the postinjection light absorption of tumor areas in ICG- and ICG/SWCNT-injected mice. It is shown that ICG is able to provide 33% enhancement at approximately 20 min peak response time with reference to the preinjection PAT level, while ICG/SWCNT provides 128% enhancement at 80 min and even higher enhancement of 196% at the end point of experiments (120 min on average). Additionally, the ICG/SWCNT enhancement was mainly observed at the tumor periphery, which was confirmed by fluorescence images of the tumor samples. This feature is highly valuable in guiding surgeons to assess tumor boundaries and dimensions in vivo and to achieve clean tumor margins to improve surgical resection of tumors.
    Journal of Biomedical Optics 09/2013; 18(9):96006. DOI:10.1117/1.JBO.18.9.096006 · 2.75 Impact Factor
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    ABSTRACT: We present the design and construction of a prototype imaging probe capable of co-registered pulse-echo ultrasound and photoacoustic (optoacoustic) imaging in real time. The probe consists of 36 fibers of 200 micron core diameter each that are distributed around a commercial transvaginal ultrasound transducer, and housed in a protective shield. Its performance was demonstrated by two sets of experiments. The first set involved imaging of blood flowing through a tube mimicking a blood vessel, the second set involved imaging of human ovaries ex vivo. The results suggest that the system along with the probe has great potential for imaging and characterizing of ovarian tissue in vivo. (© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
    Journal of Biophotonics 06/2013; 6(6-7). DOI:10.1002/jbio.201200163 · 3.86 Impact Factor
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    ABSTRACT: In this paper, we present the construction of an optical-resolution photoacoustic microscopy (OR-PAM) system and studies done on the characterization of human ovarian tissue with malignant and benign features ex vivo. PAM images of the ovaries showed more detailed blood vessel distributions with much higher resolution compared with conventional photoacoustic images obtained with array transducers. In all, 29 PAM images (20 from normal ovaries and 9 from malignant ovaries) were studied. Eight different features were extracted quantitatively from the PAM images, and a generalized linear model (GLM) was used to classify the ovaries as normal or malignant. By using the GLM, a specificity of 100% and a sensitivity of 100% were obtained for the training set. These preliminary results demonstrate the feasibility of our PAM system in mapping microvasculature networks, as well as characterizing the ovarian tissue, and could be extremely valuable in assisting surgeons for in vivo evaluation of ovarian tissue.
    Photons Plus Ultrasound: Imaging and Sensing 2013; 03/2013
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    ABSTRACT: Unique features in co-registered ultrasound and photoacoustic images of ex vivo ovarian tissue are introduced, along with the hypotheses of how these features may relate to the physiology of tumors. The images are compressed with wavelet transform, after which the mean Radon transform of the photoacoustic image is computed and fitted with a Gaussian function to find the centroid of the suspicious area for shift-invariant recognition process. In the next step, 24 features are extracted from a training set of images by several methods; including features from the Fourier domain, image statistics, and the outputs of different composite filters constructed from the joint frequency response of different cancerous images. The features were chosen from more than 400 training images obtained from 33 ex vivo ovaries of 24 patients, and used to train a support vector machine (SVM) structure. The SVM classifier was able to exclusively separate the cancerous from the non-cancerous cases with 100% sensitivity and specificity. At the end, the classifier was used to test 95 new images, obtained from 37 ovaries of 20 additional patients. The SVM classifier achieved 76.92% sensitivity and 95.12% specificity. Furthermore, if we assume that recognizing one image as a cancerous case is sufficient to consider the ovary as malignant, then the SVM classifier achieves 100% sensitivity and 87.88% specificity.
    Photons Plus Ultrasound: Imaging and Sensing 2013; 03/2013
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    ABSTRACT: In this paper, we report an ultrafast co-registered ultrasound and photoacoustic imaging system based on FPGA parallel processing. The system features 128-channel parallel acquisition and digitization, along with FPGA-based reconfigurable processing for real-time co-registered imaging of up to 15 frames per second that is only limited by the laser pulse repetition frequency of 15 Hz. We demonstrated the imaging capability of the system by live imaging of a mouse tumor model in vivo, and imaging of human ovaries ex vivo. A compact transvaginal probe that includes the PAT illumination using a fiber-optic assembly was used for this purpose. The system has the potential ability to assist a clinician to perform transvaginal ultrasound scanning and to localize the ovarian mass, while simultaneously mapping the light absorption of the ultrasound detected mass to reveal its vasculature using the co-registered PAT.
