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Sample records for quantitative phase tomography

  1. Quantitative phase microscopy and synthetic aperture tomography of live cells

    NASA Astrophysics Data System (ADS)

    Lue, Niyom

    For more than a decade MIT's George R. Harrison Spectroscopy Laboratory has been developing quantitative phase microscopy (QPM) for biological study. Measurements of a point field were made in the mid 90s, then extended to the full 2D field, and recently, to 3D by using tomography. In the first part of this thesis improvements in the techniques of Fourier Phase Microscopy (FPM) and Hilbert Phase Microscopy (HPM) and their applications to characterize cells and tissues are reported. Tomographic phase microscopy (TPM) provides quantitative information and highly detailed structural information about a live cell, but in its current form it can only examine one cell at a time. Many biological applications including statistical analysis of a large collection of cells such as flow cytometry need a tomography technique that can measure many cells at a time. For the second part of this thesis we have developed a new tomography technique that can measure many cells continuously. In this study we demonstrate the new technique by translating a live cell across a focused beam. This beam is composed of many angular plane waves, and by applying a so-called synthetic aperture algorithm we retrieve individual wave components of the focused beam. We demonstrate for the first time that we can retrieve the field of the focused beam and synthesize any arbitrary angular plane wave. We then construct a 3D map of the variations of the refractive index in a live cell from a series of these synthesized angular plane waves. This new technique is the first step needed to analyze cells flowing through a beam to provide a high-throughput 3D refractive index tomograms that can be used as a new kind of statistical optical assay of living cells.

  2. Quantitative ultrasonic computed tomography using phase-insensitive pyroelectric detectors

    NASA Astrophysics Data System (ADS)

    Zeqiri, Bajram; Baker, Christian; Alosa, Giuseppe; Wells, Peter N. T.; Liang, Hai-Dong

    2013-08-01

    The principle of using ultrasonic computed tomography (UCT) clinically for mapping tissue acoustic properties was suggested almost 40 years ago. Despite strong research activity, UCT been unable to rival its x-ray counterpart in terms of the ability to distinguish tissue pathologies. Conventional piezoelectric detectors deployed in UCT are termed phase-sensitive (PS) and it is well established that this property can lead to artefacts related to refraction and phase-cancellation that mask true tissue structure, particularly for reconstructions involving attenuation. Equally, it has long been known that phase-insensitive (PI) detectors are more immune to this effect, although sufficiently sensitive devices for clinical use have not been available. This paper explores the application of novel PI detectors to UCT. Their operating principle is based on exploiting the pyroelectric properties of the piezoelectric polymer polyvinylidene difluoride. An important detector performance characteristic which makes it particularly suited to UCT, is the lack of directionality of the PI response, relative to the PS detector mode of operation. The performance of the detectors is compared to conventional PS detection methods, for quantitatively assessing the attenuation distribution within various test objects, including a two-phase polyurethane phantom. UCT images are presented for a range of single detector apertures; tomographic reconstruction images being compared with the known structure of phantoms containing inserts as small as 3 mm, which were readily imaged. For larger diameter inserts (>10 mm), the transmitter-detector combination was able to establish the attenuation coefficient of the insert to within ±10% of values determined separately from plane-wave measurements on representative material plaques. The research has demonstrated that the new PI detectors are significantly less susceptible to refraction and phase-cancellation artefacts, generating realistic images in

  3. Quantitative phase tomography by using x-ray microscope with Foucault knife-edge scanning filter

    NASA Astrophysics Data System (ADS)

    Watanabe, Norio; Tsuburaya, Yuji; Shimada, Akihiro; Aoki, Sadao

    2016-01-01

    Quantitative phase tomography was evaluated by using a differential phase microscope with a Foucault knife-edge scanning filter. A 3D x-ray phase image of polystyrene beads was obtained at 5.4 keV. The reconstructed refractive index was fairly good agreement with the Henke's tabulated data.

  4. Controllable tomography phase microscopy

    NASA Astrophysics Data System (ADS)

    Xiu, Peng; Zhou, Xin; Kuang, Cuifang; Xu, Yingke; Liu, Xu

    2015-03-01

    Tomography phase microscopy (TPM) is a new microscopic method that can quantitatively yield the volumetric 3D distribution of a sample's refractive index (RI), which is significant for cell biology research. In this paper, a controllable TPM system is introduced. In this system a circulatory phase-shifting method and piezoelectric ceramic are used which enable the TPM system to record the 3D RI distribution at a more controllable speed, from 1 to 40 fps, than in the other TPM systems reported. The resolution of the RI distribution obtained by this controllable TPM is much better than that in images recorded by phase contrast microscopy and interference tomography microscopy. The realization of controllable TPM not only allows for the application of TPM to the measurement of kinds of RI sample, but also contributes to academic and technological support for the practical use of TPM.

  5. Quantitative X-ray phase tomography with sub-micron resolution

    NASA Astrophysics Data System (ADS)

    McMahon, P. J.; Peele, A. G.; Paterson, D.; Lin, J. J. A.; Irving, T. H. K.; McNulty, I.; Nugent, K. A.

    2003-03-01

    Tomographic X-ray phase reconstructions of an atomic force microscope tip with a spatial resolution of better than 900 nm are presented. The data was acquired using an X-ray energy of 1.83 keV using a zone plate based microscope at a third generation synchrotron, the Advanced Photon Source at the Argonne National Laboratory. The phase tomographic data is quantitatively accurate and we confirm that the deduced refractive index is in agreement with the known properties of the sample. Our results open the way for full 3D imaging of the complex refractive index with sub-micron spatial resolution.

