Browsing by Subject "Imaging"

Now showing 1 - 12 of 12

Open Access
Accelerated phase-cycled SSFP imaging with compressed sensing
(Institute of Electrical and Electronics Engineers Inc., 2015) Çukur, T.
Balanced steady-state free precession (SSFP) imaging suffers from irrecoverable signal losses, known as banding artifacts, in regions of large B0 field inhomogeneity. A common solution is to acquire multiple phase-cycled images each with a different frequency sensitivity, such that the location of banding artifacts are shifted in space. These images are then combined to alleviate signal loss across the entire field-of-view. Although high levels of artifact suppression are viable using a large number of images, this is a time costly process that limits clinical utility. Here, we propose to accelerate individual acquisitions such that the overall scan time is equal to that of a single SSFP acquisition. Aliasing artifacts and noise are minimized by using a variable-density random sampling pattern in k-space, and by generating disjoint sampling patterns for separate acquisitions. A sparsity-enforcing method is then used for image reconstruction. Demonstrations on realistic brain phantom images, and in vivo brain and knee images are provided. In all cases, the proposed technique enables robust SSFP imaging in the presence of field inhomogeneities without prolonging scan times. © 2014 IEEE.
Open Access
Density profile of a Bose-Einstein condensate inside a pancake-shaped trap: Observational consequences of the dimensional cross-over in the scattering properties
(Elsevier Science B.V., 2002) Tanatar, Bilal; Minguzzi, A.; Vignolo, P.; Tosi, M. P.
It is theoretically well known that two-dimensionality of the scattering events in a Bose-Einstein condensate introduces a logarithmic dependence on density in the coupling constant entering a mean-field theory of the equilibrium density profile, which becomes dominant as the s-wave scattering length gets larger than the condensate thickness. We trace the regions of experimentally accessible system parameters for which the cross-over between different dimensionality behaviors in the scattering properties may become observable through in situ imaging of the condensed cloud with varying trap anisotropy and scattering length.
Open Access
Detection of a long non-coding RNA (CCAT1) in living cells and human adenocarcinoma of colon tissues using FIT–PNA molecular beacons
(Elsevier Ireland Ltd., 2014-09-28) Kam, Y.; Rubinstein, A.; Naik, S.; Djavsarov, I.; Halle, D.; Ariel, I.; Gure, A. O.; Stojadinovic, A.; Pan, H. G.; Tsivin, V.; Nissan, A.; Yavin, E.
Although the function and mechanism of action of long non-coding RNAs (lncRNA) is still not completely known, studies have shown their potential role in the control of gene expression and regulation, in cellular proliferation and invasiveness at the transcriptional level via multiple mechanisms. Recently, colon cancer associated transcript 1 (CCAT1) lncRNA was found to be expressed in colorectal cancer (CRC) tumors but not in normal tissue. This study aimed to study the ability of a CCAT1-specific peptide nucleic acid (PNA) based molecular beacons (TO-PNA-MB) to serve as a diagnostic probe for in vitro, ex vivo, and in situ (human colon biopsies) detection of CRC. The data showed enhanced fluorescence upon in vitro hybridization to RNA extracted from CCAT1 expressing cells (HT-29, SW-480) compared to control cells (SK-Mel-2). Uptake of TO-PNA-MBs into cells was achieved by covalently attaching cell penetrating peptides (CPPs) to the TO-PNA-MB probes. In situ hybridization of selected TO-PNA-MB in human CRC specimens was shown to detect CCAT1 expression in all (4/4) subjects with pre-cancerous adenomas, and in all (8/8) patients with invasive adenocarcinoma (penetrating the bowel wall) tumors. The results showed that CCAT1 TO-PNA-MB is a powerful diagnostic tool for the specific identification of CRC, suggesting that with the aid of an appropriate pharmaceutical vehicle, real time in vivo imaging is feasible. TO-PNA-MB may enable identifying occult metastatic disease during surgery, or differentiating in real time in vivo imaging, between benign and malignant lesions.
Open Access
Editorial: machine learning methods for human brain imaging
(Frontiers Research Foundation, 2023-02-28) Vural, Y.; Tunay, F.; Newman, S.D.; Çukur, Tolga; Önal Ertuğrul, I.
