Browsing by Subject "Imaging techniques"
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Item Open Access Activatable photosensitizers: agents for selective photodynamic therapy(Wiley-VCH Verlag, 2017) Li, X.; Kolemen, S.; Yoon, J.; Akkaya, E. U.Recent developments in the design of bifunctional and activatable photosensitizers rejuvenate the aging field of photodynamic sensitization and photodynamic therapy. While systematic studies have uncovered new dyes that can serve as potential photosensitizers, the most promising results have come from studies aimed at gaining precise control over the location and rate of cytotoxic singlet oxygen generation. As a consequence, higher selectivities and efficiencies in photodynamic treatment protocols are now within reach. This feature article highlights the variety of approaches that have been pursued to improve photodynamic therapy and to transform simple photosensitizers into smarter theranostic agents.Item Open Access Amphiphilic peptide coated superparamagnetic iron oxide nanoparticles for in vivo MR tumor imaging(Royal Society of Chemistry, 2016) Ozdemir, A.; Ekiz, M. S.; Dilli, A.; Güler, Mustafa O.; Tekinay, A. B.Magnetic resonance imaging (MRI) is a noninvasive imaging technique that provides high spatial resolution and depth with pronounced soft-tissue contrast for in vivo imaging. A broad variety of strategies have been employed to enhance the diagnostic value of MRI and detect tissue abnormalities at an earlier stage. Superparamagnetic iron oxide nanoparticles (SPIONs) are considered to be suitable candidates for effective imaging due to their small size, versatile functionality and better biocompatibility. Here, we demonstrate that coating SPIONs with proline-rich amphiphilic peptide molecules through noncovalent interactions leads to a water-dispersed hybrid system suitable as an MRI contrast agent. Cellular viability and uptake of amphiphilic peptide coated SPIONs (SPION/K-PA) were evaluated with human vascular endothelial cells (HUVEC) and estrogen receptor (ER) positive human breast adenocarcinoma (MCF-7) cells. The efficiency of SPION/K-PA as MRI contrast agents was analyzed in Sprague-Dawley rats with mammary gland tumors. MR imaging showed that SPION/K-PA effectively accumulated in tumor tissues, enhancing their imaging potential. Although nanoparticles were observed in reticuloendothelial system organs (RES) and especially in the liver and kidney immediately after administration, the MR signal intensity in these organs diminished after 1 h and nanoparticles were subsequently cleared from these organs within two weeks. Histological observations also validated the accumulation of nanoparticles in tumor tissue at 4 h and their bioelimination from the organs of both healthy and tumor-bearing rats after two weeks.Item Open Access Characterization and imaging with lamb wave lens at gigahertz frequencies(IEEE, 1994-10-11) Bozkurt, Ayhan; Yaralıoğlu, Göksenin; Atalar, Abdullah; Köymen, Hayrettin; Kramer, K.Lamb wave lenses with conical refracting surfaces are fabricated for use at 400 MHz and 1 GHz. The conical surfaces are ground and polished with mechanical means and they are sufficiently smooth for the frequencies of interest. The wide bandwidth of transducers allow frequency tuning necessary for Lamb wave lenses. The fabricated lenses show the expected V(Z) performance. At high frequencies the attenuation in the coupling medium can be very high, but due to the smaller wavelength the resolution is better and defocus distance can be reduced. Inherently higher leaky wave sensitivity of Lamb wave lens enables a good V(Z) characterization ability at higher frequencies as compared to the conventional spherical lens. Subsurface imaging with these Lamb wave lenses gives satisfactory results for layered structures. Chosen object has leaky wave modes within the angular coverage of the lens. The images exhibit a resolution close to the diffraction limit. Experimental V(Z) curves obtained with these lenses along with images are presented.Item Open Access CO2 laser polishing of microfluidic channels fabricated by femtosecond laser assisted carving(Institute of Physics Publishing, 2016-10) Serhatlioglu, M.; Ortaç, B.; Elbuken, C.; Bıyıklı, Necmi; Solmaz, M. E.In this study, we investigate the effects of CO2 laser polishing on microscopic structures fabricated by femtosecond laser assisted carving (FLAC). FLAC is the peripheral laser irradiation of 2.5D structures suitable for low repetition rate lasers and is first used to define the microwell structures in fused silica followed by chemical etching. Subsequently, the bottom surface of patterned microwells is irradiated with a pulsed CO2 laser. The surfaces were characterized using an atomic force microscope (AFM) and scanning electron microscope (SEM) in terms of roughness and high quality optical imaging before and after the CO2 laser treatment. The AFM measurements show that the surface roughness improves more than threefold after CO2 laser polishing, which promises good channel quality for applications that require optical imaging. In order to demonstrate the ability of this method to produce low surface roughness systems, we have fabricated a microfluidic channel. The channel is filled with polystyrene bead-laden fluid and imaged with transmission mode microscopy. The high quality optical images prove CO2 