  6. Quantitative photoacoustic tomography

    PubMed Central

    Yuan, Zhen; Jiang, Huabei

    2009-01-01

    In this paper, several algorithms that allow for quantitative photoacoustic reconstruction of tissue optical, acoustic and physiological properties are described in a finite-element method based framework. These quantitative reconstruction algorithms are compared, and the merits and limitations associated with these methods are discussed. In addition, a multispectral approach is presented for concurrent reconstructions of multiple parameters including deoxyhaemoglobin, oxyhaemoglobin and water concentrations as well as acoustic speed. Simulation and in vivo experiments are used to demonstrate the effectiveness of the reconstruction algorithms presented. PMID:19581254

  7. Compressive Phase Contrast Tomography

    SciTech Connect

    Maia, Filipe; MacDowell, Alastair; Marchesini, Stefano; Padmore, Howard A.; Parkinson, Dula Y.; Pien, Jack; Schirotzek, Andre; Yang, Chao

    2010-09-01

    When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher contrast datasets have a sparse solution. We apply basis pursuit solvers to improve SNR, remove ring artifacts, reduce the number of views and radiation dose from phase contrast datasets collected at the Hard X-Ray Micro Tomography Beamline at the Advanced Light Source. We report a GPU code for the most computationally intensive task, the gridding and inverse gridding algorithm (non uniform sampled Fourier transform).

  8. Quantitative optical phase microscopy.

    PubMed

    Barty, A; Nugent, K A; Paganin, D; Roberts, A

    1998-06-01

    We present a new method for the extraction of quantitative phase data from microscopic phase samples by use of partially coherent illumination and an ordinary transmission microscope. The technique produces quantitative images of the phase profile of the sample without phase unwrapping. The technique is able to recover phase even in the presence of amplitude modulation, making it significantly more powerful than existing methods of phase microscopy. We demonstrate the technique by providing quantitatively correct phase images of well-characterized test samples and show that the results obtained for more-complex samples correlate with structures observed with Nomarski differential interference contrast techniques.

  9. Quantitative Three-Dimensional Imaging of Lipid, Protein, and Water Contents via X-Ray Phase-Contrast Tomography

    PubMed Central

    Willner, Marian; Viermetz, Manuel; Marschner, Mathias; Scherer, Kai; Braun, Christian; Fingerle, Alexander; Noël, Peter; Rummeny, Ernst; Pfeiffer, Franz; Herzen, Julia

    2016-01-01

    X-ray phase-contrast computed tomography is an emerging imaging technology with powerful capabilities for three-dimensional (3D) visualization of weakly absorbing objects such as biological soft tissues. This technique is an extension of existing X-ray applications because conventional attenuation-contrast images are simultaneously acquired. The complementary information provided by both the contrast modalities suggests that enhanced material characterization is possible when performing combined data analysis. In this study, we describe how protein, lipid, and water concentrations in each 3D voxel can be quantified by vector decomposition. Experimental results of dairy products, porcine fat and rind, and different human soft tissue types are presented. The results demonstrate the potential of phase-contrast imaging as a new analysis tool. The 3D representations of protein, lipid, and water contents open up new opportunities in the fields of biology, medicine, and food science. PMID:27003308

  10. Phase contrast imaging X-ray computed tomography: quantitative characterization of human patellar cartilage matrix with topological and geometrical features

    NASA Astrophysics Data System (ADS)

    Nagarajan, Mahesh B.; Coan, Paola; Huber, Markus B.; Diemoz, Paul C.; Wismüller, Axel

    2014-03-01

    Current assessment of cartilage is primarily based on identification of indirect markers such as joint space narrowing and increased subchondral bone density on x-ray images. In this context, phase contrast CT imaging (PCI-CT) has recently emerged as a novel imaging technique that allows a direct examination of chondrocyte patterns and their correlation to osteoarthritis through visualization of cartilage soft tissue. This study investigates the use of topological and geometrical approaches for characterizing chondrocyte patterns in the radial zone of the knee cartilage matrix in the presence and absence of osteoarthritic damage. For this purpose, topological features derived from Minkowski Functionals and geometric features derived from the Scaling Index Method (SIM) were extracted from 842 regions of interest (ROI) annotated on PCI-CT images of healthy and osteoarthritic specimens of human patellar cartilage. The extracted features were then used in a machine learning task involving support vector regression to classify ROIs as healthy or osteoarthritic. Classification performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). The best classification performance was observed with high-dimensional geometrical feature vectors derived from SIM (0.95 ± 0.06) which outperformed all Minkowski Functionals (p < 0.001). These results suggest that such quantitative analysis of chondrocyte patterns in human patellar cartilage matrix involving SIM-derived geometrical features can distinguish between healthy and osteoarthritic tissue with high accuracy.