Open Access
MaterialVis: material visualization tool using direct volume and surface rendering techniques
(Elsevier Inc., 2014) Okuyan, E.; Güdükbay, Uğur; Bulutay, C.; Heinig, Karl-Heinz
Visualization of the materials is an indispensable part of their structural analysis. We developed a visualization tool for amorphous as well as crystalline structures, called MaterialVis. Unlike the existing tools, MaterialVis represents material structures as a volume and a surface manifold, in addition to plain atomic coordinates. Both amorphous and crystalline structures exhibit topological features as well as various defects. MaterialVis provides a wide range of functionality to visualize such topological structures and crystal defects interactively. Direct volume rendering techniques are used to visualize the volumetric features of materials, such as crystal defects, which are responsible for the distinct fingerprints of a specific sample. In addition, the tool provides surface visualization to extract hidden topological features within the material. Together with the rich set of parameters and options to control the visualization, MaterialVis allows users to visualize various aspects of materials very efficiently as generated by modern analytical techniques such as the Atom Probe Tomography.
Open Access
Microscopic characterization of peptide nanostructures
(Elsevier, 2012) Mammadov, Rashad; Tekinay, Ayse B.; Dana, Aykutlu; Güler, Mustafa O.
Peptide-based nanomaterials have been utilized for various applications from regenerative medicine to electronics since they provide several advantages including easy synthesis methods, numerous routes for functionalization and biomimicry of secondary structures of proteins which leads to design of self-assembling peptide molecules to form nanostructures. Microscopic characterization at nanoscale is critical to understand processes directing peptide molecules to self-assemble and identify structure-function relationship of the nanostructures. Here, fundamental studies in microscopic characterization of peptide nanostructures are discussed to provide insights in widely used microscopy tools. In this review, we will encompass characterization studies of peptide nanostructures with modern microscopes, such as TEM, SEM, AFM, and advanced optical microscopy techniques. We will also mention specimen preparation methods and describe interpretation of the images. © 2011 Elsevier Ltd.
Open Access
Power dissipation analysis in tapping-mode atomic force microscopy
(American Physical Society, 2003) Balantekin, M.; Atalar, Abdullah
In a tapping-mode atomic force microscope, a power is dissipated in the sample during the imaging process. While the vibrating tip taps on the sample surface, some part of its energy is coupled to the sample. Too much dissipated power may mean the damage of the sample or the tip. The amount of power dissipation is related to the mechanical properties of a sample such as viscosity and elasticity. In this paper, we first formulate the steady-state tip-sample interaction force by a simple analytical expression, and then we derive the expressions for average and maximum power dissipated in the sample by means of sample parameters. Furthermore, for a given sample elastic properties we can determine approximately the sample damping constant by measuring the average power dissipation. Simulation results are in close agreement with our analytical approach.
Open Access
Profile-encoding reconstruction for multiple-acquisition balanced steady-state free precession imaging
(John Wiley and Sons Inc., 2017) Ilicak, Efe; Senel, Lutfi Kerem; Biyik, Erdem; Çukur, Tolga
Purpose: The scan-efficiency in multiple-acquisition balanced steady-state free precession imaging can be maintained by accelerating and reconstructing each phase-cycled acquisition individually, but this strategy ignores correlated structural information among acquisitions. Here, an improved acceleration framework is proposed that jointly processes undersampled data across N phase cycles. Methods: Phase-cycled imaging is cast as a profile-encoding problem, modeling each image as an artifact-free image multiplied with a distinct balanced steady-state free precession profile. A profile-encoding reconstruction (PE-SSFP) is employed to recover missing data by enforcing joint sparsity and total-variation penalties across phase cycles. PE-SSFP is compared with individual compressed-sensing and parallel-imaging (ESPIRiT) reconstructions. Results: In the brain and the knee, PE-SSFP yields improved image quality compared to individual compressed-sensing and other tested methods particularly for higher N values. On average, PE-SSFP improves peak SNR by 3.8 ± 3.0 dB (mean ± s.e. across N = 2–8) and structural similarity by 1.4 ± 1.2% over individual compressed-sensing, and peak SNR by 5.6 ± 0.7 dB and structural similarity by 7.1 ± 0.5% over ESPIRiT. Conclusion: PE-SSFP attains improved image quality and preservation of high-spatial-frequency information at high acceleration factors, compared to conventional reconstructions. PE-SSFP is a promising technique for scan-efficient balanced steady-state free precession imaging with improved reliability against field inhomogeneity. Magn Reson Med 78:1316–1329, 2017.