laser processing as a practical method to reduce the surface roughness of microfluidic channels fabricated by femtosecond laser irradiation. We further compared the traditional and laser-based glass micromachining approaches, which includes FLAC followed by the CO2 polishing technique.Item Open Access Concentric ring structures as efficient SERS substrates(Institute of Electrical and Electronics Engineers, 2013) Cinel, N. A.; Cakmakyapan, S.; Ertas, G.; Özbay, EkmelPlasmonic nanopatterned structures that can work as highly efficient surface-enhanced Raman scattering (SERS) substrates are presented in this study. A 'coupled' concentric ring structure has been designed, fabricated, tuned, and compared to an 'etched' concentric ring structure and plain gold film via SERS experiments. The proposed design gives Raman signal intensity 630 times larger than plain gold film and 8 times larger than an 'etched' concentric ring structure. The surface plasmons were imaged with the fluorescence imaging technique and supporting numerical simulations were done.Item Open Access High-resolution imaging of elastic properties using harmonic cantilevers(Elsevier, 2004) Sahin, O.; Yaralioglu, G.; Grow, R.; Zappe, S. F.; Atalar, Abdullah; Quate, C.; Solgaard, O.We present a micromachined scanning probe cantilever, in which a specific higher-order flexural mode is designed to be resonant at an exact integer multiple of the fundamental resonance frequency. We have fabricated such cantilevers by reducing the stiffness of the third order flexural mode relative to the fundamental mode, and we have demonstrated that these cantilevers enable sensing of non-linear mechanical interactions between the atomically sharp tip at the free end of the cantilever and a surface with unknown mechanical properties in tapping-mode atomic force microscopy. Images of surfaces with large topographical variations show that for such samples harmonic imaging has better resolution than standard tapping-mode imaging.Item Open Access Localization of diagnostically relevant regions of interest in whole slide images: a comparative study(Springer New York LLC, 2016-08) Mercan, E.; Aksoy, S.; Shapiro, L. G.; Weaver, D. L.; Brunyé, T. T.; Elmore, J. G.Whole slide digital imaging technology enables researchers to study pathologists’ interpretive behavior as they view digital slides and gain new understanding of the diagnostic medical decision-making process. In this study, we propose a simple yet important analysis to extract diagnostically relevant regions of interest (ROIs) from tracking records using only pathologists’ actions as they viewed biopsy specimens in the whole slide digital imaging format (zooming, panning, and fixating). We use these extracted regions in a visual bag-of-words model based on color and texture features to predict diagnostically relevant ROIs on whole slide images. Using a logistic regression classifier in a cross-validation setting on 240 digital breast biopsy slides and viewport tracking logs of three expert pathologists, we produce probability maps that show 74 % overlap with the actual regions at which pathologists looked. We compare different bag-of-words models by changing dictionary size, visual word definition (patches vs. superpixels), and training data (automatically extracted ROIs vs. manually marked ROIs). This study is a first step in understanding the scanning behaviors of pathologists and the underlying reasons for diagnostic errors. © 2016, Society for Imaging Informatics in Medicine.Item Open Access Low-amplitude, force gradient imaging of Cu(100) surface using tunnel current feedback(Institute of Physics Publishing, 2004) Özer, H. Ö.; Norris, A.; Oral, A.; Hoffmann, P. M.; Pethica, J. B.The large corrugation amplitudes in scanning tunnelling microscope (STM) images of metal surfaces have been commonly attributed to the action of forces between the tip and the sample. We have investigated the Cu(100) surface using a high-resolution non-contact atomic force microscope/scanning tunnelling microscope (nc-AFM/STM) in UHV. Force gradient and STM topography images were acquired simultaneously using constant tunnelling current feedback. Force gradient images showed atomic resolution whereas STM scans exhibited almost no contrast, corresponding to a flat tip trajectory during scans. The corrugation height in force gradient images was found to increase as the set tunnelling current was increased. Force gradient and tunnel current were directly measured as a function of separation, to determine the operating conditions during imaging. The STM operation regime is found to lie between the minimum of the stiffness curve and the start of repulsive force.Item Unknown Observation of negative refraction and focusing in two-dimensional photonic crystals(Institute of Physics Publishing Ltd., 2006) Özbay, Ekmel; Bulu, M.; Guven, K.; Caglayan, H.; Aydin, K.We experimentally and theoretically demonstrate the negative refraction and focusing of electromagnetic (EM) waves by twodimensional photonic crystal slabs at microwave frequencies. The negative refraction is observed both for transverse magnetic (TM) and transverse electric (TE) polarized incident EM waves. Gaussian beam shifting method is used to verify the negative refractive index. The Subwavelength imaging and flat lens behavior of photonic crystals are succesfully demonstrated. We