  11. Laser refractive tomography of phase objects

    SciTech Connect

    Raskovskaya, I L

    2013-06-30

    The principles are outlined of laser refractive tomography - a method for reconstructing the values of the refractive index in the cross sections of phase objects, which involves the use of three-dimensional refractive images (3D refractograms) of structured laser radiation. A simulation algorithm is realised and examples are provided of characteristic 3D refractograms obtained by solving the direct problem of refraction of structured radiation. A method was developed for reconstructing the values of refractive index under conditions of strong refraction, which is based on the visualisation of ray trajectories inside an optically inhomogeneous medium. A classification is made of possible approaches to the solution of the inverse problem of refraction based on the visualisation of ray trajectories. Examples are given of cross section reconstruction and quantitative diagnostics of phase objects. (laser imaging)

  12. Fourier phase in Fourier-domain optical coherence tomography

    PubMed Central

    Uttam, Shikhar; Liu, Yang

    2015-01-01

    Phase of an electromagnetic wave propagating through a sample-of-interest is well understood in the context of quantitative phase imaging in transmission-mode microscopy. In the past decade, Fourier-domain optical coherence tomography has been used to extend quantitative phase imaging to the reflection-mode. Unlike transmission-mode electromagnetic phase, however, the origin and characteristics of reflection-mode Fourier phase are poorly understood, especially in samples with a slowly varying refractive index. In this paper, the general theory of Fourier phase from first principles is presented, and it is shown that Fourier phase is a joint estimate of subresolution offset and mean spatial frequency of the coherence-gated sample refractive index. It is also shown that both spectral-domain phase microscopy and depth-resolved spatial-domain low-coherence quantitative phase microscopy are special cases of this general theory. Analytical expressions are provided for both, and simulations are presented to explain and support the theoretical results. These results are further used to show how Fourier phase allows the estimation of an axial mean spatial frequency profile of the sample, along with depth-resolved characterization of localized optical density change and sample heterogeneity. Finally, a Fourier phase-based explanation of Doppler optical coherence tomography is also provided. PMID:26831383

  13. Optical Coherence Tomography for nanoparticles quantitative characterization

    NASA Astrophysics Data System (ADS)

    Trojanowski, Michał; Kraszewski, Maciej; StrÄ kowski, Marcin R.; Pluciński, Jerzy

    2015-08-01

    The unique features of nanocomposite materials depend on the type and size of nanoparticles, as well as their placement in the composite matrices. Therefore the nanocomposites manufacturing process requires inline control over certain parameters of nanoparticles such as dispersion and concentration. Keeping track of nanoparticles parameters inside a matrix is currently a difficult task due to lack of a fast, reliable and cost effective way of measurement that can be used for large volume samples. For this purpose the Optical Coherence Tomography (OCT) has been used. OCT is an optical measurement method, which is a non-destructive and non-invasive technique. It is capable of creating tomographic images of inner structure by gathering depth related backscattered signal from scattering particles. In addition, it can analyse, in a single shot, area of the centimetre range with resolution up to single micrometres. Still to increase OCT measurement capabilities we are using additional system extensions such as Spectroscopic OCT (SOCT). With such addition, we are able to measure depth related parameters such as scattering spectra and intensity of backscattered signal. Those parameters allow us to quantitatively estimate nanoparticles concentration. Gaining those, information allows to calculate volume concentration of nanoparticles. In addition, we analyse metallic oxides nanoparticles. To fully characterize nanoparticles it is necessary to find and differentiate those that are single particles from agglomerated ones. In this contribution we present our research results on using the LCI based measurement techniques for evaluation of materials with nanoparticles. The laboratory system and signal processing algorithms are going to be shown in order to express the usefulness of this method for inline constant monitoring of the nanocomposite material fabrication.

  14. Optical coherence Doppler tomography for quantitative cerebral blood flow imaging

    PubMed Central

    You, Jiang; Du, Congwu; Volkow, Nora D.; Pan, Yingtian

    2014-01-01

    Optical coherence Doppler tomography (ODT) is a promising neurotechnique that permits 3D imaging of the cerebral blood flow (CBF) network; however, quantitative CBF velocity (CBFv) imaging remains challenging. Here we present a simple phase summation method to enhance slow capillary flow detection sensitivity without sacrificing dynamic range for fast flow and vessel tracking to improve angle correction for absolute CBFv quantification. Flow phantom validation indicated that the CBFv quantification accuracy increased from 15% to 91% and the coefficient of variation (CV) decreased 9.3-fold; in vivo mouse brain validation showed that CV decreased 4.4-/10.8- fold for venular/arteriolar flows. ODT was able to identify cocaine-elicited microischemia and quantify CBFv disruption in branch vessels and capillaries that otherwise would have not been possible. PMID:25401033

  15. Quantitative phase imaging of arthropods

    PubMed Central

    Sridharan, Shamira; Katz, Aron; Soto-Adames, Felipe; Popescu, Gabriel

    2015-01-01

    Abstract. Classification of arthropods is performed by characterization of fine features such as setae and cuticles. An unstained whole arthropod specimen mounted on a slide can be preserved for many decades, but is difficult to study since current methods require sample manipulation or tedious image processing. Spatial light interference microscopy (SLIM) is a quantitative phase imaging (QPI) technique that is an add-on module to a commercial phase contrast microscope. We use SLIM to image a whole organism springtail Ceratophysella denticulata mounted on a slide. This is the first time, to our knowledge, that an entire organism has been imaged using QPI. We also demonstrate the ability of SLIM to image fine structures in addition to providing quantitative data that cannot be obtained by traditional bright field microscopy. PMID:26334858

  16. Quantitative phase imaging of arthropods.

    PubMed

    Sridharan, Shamira; Katz, Aron; Soto-Adames, Felipe; Popescu, Gabriel

    2015-01-01

    Classification of arthropods is performed by characterization of fine features such as setae and cuticles. An unstained whole arthropod specimen mounted on a slide can be preserved for many decades, but is difficult to study since current methods require sample manipulation or tedious image processing. Spatial light interference microscopy (SLIM) is a quantitative phase imaging (QPI) technique that is an add-on module to a commercial phase contrast microscope. We use SLIM to image a whole organism springtail Ceratophysella denticulata mounted on a slide. This is the first time, to our knowledge, that an entire organism has been imaged using QPI. We also demonstrate the ability of SLIM to image fine structures in addition to providing quantitative data that cannot be obtained by traditional bright field microscopy. PMID:26334858