    Photons Plus Ultrasound: Imaging and Sensing 2013; 03/2013
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    ABSTRACT: This paper presents a real-time transvaginal photoacoustic imaging probe for imaging human ovaries in vivo. The probe consists of a high-throughput (up to 80%) fiber-optic 1 x 19 beamsplitters, a commercial array ultrasound transducer, and a fiber protective sheath. The beamsplitter has a 940-micron core diameter input fiber and 240-micron core diameter output fibers numbering 36. The 36 small-core output fibers surround the ultrasound transducer and delivers light to the tissue during imaging. A protective sheath, modeled in the form of the transducer using a 3-D printer, encloses the transducer with array of fibers. A real-time image acquisition system collects and processes the photoacoustic RF signals from the transducer, and displays the images formed on a monitor in real time. Additionally, the system is capable of coregistered pulse-echo ultrasound imaging. In this way, we obtain both morphological and functional information from the ovarian tissue. Photoacousitc images of malignant human ovaries taken ex vivo with the probe revealed blood vascular and networks that was distinguishable from normal ovaries, making the probe potential useful for characterizing ovarian tissue.
    Photons Plus Ultrasound: Imaging and Sensing 2013; 03/2013
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    ABSTRACT: In this study, we present a novel photoacoustic contrast agent which is based on bis-carboxylic acid derivative of Indocyanine green (ICG) covalently conjugated to single-wall carbon nanotubes (ICG/SWCNT). Covalently attaching ICG to the functionalized SWCNT provides a more robust system that delivers much more ICG to the tumor site. The detection sensitivity of the new contrast agent in mouse tumor model is demonstrated in vivo by our custom built photoacoustic imaging system. PAT summation signal is defined to show the long-term light absorption of tumor areas in ICG injected mice and ICG/SWCNT injected mice. It is shown that ICG is able to provide 33% enhancement at approximately 20 minutes peak response time referred to pre-injection PAT summation level, while ICG/SWCNT provides 128% enhancement at 80 minutes and even higher enhancement of 196% at the end point of experiments (120 minutes on average). Additionally, the ICG/SWCNT enhancement was mainly observed at the tumor periphery as confirmed by fluorescence images of the tumor samples. This feature is highly valuable in guiding surgeons to assess tumor boundaries and dimensions in vivo and improve surgical resection of tumors for achieving clean tumor margins.
    Photons Plus Ultrasound: Imaging and Sensing 2013; 03/2013
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    ABSTRACT: In this paper, human ovarian tissue with malignant and benign features was imaged ex vivo using an optical-resolution photoacoustic microscopy (OR-PAM) system. The feasibility of PAM to differentiate malignant from normal ovarian tissues was explored by comparing the PAM images morphologically. Based on the observed differences between PAM images of normal and malignant ovarian tissues in microvasculature features and distributions, seven features were quantitatively extracted from the PAM images, and a logistic model was used to classify ovaries as normal or malignant. 106 PAM images from 18 ovaries were studied. 57 images were used to train the seven-parameter logistic model, and a specificity of 92.1% and a sensitivity of 89.5% were achieved; 49 images were then tested, and a specificity of 81.3% and a sensitivity of 88.2% were achieved. These preliminary results demonstrate the feasibility of our PAM system in mapping microvasculature networks as well as characterizing the ovarian tissue, and could be extremely valuable in assisting surgeons for in vivo evaluation of ovarian tissue during minimally invasive surgery.
    Biomedical Optics Express 01/2013; 4(12):2763-8. DOI:10.1364/BOE.4.002763 · 3.50 Impact Factor
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    ABSTRACT: Unique features and the underlining hypotheses of how these features may relate to the tumor physiology in coregistered ultrasound and photoacoustic images of ex vivo ovarian tissue are introduced. The images were first compressed with wavelet transform. The mean Radon transform of photoacoustic images was then computed and fitted with a Gaussian function to find the centroid of a suspicious area for shift-invariant recognition process. Twenty-four features were extracted from a training set by several methods, including Fourier transform, image statistics, and different composite filters. The features were chosen from more than 400 training images obtained from 33 ex vivo ovaries of 24 patients, and used to train three classifiers, including generalized linear model, neural network, and support vector machine (SVM). The SVM achieved the best training performance and was able to exclusively separate cancerous from non-cancerous cases with 100% sensitivity and specificity. At the end, the classifiers were used to test 95 new images obtained from 37 ovaries of 20 additional patients. The SVM classifier achieved 76.92% sensitivity and 95.12% specificity. Furthermore, if we assume that recognizing one image as a cancer is sufficient to consider an ovary as malignant, the SVM classifier achieves 100% sensitivity and 87.88% specificity.