have been able to overcome the diffraction limit and focus the EM waves to a spot size of 0.21λ. Metallodielectric photonic crystals are employed to increase the range of angle of incidence that results in negative refraction. Experimental results and theoretical calculations are in good agreement throughout the work. © 2006 The Japan Society of Applied Physics.Item Unknown Perception of 3-D Surfaces from 2-D Contours(1993) Ulupinar F.; Nevatia, R.Inference of 3-D shape from 2-D contours in a single image is an important problem in machine vision. We survey classes of techniques proposed in the past and provide a critical analysis. We propose that two kinds of symmetries in figures, which are known as parallel and skew symmetries, give significant information about surface shape for a variety of objects. We derive the constraints imposed by these symmetries and show how to use them to infer 3-D shape. We discuss the zero Gaussian curvature (ZGC) surfaces in depth and show results on the recovery of surface orientation for various ZGC surfaces. © 1993 IEEEItem Unknown A phase aberration correction method for ultrasound imaging(IEEE, 1993) Karaman, M.; Atalar, Abdullah; Köymen, Hayrettin; O'Donnell, M.A computationally efficient method for phase aberration correction in ultrasound imaging is presented. The method is based on time delay estimation via minimization of the sum of absolute differences between radio frequency samples of adjacent array elements. Effects of averaging estimated aberration patterns over scan angles, and truncation to a single bit wordlength are examined. Phase distortions due to near-field inhomogeneities are simulated using silicone rubber aberrators. Performance of the method is tested using experimental data. Simulation studies addressing different factors affecting efficiency of the method, such as the number of iterations, window length, and the number of scan angles used for averaging, are presented. Images of a standard resolution phantom are reconstructed and used for qualitative testing.Item Unknown Real-time imaging of vortex-antivortex annihilation in Bi 2Sr2CaCu2O8+δ single crystals by low temperature scanning hall probe microscopy(IOP Institute of Physics Publishing, 2006) Dede, M.; Oral, A.; Yamamoto, T.; Kadowaki, K.; Shtrikman, H.Vortices in superconductors play an important role in operating limits and applications of the superconductors. Scanning Hall probe microscopes have proven themselves to be quantitative and non-invasive tools for investigating magnetic samples down to 50 nm scale. Penetration of vortices in high quality single crystal Bi2Sr2CaCu2O8+δ superconductor has been studied in real-time with single vortex resolution at 77 K using a low temperature scanning Hall probe microscope (LT-SHPM). Vortices have been observed to be annihilated by the antivortices in small M-H loops.Item Unknown Room temperature sub-micron magnetic imaging by scanning hall probe microscopy(Japan Society of Applied Physics, 2001) Sandhu, A.; Masuda, H.; Oral, A.; Bending, S. J.An ultra-high sensitive room temperature scanning Hall probe microscope (RT-SHPM) system incorporating a GaAs/A1GaAs micro-Hall probe was used for the direct magnetic imaging of localized magnetic field fluctuations in very close proximity to the surface of ferromagnetic materials. The active area, Hall coefficient and field sensitivity of the Hall probe were 0.8 μm×0.8 μm, 0.3 Ω/G and 0.04 G/√Hz, respectively. The use of a semiconducting Hall probe sensor enabled measurements in the presence of externally applied magnetic fields. Samples studied included magnetic recording media, demagnetized strontium ferrite permanent magnets, and low coercivity perpendicular garnet thin films. The RT-SHPM offers a simple means for quantitatively monitoring sub-micron magnetic domain structures at room temperature.Item Unknown Room-temperature scanning Hall probe microscope (RT-SHPM) imaging of garnet films using new high-performance InSb sensors(IEEE, 2002) Oral, Ahmet; Kaval, Murat; Dede, Münir; Masuda, H.; Okamoto, A.; Shibasaki, I.; Sandhu, A.The room-temperature scanning Hall probe microscopy (RT-SHPM) imaging of garnet films using high-performance InSb sensors was discussed. The high-performance InSb micro-Hall sensors were fabricated by optical lithography. It was found that the room-temperature noise figure of the InSb sensors was 6-10 mG/√Hz, which was an order of magnitude better than GaAs-AlGaAs two-dimensional electron gas sensors.Item Unknown RT-SHPM imaging of permalloy microstructures and garnet films using new high performance INSB sensors(IEEE, 2002) Oral, Ahmet; Kaval, Murat; Dede, Münir; Sandhu, A.The room temperature scanning Hall probe microscopy (RT-SHPM) imaging of permalloy microstructures and garnet films was discussed. The high performance InSb Hall sensors were used for this purpose. It was shown that the InSb Hall probes were highly sensitive and low noise alternatives to GaAs sensors for RT-SHPM.Item Unknown SAR image reconstruction by expectation maximization based matching pursuit(Academic Press, 2015) Ugur, S.; Arıkan, Orhan; Gürbüz, A. C.Synthetic Aperture Radar (SAR) provides high resolution images of terrain and target reflectivity. SAR systems are indispensable in many remote sensing applications. Phase errors due to uncompensated platform motion degrade resolution in reconstructed