  17. Quantitative phase imaging of arthropods

    NASA Astrophysics Data System (ADS)

    Sridharan, Shamira; Katz, Aron; Soto-Adames, Felipe; Popescu, Gabriel

    2015-11-01

    Classification of arthropods is performed by characterization of fine features such as setae and cuticles. An unstained whole arthropod specimen mounted on a slide can be preserved for many decades, but is difficult to study since current methods require sample manipulation or tedious image processing. Spatial light interference microscopy (SLIM) is a quantitative phase imaging (QPI) technique that is an add-on module to a commercial phase contrast microscope. We use SLIM to image a whole organism springtail Ceratophysella denticulata mounted on a slide. This is the first time, to our knowledge, that an entire organism has been imaged using QPI. We also demonstrate the ability of SLIM to image fine structures in addition to providing quantitative data that cannot be obtained by traditional bright field microscopy.

  18. Quantitative phase imaging of arthropods.

    PubMed

    Sridharan, Shamira; Katz, Aron; Soto-Adames, Felipe; Popescu, Gabriel

    2015-01-01

    Classification of arthropods is performed by characterization of fine features such as setae and cuticles. An unstained whole arthropod specimen mounted on a slide can be preserved for many decades, but is difficult to study since current methods require sample manipulation or tedious image processing. Spatial light interference microscopy (SLIM) is a quantitative phase imaging (QPI) technique that is an add-on module to a commercial phase contrast microscope. We use SLIM to image a whole organism springtail Ceratophysella denticulata mounted on a slide. This is the first time, to our knowledge, that an entire organism has been imaged using QPI. We also demonstrate the ability of SLIM to image fine structures in addition to providing quantitative data that cannot be obtained by traditional bright field microscopy.

  19. Effect of dexamethasone on mandibular bone biomechanics in rats during the growth phase as assessed by bending test and peripheral quantitative computerized tomography.

    PubMed

    Bozzini, Clarisa; Champin, Graciela; Alippi, Rosa M; Bozzini, Carlos E

    2015-04-01

    Long-term glucocorticoid administration to growing rats induces osteopenia and alterations in the biomechanical behavior of the bone. This study was performed to estimate the effects of dexamethasone (DTX), a synthetic steroid with predominant glucocorticoid activity, on the biomechanical properties of the mandible of rats during the growth phase, as assessed by bending test and peripheral quantitative computed tomographic (pQCT) analysis. The data obtained by the two methods will provide more precise information when analyzed together than separately. Female rats aged 23 d (n=7) received 500μg.kg-1 per day of DXT for 4 weeks. At the end of the treatment period, their body weight and body length were 51.3% and 20.6% lower, respectively, than controls. Hemimandible weight and area (an index of mandibular size) were 27.3% and 9.7% lower, respectively. The right hemimandible of each animal was subjected to a mechanical 3-point bending test. Significant weakening of the bone, as shown by a correlative impairment of strength and stiffness, was observed in experimental rats. Bone density and cross-sectional area were measured by pQCT. Cross-sectional, cortical and trabecular areas were reduced by 20% to 30% in the DTX group, as were other cortical parameters, including the bone density, mineral content and cross-sectional moment of inertia. The "bone strength index" (BSI, the product of the pQCT-assessed xCSMI and vCtBMD) was 56% lower in treated rats, which compares well with the 54% and 52% reduction observed in mandibular strength and stiffness determined through the bending test. Data suggest that the corticosteroid exerts a combined, negative action on bone geometry (mass and architecture) and volumetric bone mineral density of cortical bone, which would express independent effects on both cellular (material quality) and tissue (cross-sectional design) levels of biological organization of the skeleton in the species. PMID:25950168

  20. Effect of dexamethasone on mandibular bone biomechanics in rats during the growth phase as assessed by bending test and peripheral quantitative computerized tomography.

    PubMed

    Bozzini, Clarisa; Champin, Graciela; Alippi, Rosa M; Bozzini, Carlos E

    2015-04-01

    Long-term glucocorticoid administration to growing rats induces osteopenia and alterations in the biomechanical behavior of the bone. This study was performed to estimate the effects of dexamethasone (DTX), a synthetic steroid with predominant glucocorticoid activity, on the biomechanical properties of the mandible of rats during the growth phase, as assessed by bending test and peripheral quantitative computed tomographic (pQCT) analysis. The data obtained by the two methods will provide more precise information when analyzed together than separately. Female rats aged 23 d (n=7) received 500μg.kg-1 per day of DXT for 4 weeks. At the end of the treatment period, their body weight and body length were 51.3% and 20.6% lower, respectively, than controls. Hemimandible weight and area (an index of mandibular size) were 27.3% and 9.7% lower, respectively. The right hemimandible of each animal was subjected to a mechanical 3-point bending test. Significant weakening of the bone, as shown by a correlative impairment of strength and stiffness, was observed in experimental rats. Bone density and cross-sectional area were measured by pQCT. Cross-sectional, cortical and trabecular areas were reduced by 20% to 30% in the DTX group, as were other cortical parameters, including the bone density, mineral content and cross-sectional moment of inertia. The "bone strength index" (BSI, the product of the pQCT-assessed xCSMI and vCtBMD) was 56% lower in treated rats, which compares well with the 54% and 52% reduction observed in mandibular strength and stiffness determined through the bending test. Data suggest that the corticosteroid exerts a combined, negative action on bone geometry (mass and architecture) and volumetric bone mineral density of cortical bone, which would express independent effects on both cellular (material quality) and tissue (cross-sectional design) levels of biological organization of the skeleton in the species.