    Journal of Biomedical Optics 12/2012; 17(12):126003. DOI:10.1117/1.JBO.17.12.126003 · 2.75 Impact Factor
  • Umar Alqasemi, Hai Li, Andrés Aguirre, Quing Zhu
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    ABSTRACT: In this paper, we report, to the best of our knowledge, a unique field-programmable gate array (FPGA)-based reconfigurable processor for real-time interlaced co-registered ultrasound and photoacoustic imaging and its application in imaging tumor dynamic response. The FPGA is used to control, acquire, store, delay-and-sum, and transfer the data for real-time co-registered imaging. The FPGA controls the ultrasound transmission and ultrasound and photoacoustic data acquisition process of a customized 16-channel module that contains all of the necessary analog and digital circuits. The 16-channel module is one of multiple modules plugged into a motherboard; their beamformed outputs are made available for a digital signal processor (DSP) to access using an external memory interface (EMIF). The FPGA performs a key role through ultrafast reconfiguration and adaptation of its structure to allow real-time switching between the two imaging modes, including transmission control, laser synchronization, internal memory structure, beamforming, and EMIF structure and memory size. It performs another role by parallel accessing of internal memories and multi-thread processing to reduce the transfer of data and the processing load on the DSP. Furthermore, because the laser will be pulsing even during ultrasound pulse-echo acquisition, the FPGA ensures that the laser pulses are far enough from the pulse-echo acquisitions by appropriate time-division multiplexing (TDM). A co-registered ultrasound and photoacoustic imaging system consisting of four FPGA modules (64-channels) is constructed, and its performance is demonstrated using phantom targets and in vivo mouse tumor models.
    IEEE transactions on ultrasonics, ferroelectrics, and frequency control 07/2012; 59(7):1344-53. DOI:10.1109/TUFFC.2012.2335 · 1.50 Impact Factor
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    ABSTRACT: Co-registered Ultrasound and Photoacoustic images provide complimentary structure and functional information for cancer diagnosis and assessment of therapy response. In SPIE Photonics West 2011, we reported a system that acquires from 64 channels and displays up to 1 frame per second (fps) ultrasound pulse-echo images, 5 fps photoacoustic images, and 0.5 fps co-registered images. In this year, we report an upgraded system which acquires from 128 channels and displays up to 15 fps co-registered ultrasound and photoacoustic images limited by our laser pulse repetition rate. The system architecture is novel and it provides real-time co-registration of images, the ability of acquiring the channel RF data for both modalities, and the flexibility of adjusting every parameter involved in the imaging process for both modalities. The digital signal processor board is upgraded to an FPGA-based PCIe board that collects the data from the acquisition modules and transfers them to the PC memory at 2.5GT/s rate through an x8 DDR PCIe bus running at 100MHz clock frequency. The modules FPGA code is also upgraded to form a beam line in 90 microseconds and to communicate through ultrafast differential tracks with the PCIe board. Furthermore, the printed circuit board (PCB) design of the system was adjusted to provide a maximum of 80dB signal-to-noise ratio at 60dB gain, which is comparable to some commercial ultrasound machines. The real-time system allows capturing co-registered US/PAT images free of motion artifacts and also provides ultrafast dynamic information when a contrast agent is used. The system is built for clinical use to assist the diagnosis of ovarian cancer. However, the hardware is still under testing and evaluation stage, experimental and clinical results will be reported later.
    Photons Plus Ultrasound: Imaging and Sensing 2012; 02/2012
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    ABSTRACT: We present a photoacoustic tomography-guided diffuse optical tomography approach using a hand-held probe for detection and characterization of deeply-seated targets embedded in a turbid medium. Diffuse optical tomography guided by coregistered ultrasound, MRI, and x ray has demonstrated a great clinical potential to overcome lesion location uncertainty and to improve light quantification accuracy. However, due to the different contrast mechanisms, some lesions may not be detectable by a nonoptical modality but yet have high optical contrast. Photoacoustic tomography utilizes a short-pulsed laser beam to diffusively penetrate into tissue. Upon absorption of the light by the target, photoacoustic waves are generated and used to reconstruct, at ultrasound resolution, the optical absorption distribution that reveals optical contrast. However, the robustness of optical property quantification of targets by photoacoustic tomography is complicated because of the wide range of ultrasound transducer sensitivity, the orientation and shape of the targets relative to the ultrasound array, and the uniformity of the laser beam. We show in this paper that the relative optical absorption map provided by photoacoustic tomography can potentially guide the diffuse optical tomography to accurately reconstruct target absorption maps.
    Journal of Biomedical Optics 04/2011; 16(4):046010. DOI:10.1117/1.3563534 · 2.75 Impact Factor