Open Access
Resonant harmonic response in tapping-mode atomic force microscopy
(American Physical Society, 2004) Sahin, O.; Quate, C. F.; Solgaard, O.; Atalar, Abdullah
Higher harmonics in tapping-mode atomic force microscopy offers the potential for imaging and sensing material properties at the nanoscale. The signal level at a given harmonic of the fundamental mode can be enhanced if the cantilever is designed in such a way that the frequency of one of the higher harmonics of the fundamental mode (designated as the resonant harmonic) matches the resonant frequency of a higher-order flexural mode. Here we present an analytical approach that relates the amplitude and phase of the cantilever vibration at the frequency of the resonant harmonic to the elastic modulus of the sample. The resonant harmonic response is optimized for different samples with a proper design of the cantilever. It is found that resonant harmonics are sensitive to the stiffness of the material under investigation.
Open Access
Roadmap on wavefront shaping and deep imaging in complex media
(Institute of Physics, 2022-10) Gigan, Sylvain; Katz, Ori; De Aguiar, Hilton B.; Andresen, Esben Ravn; Aubry, Alexandre; Bertolotti, Jacopo; Bossy, Emmanuel; Bouchet, Dorian; Brake, Joshua; Brasselet, Sophie; Bromberg, Yaron; Cao, Hui; Chaigne, Thomas; Cheng, Zhongtao; Choi, Wonshik; Čižmár, Tomáš; Cui, Meng; Curtis, Vincent R.; Defienne, Hugo; Hofer, Matthias; Horisaki, Ryoichi; Horstmeyer, Roarke; Ji, Na; LaViolette, Aaron K.; Mertz, Jerome; Moser, Christophe; Mosk, Allard P; Pégard, Nicolas C; Piestun, Rafael; Popoff, Sebastien; Phillips, David B.; Psaltis, Demetri; Rahmani, Babak; Rigneault, Hervé; Rotter, Stefan; Tian, Lei; Vellekoop, Ivo M.; Waller, Laura; Wang, Lihong; Weber, Timothy; Xiao, Sheng; Xu, Chris; Yamilov, Alexey; Yang, Changhuei; Yılmaz, Hasan
The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow us to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. A vibrant and diverse community is now working in this field, which has revolutionized the prospect of diffraction-limited imaging at depth in tissues. This roadmap highlights several key aspects of this fast developing field, and some of the challenges and opportunities ahead. © 2022 The Author(s). Published by IOP Publishing Ltd.
Open Access
Room temperature scanning Hall probe microscopy using GaAs/AlGaAs and Bi micro-hall probes
(Elsevier Science B.V., 2002) Sandhu, A.; Masuda, H.; Oral, A.; Yamada, A.; Konagai, M.
A room temperature scanning Hall probe microscope system utilizing GaAs/AlGaAs and bismuth micro-Hall probes was used for magnetic imaging of ferromagnetic domain structures on the surfaces of crystalline thin film garnets and permanent magnets. The Bi micro-Hall probes had dimensions ranging between 0.25 and 2.8μm2 and were fabricated using a combination of optical lithography and focused ion beam milling. The use of bismuth was found to overcome surface depletion effects associated with semiconducting micro-Hall probes. Our experiments demonstrated that Bi is a practical choice of material for fabricating sub-micron sized Hall sensors.
Open Access
Uniqueness and reconstruction in magnetic resonance-electrical impedance tomography (MR-EIT)
(Institute of Physics Publishing, 2003) İder, Y. Z.; Onart, S.; Lionheart, W. R. B.
Magnetic resonance-electrical impedance tomography (MR-EIT) was first proposed in 1992. Since then various reconstruction algorithms have been suggested and applied. These algorithms use peripheral voltage measurements and internal current density measurements in different combinations. In this study the problem of MR-EIT is treated as a hyperbolic system of first-order partial differential equations, and three numerical methods are proposed for its solution. This approach is not utilized in any of the algorithms proposed earlier. The numerical solution methods are integration along equipotential surfaces (method of characteristics), integration on a Cartesian grid, and inversion of a system matrix derived by a finite difference formulation. It is shown that if some uniqueness conditions are satisfied, then using at least two injected current patterns, resistivity can be reconstructed apart from a multiplicative constant. This constant can then be identified using a single voltage measurement. The methods proposed are direct, non-iterative, and valid and feasible for 3D reconstructions. They can also be used to easily obtain slice and field-of-view images from a 3D object. 2D simulations are made to illustrate the performance of the algorithms.