  1. GPC and quantitative phase imaging

    NASA Astrophysics Data System (ADS)

    Palima, Darwin; Bañas, Andrew Rafael; Villangca, Mark Jayson; Glückstad, Jesper

    2016-03-01

    Generalized Phase Contrast (GPC) is a light efficient method for generating speckle-free contiguous optical distributions using binary-only or analog phase levels. It has been used in applications such as optical trapping and manipulation, active microscopy, structured illumination, optical security, parallel laser marking and labelling and recently in contemporary biophotonics applications such as for adaptive and parallel two-photon optogenetics and neurophotonics. We will present our most recent GPC developments geared towards these applications. We first show a very compact static light shaper followed by the potential of GPC for biomedical and multispectral applications where we experimentally demonstrate the active light shaping of a supercontinuum laser over most of the visible wavelength range. Finally, we discuss how GPC can be advantageously applied for Quantitative Phase Imaging (QPI).

  2. Toward quantitative core-loss EFTEM tomography.

    PubMed

    Jin-Phillipp, N Y; Koch, C T; van Aken, P A

    2011-07-01

    Core-loss EFTEM tomography provides three-dimensional structural and chemical information. Multiple inelastic scattering occurring in thick specimens as well as orientation-dependent diffraction contrast due to multiple elastic scattering, however, often limit its applications. After demonstrating the capability of core-loss EFTEM tomography to reconstruct just a few monolayers thin carbon layer covering a Fe catalyst particle we discuss its application to thicker samples. We propose an approximate multiple-scattering correction method based on the use of zero-loss images and apply it successfully to copper whiskers, providing a significant improvement of the reconstructed 3D elemental distribution. We conclude this paper by a general discussion on experimental parameters affecting the accuracy of EFTEM 3D elemental mapping. PMID:21864765

  3. Gold Nanoparticle Quantitation by Whole Cell Tomography.

    PubMed

    Sanders, Aric W; Jeerage, Kavita M; Schwartz, Cindi L; Curtin, Alexandra E; Chiaramonti, Ann N

    2015-12-22

    Many proposed biomedical applications for engineered gold nanoparticles require their incorporation by mammalian cells in specific numbers and locations. Here, the number of gold nanoparticles inside of individual mammalian stem cells was characterized using fast focused ion beam-scanning electron microscopy based tomography. Enhanced optical microscopy was used to provide a multiscale map of the in vitro sample, which allows cells of interest to be identified within their local environment. Cells were then serially sectioned using a gallium ion beam and imaged using a scanning electron beam. To confirm the accuracy of single cross sections, nanoparticles in similar cross sections were imaged using transmission electron microscopy and scanning helium ion microscopy. Complete tomographic series were then used to count the nanoparticles inside of each cell and measure their spatial distribution. We investigated the influence of slice thickness on counting single particles and clusters as well as nanoparticle packing within clusters. For 60 nm citrate stabilized particles, the nanoparticle cluster packing volume is 2.15 ± 0.20 times the volume of the bare gold nanoparticles.

  4. Quantitative contrast-enhanced optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Winetraub, Yonatan; SoRelle, Elliott D.; Liba, Orly; de la Zerda, Adam

    2016-01-01

    We have developed a model to accurately quantify the signals produced by exogenous scattering agents used for contrast-enhanced Optical Coherence Tomography (OCT). This model predicts distinct concentration-dependent signal trends that arise from the underlying physics of OCT detection. Accordingly, we show that real scattering particles can be described as simplified ideal scatterers with modified scattering intensity and concentration. The relation between OCT signal and particle concentration is approximately linear at concentrations lower than 0.8 particle per imaging voxel. However, at higher concentrations, interference effects cause signal to increase with a square root dependence on the number of particles within a voxel. Finally, high particle concentrations cause enough light attenuation to saturate the detected signal. Predictions were validated by comparison with measured OCT signals from gold nanorods (GNRs) prepared in water at concentrations ranging over five orders of magnitude (50 fM to 5 nM). In addition, we validated that our model accurately predicts the signal responses of GNRs in highly heterogeneous scattering environments including whole blood and living animals. By enabling particle quantification, this work provides a valuable tool for current and future contrast-enhanced in vivo OCT studies. More generally, the model described herein may inform the interpretation of detected signals in modalities that rely on coherence-based detection or are susceptible to interference effects.

  5. Reduction of phase artifacts in differential phase contrast computed tomography.

    PubMed

    Jerjen, Iwan; Revol, Vincent; Schuetz, Philipp; Kottler, Christian; Kaufmann, Rolf; Luethi, Thomas; Jefimovs, Konstantins; Urban, Claus; Sennhauser, Urs

    2011-07-01

    X-ray differential phase contrast computed tomography (DPC CT) with a Talbot-Lau interferometer setup allows visualizing the three-dimensional distribution of the refractive index by measuring the shifts of an interference pattern due to phase variations of the X-ray beam. Unfortunately, severe reconstruction artifacts appear in the presence of differential phase wrapping and clipping. In this paper, we propose to use the attenuation contrast, which is obtained from the same measurement, for correcting the DPC signal. Using the example of a DPC CT measurement with pronounced phase artifacts, we will discuss the efficiency of our phase artifact correction method. PMID:21747516

  6. Longitudinal phase space tomography with space charge

    NASA Astrophysics Data System (ADS)

    Hancock, S.; Lindroos, M.; Koscielniak, S.