images. A multitude of autofocusing techniques has been proposed to estimate and correct phase errors in SAR images. Some autofocus techniques work as a post-processor on reconstructed images and some are integrated into the image reconstruction algorithms. Compressed Sensing (CS), as a relatively new theory, can be applied to sparse SAR image reconstruction especially in detection of strong targets. Autofocus can also be integrated into CS based SAR image reconstruction techniques. However, due to their high computational complexity, CS based techniques are not commonly used in practice. To improve efficiency of image reconstruction we propose a novel CS based SAR imaging technique which utilizes recently proposed Expectation Maximization based Matching Pursuit (EMMP) algorithm. EMMP algorithm is greedy and computationally less complex enabling fast SAR image reconstructions. The proposed EMMP based SAR image reconstruction technique also performs autofocus and image reconstruction simultaneously. Based on a variety of metrics, performance of the proposed EMMP based SAR image reconstruction technique is investigated. The obtained results show that the proposed technique provides high resolution images of sparse target scenes while performing highly accurate motion compensation.Item Unknown Simultaneous non-contact atomic force microscopy (nc-AFM)/STM imaging and force spectroscopy of Si(1 0 0)(2 × 1) with small oscillation amplitudes(Elsevier Science B.V., 2002) Özer, H. Ö.; Atabak, M.; Ellialtoğlu, R. M.; Oral, A.Si(1 0 0)(2 × 1) surface is imaged using a new non-contact atomic force microscopy (nc-AFM)/STM with sub-Ångström oscillation amplitudes using stiff tungsten levers. Simultaneous force gradient and STM images of individual dimers and atomic scale defects are obtained. We measured force-distance (f-d) curves with different tips. Some of the tips show long force interactions, whereas some others resolve short-range interatomic force interactions. We observed that the tips showing short-range force interaction give atomic resolution in force gradient scans. This result suggests that short-range force interactions are responsible for atomic resolution in nc-AFM.Item Unknown VLSI circuits for adaptive digital beamforming in ultrasound imaging(IEEE, 1993) Karaman, M.; Atalar, Abdullah; Köymen, HayrettinFor phased-array ultrasound imaging, alternative beamforming techniques and their VLSI circuits are studied to form a fully digital receive front-end hardware. In order to increase the timing accuracy in beamforming, a computationally efficient interpolation scheme to increase the sampling rate is examined. For adaptive beamforming, a phase aberration correction method with very low computational complexity is described. Image quality performance of the method is examined by processing the non-aberrated and aberrated phased-array experimental data sets of an ultrasound resolution phantom. A digital beamforming scheme based on receive focusing at the raster focal points is examined. The sector images of the resolution phantom, reconstructed from the phased-array experimental data by beamforming at the radial and raster focal points, are presented for comparison of the image resolution performances of the two beamforming schemes. VLSI circuits and their implementations for the proposed techniques are presented.Item Unknown White-emitting conjugated polymer nanoparticles with cross-linked shell for mechanical stability and controllable photometric properties in color-conversion LED applications(2011) Park, Eun-Ju; Erdem, T.; Ibrahimova, V.; Nizamoglu, S.; Demir, Hilmi Volkan; Tuncel, D.We report on the synthesis and characterization of water-dispersible, mechanically stable conjugated polymer nanoparticles (CPNs) in shelled architecture with tunable emission and controllable photometric properties via cross-linking. Using a reprecipitation method, whiteemitting polymer nanoparticles are prepared in different sizes by varying the concentration of polymer; the emission kinetics are tuned by controlling the shell formation. For this purpose, polyfluorene derivatives containing azide groups are selected that can be decomposed under UV light to generate very reactive species, which opportunely facilitate the inter- and intra-cross-linking of polymer chains to form shells. Nanoparticles before and after UV treatment are characterized by various techniques. Their size and morphologies are determined by using dynamic light scattering (DLS) measurements and imaging techniques including scanning electron microscopy (SEM) and atomic force microscopy (AFM). For optical characterization, UV vis and steady-state and timeresolved fluorescent spectroscopies are performed. Solid-state behaviors of these CPNs are also investigated by forming films through drop-casting. Moreover, the photometric calculations are also performed for films and dispersions to determine the color quality. A device has been constructed to show proof-of-principle white light generation from these nanoparticles. Additionally, mechanical stability studies are performed and demonstrated that these nanoparticles are indeed mechanically stable by removing the solvent after cross-linking using a freeze-dryer and redispersing in water and THF. Optical and imaging data confirm that the redispersed particles preserve their shapes and sizes after cross-linking.