    2000-12-01

    Tomography is now a very broad topic with a wealth of algorithms for the reconstruction of both qualitative and quantitative images. In an extension in the domain of particle accelerators, one of the simplest algorithms has been modified to take into account the nonlinearity of large-amplitude synchrotron motion. This permits the accurate reconstruction of longitudinal phase space density from one-dimensional bunch profile data. The method is a hybrid one which incorporates particle tracking. Hitherto, a very simple tracking algorithm has been employed because only a brief span of measured profile data is required to build a snapshot of phase space. This is one of the strengths of the method, as tracking for relatively few turns relaxes the precision to which input machine parameters need to be known. The recent addition of longitudinal space charge considerations as an optional refinement of the code is described. Simplicity suggested an approach based on the derivative of bunch shape with the properties of the vacuum chamber parametrized by a single value of distributed reactive impedance and by a geometrical coupling coefficient. This is sufficient to model the dominant collective effects in machines of low to moderate energy. In contrast to simulation codes, binning is not an issue since the profiles to be differentiated are measured ones. The program is written in Fortran 90 with high-performance Fortran extensions for parallel processing. A major effort has been made to identify and remove execution bottlenecks, for example, by reducing floating-point calculations and recoding slow intrinsic functions. A pointerlike mechanism which avoids the problems associated with pointers and parallel processing has been implemented. This is required to handle the large, sparse matrices that the algorithm employs. Results obtained with and without the inclusion of space charge are presented and compared for proton beams in the CERN protron synchrotron booster. Comparisons

  7. Fluorescence-enhanced optical tomography using phase information

    NASA Astrophysics Data System (ADS)

    Lu, Yujie; Sevick-Muraca, Eva M.

    2011-02-01

    Fluorescence-enhanced optical imaging/tomography (FEOI/FEOT) could play an important role in drug discovery and clinical diagnostics. In recent years, improvement in spatial resolution and quantitative biological information has been increasingly promised. Time- and frequency-resolved FEOT has great potential to obtain improved reconstruction information compared with continuous wave (CW) mode due to the acquisition of more measurement information. In this paper, a phase-only FEOT(PO-FEOT) is proposed and evaluated. In PO-FEOT, a finite element-based linear relationship between the unknown fluorophore variables and phase information obtained from time- and frequency-domain boundary measurements is used in FEOT reconstruction. Synthetic data shows that, compared to the amplitude and phase-based reconstruction, the reconstruction time cost is remarkably reduced when phase is used alone. The reconstructed results show that PO-FEOT with high frequency information can acquire preferable reconstruction quality.

  8. Quantitative cone beam X-ray luminescence tomography/X-ray computed tomography imaging

    SciTech Connect

    Chen, Dongmei; Zhu, Shouping Chen, Xueli; Chao, Tiantian; Cao, Xu; Zhao, Fengjun; Huang, Liyu; Liang, Jimin

    2014-11-10

    X-ray luminescence tomography (XLT) is an imaging technology based on X-ray-excitable materials. The main purpose of this paper is to obtain quantitative luminescence concentration using the structural information of the X-ray computed tomography (XCT) in the hybrid cone beam XLT/XCT system. A multi-wavelength luminescence cone beam XLT method with the structural a priori information is presented to relieve the severe ill-posedness problem in the cone beam XLT. The nanophosphors and phantom experiments were undertaken to access the linear relationship of the system response. Then, an in vivo mouse experiment was conducted. The in vivo experimental results show that the recovered concentration error as low as 6.67% with the location error of 0.85 mm can be achieved. The results demonstrate that the proposed method can accurately recover the nanophosphor inclusion and realize the quantitative imaging.

  9. The APOSTEL recommendations for reporting quantitative optical coherence tomography studies

    PubMed Central

    Cruz-Herranz, Andrés; Balk, Lisanne J.; Oberwahrenbrock, Timm; Saidha, Shiv; Martinez-Lapiscina, Elena H.; Lagreze, Wolf A.; Schuman, Joel S.; Villoslada, Pablo; Calabresi, Peter; Balcer, Laura; Petzold, Axel; Green, Ari J.; Paul, Friedemann; Brandt, Alexander U.

    2016-01-01

    Objective: To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. Methods: A panel of experienced OCT researchers (including 11 neurologists, 2 ophthalmologists, and 2 neuroscientists) discussed requirements for performing and reporting quantitative analyses of retinal morphology and developed a list of initial recommendations based on experience and previous studies. The list of recommendations was subsequently revised during several meetings of the coordinating group. Results: We provide a 9-point checklist encompassing aspects deemed relevant when reporting quantitative OCT studies. The areas covered are study protocol, acquisition device, acquisition settings, scanning protocol, funduscopic imaging, postacquisition data selection, postacquisition data analysis, recommended nomenclature, and statistical analysis. Conclusions: The Advised Protocol for OCT Study Terminology and Elements recommendations include core items to standardize and improve quality of reporting in quantitative OCT studies. The recommendations will make reporting of quantitative OCT studies more consistent and in line with existing standards for reporting research in other biomedical areas. The recommendations originated from expert consensus and thus represent Class IV evidence. They will need to be regularly adjusted according to new insights and practices. PMID:27225223

  10. Quantitative fluorescence tomography using a trimodality system: in vivo validation

    NASA Astrophysics Data System (ADS)

    Lin, Yuting; Barber, William C.; Iwanczyk, Jan S.; Roeck, Werner W.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-07-01

    A fully integrated trimodality fluorescence, diffuse optical, and x-ray computed tomography (FT/DOT/XCT) system for small animal imaging is reported in this work. The main purpose of this system is to obtain quantitatively accurate fluorescence concentration images using a multimodality approach. XCT offers anatomical information, while DOT provides the necessary background optical property map to improve FT image accuracy. The quantitative accuracy of this trimodality system is demonstrated in vivo. In particular, we show that a 2-mm-diam fluorescence inclusion located 8 mm deep in a nude mouse can only be localized when functional a priori information from DOT is available. However, the error in the recovered fluorophore concentration is nearly 87%. On the other hand, the fluorophore concentration can be accurately recovered within 2% error when both DOT functional and XCT structural a priori information are utilized together to guide and constrain the FT reconstruction algorithm.

  11. Assessment of metabolic bone diseases by quantitative computed tomography

    SciTech Connect

    Richardson, M.L.; Genant, H.K.; Cann, C.E.; Ettinger, B.; Gordan, G.S.; Kolb, F.O.; Reiser, U.J.

    1985-05-01

    Advances in the radiologic sciences have permitted the development of numerous noninvasive techniques for measuring the mineral content of bone, with varying degrees of precision, accuracy, and sensitivity. The techniques of standard radiography, radiogrammetry, photodensitometry, Compton scattering, neutron activation analysis, single and dual photon absorptiometry, and quantitative computed tomography (QCT) are described and reviewed in depth. Results from previous cross-sectional and longitudinal QCT investigations are given. They then describe a current investigation in which they studied 269 subjects, including 173 normal women, 34 patients with hyperparathyroidism, 24 patients with steroid- induced osteoporosis, and 38 men with idiopathic osteoporosis. Spinal quantitative computed tomography, radiogrammetry, and single photon absorptiometry were performed, and a spinal fracture index was calculated on all patients. The authors found a disproportionate loss of spinal trabecular mineral compared to appendicular mineral in the men with idiopathic osteoporosis and the patients with steroid-induced osteoporosis. They observed roughly equivalent mineral loss in both the appendicular and axial regions in the hyperparathyroid patients. The appendicular cortical measurements correlated moderately well with each other but less well with spinal trabecular QCT. The spinal fracture index correlated well with QCT and less well with the appendicular measurements.

  12. Error corrections for quantitative thermal neutron computed tomography

    NASA Astrophysics Data System (ADS)

    Shi, Liang

    A state-of-the art, two mirror reflection, combination of a Li-6 scintillation screen and a cooled CCD camera high spatial resolution neutron radioscopy imaging system was designed and developed in the RSEC at Penn State. Radiation shielding was applied to the imaging system to achieve a higher spatial resolution. Modulation Transfer Function (MTF) analysis shows that a spatial resolution of 116 microns was achieved. The imaging system was successfully applied for diagnostic measurements of hydrogen fuel cells. A quantitative neutron computed tomography NCT model was developed which confirmed the fundamental computed tomography theory. The model justified the partial volume neutron computed tomography water/ice mass evaluation technique which was designed and tested by Heller. The evaluation results of the water/ice mass using the NCT method was very close to the theoretical value. Sample and background neutron scattering effects were considered as one of the errors that influenced the accuracy of the quantitative measurement using the NCT method. The neutron scattering effect induced cupping artifacts that also contributed to the error in the measurement of water/ice mass using NCT. One method was developed to reduce the cupping artifacts in the reconstruction slice of the water/ice column. The geometric unsharpness, Ug, was demonstrated as the predominant source of error for the accuracy of the 3-D water/ice mass evaluation technique. A unique method was established to reduce the divergence neutron beam associated geometric unsharpness Ug. Compared to the de-convolution algorithm used in de-blurring the image projection, the method has the advantage of minimizing the unsharpness while keeping the degree of cupping through the water column the same. For the 3-D water/ice mass evaluation purpose, this method is a better choice for the water quantification technique error correction.

  13. Phase calibration target for quantitative phase imaging with ptychography.

    PubMed

    Godden, T M; Muñiz-Piniella, A; Claverley, J D; Yacoot, A; Humphry, M J

    2016-04-01

    Quantitative phase imaging (QPI) utilizes refractive index and thickness variations that lead to optical phase shifts. This gives contrast to images of transparent objects. In quantitative biology, phase images are used to accurately segment cells and calculate properties such as dry mass, volume and proliferation rate. The fidelity of the measured phase shifts is of critical importance in this field. However to date, there has been no standardized method for characterizing the performance of phase imaging systems. Consequently, there is an increasing need for protocols to test the performance of phase imaging systems using well-defined phase calibration and resolution targets. In this work, we present a candidate for a standardized phase resolution target, and measurement protocol for the determination of the transfer of spatial frequencies, and sensitivity of a phase imaging system. The target has been carefully designed to contain well-defined depth variations over a broadband range of spatial frequencies. In order to demonstrate the utility of the target, we measure quantitative phase images on a ptychographic microscope, and compare the measured optical phase shifts with Atomic Force Microscopy (AFM) topography maps and surface profile measurements from coherence scanning interferometry. The results show that ptychography has fully quantitative nanometer sensitivity in optical path differences over a broadband range of spatial frequencies for feature sizes ranging from micrometers to hundreds of micrometers. PMID:27137054

  14. Assessment of metabolic bone diseases by quantitative computed tomography

    NASA Technical Reports Server (NTRS)

    Richardson, M. L.; Genant, H. K.; Cann, C. E.; Ettinger, B.; Gordan, G. S.; Kolb, F. O.; Reiser, U. J.

    1985-01-01

    Advances in the radiologic sciences have permitted the development of numerous noninvasive techniques for measuring the mineral content of bone, with varying degrees of precision, accuracy, and sensitivity. The techniques of standard radiography, radiogrammetry, photodensitometry, Compton scattering, neutron activation analysis, single and dual photon absorptiometry, and quantitative computed tomography (QCT) are described and reviewed in depth. Results from previous cross-sectional and longitudinal QCT investigations are given. They then describe a current investigation in which they studied 269 subjects, including 173 normal women, 34 patients with hyperparathyroidism, 24 patients with steroid-induced osteoporosis, and 38 men with idiopathic osteoporosis. Spinal quantitative computed tomography, radiogrammetry, and single photon absorptiometry were performed, and a spinal fracture index was calculated on all patients. The authors found a disproportionate loss of spinal trabecular mineral compared to appendicular mineral in the men with idiopathic osteoporosis and the patients with steroid-induced osteoporosis. They observed roughly equivalent mineral loss in both the appendicular and axial regions in the hyperparathyroid patients. The appendicular cortical measurements correlated moderately well with each other but less well with spinal trabecular QCT. The spinal fracture index correlated well with QCT and less well with the appendicular measurements. Knowledge of appendicular cortical mineral status is important in its own right but is not a valid predictor of axial trabecular mineral status, which may be disproportionately decreased in certain diseases. Quantitative CT provides a reliable means of assessing the latter region of the skeleton, correlates well with the spinal fracture index (a semiquantitative measurement of end-organ failure), and offers the clinician a sensitive means of following the effects of therapy.

  15. Bayesian parameter estimation in spectral quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Pulkkinen, Aki; Cox, Ben T.; Arridge, Simon R.; Kaipio, Jari P.; Tarvainen, Tanja

    2016-03-01

    Photoacoustic tomography (PAT) is an imaging technique combining strong contrast of optical imaging to high spatial resolution of ultrasound imaging. These strengths are achieved via photoacoustic effect, where a spatial absorption of light pulse is converted into a measurable propagating ultrasound wave. The method is seen as a potential tool for small animal imaging, pre-clinical investigations, study of blood vessels and vasculature, as well as for cancer imaging. The goal in PAT is to form an image of the absorbed optical energy density field via acoustic inverse problem approaches from the measured ultrasound data. Quantitative PAT (QPAT) proceeds from these images and forms quantitative estimates of the optical properties of the target. This optical inverse problem of QPAT is illposed. To alleviate the issue, spectral QPAT (SQPAT) utilizes PAT data formed at multiple optical wavelengths simultaneously with optical parameter models of tissue to form quantitative estimates of the parameters of interest. In this work, the inverse problem of SQPAT is investigated. Light propagation is modelled using the diffusion equation. Optical absorption is described with chromophore concentration weighted sum of known chromophore absorption spectra. Scattering is described by Mie scattering theory with an exponential power law. In the inverse problem, the spatially varying unknown parameters of interest are the chromophore concentrations, the Mie scattering parameters (power law factor and the exponent), and Gruneisen parameter. The inverse problem is approached with a Bayesian method. It is numerically demonstrated, that estimation of all parameters of interest is possible with the approach.

  16. Glasses for 3D ultrasound computer tomography: phase compensation

    NASA Astrophysics Data System (ADS)

    Zapf, M.; Hopp, T.; Ruiter, N. V.

    2016-03-01

    Ultrasound Computer Tomography (USCT), developed at KIT, is a promising new imaging system for breast cancer diagnosis, and was successfully tested in a pilot study. The 3D USCT II prototype consists of several hundreds of ultrasound (US) transducers on a semi-ellipsoidal aperture. Spherical waves are sequentially emitted by individual transducers and received in parallel by many transducers. Reflectivity volumes are reconstructed by synthetic aperture focusing (SAFT). However, straight forward SAFT imaging leads to blurred images due to system imperfections. We present an extension of a previously proposed approach to enhance the images. This approach includes additional a priori information and system characteristics. Now spatial phase compensation was included. The approach was evaluated with a simulation and clinical data sets. An increase in the image quality was observed and quantitatively measured by SNR and other metrics.

  17. Clinical efficacy of 2-phase versus 4-phase computed tomography for localization in primary hyperparathyroidism

    PubMed Central

    Ramirez, Adriana G.; Shada, Amber L.; Martin, Allison N.; Raghavan, Prashant; Durst, Christopher R.; Mukherjee, Sugoto; Gaughen, John R.; Ornan, David A.; Hanks, John B.; Smith, Philip W.

    2016-01-01

    Background Four-dimensional computed tomography is being used increasingly for localization of abnormal glands in primary hyperparathyroidism. We hypothesized that compared with traditional 4-phase imaging, 2-phase imaging would halve the radiation dose without compromising parathyroid localization and clinical outcomes. Methods A transition from 4-phase to 2-phase imaging was instituted between 2009 and 2010. A pre-post analysis was performed on patients undergoing operative treatment with a parathyroid protocol computed tomography, and relevant data were correlated with operative findings. Sensitivity, positive predictive value, technical success, and cure rates were calculated. The Fisher exact test or χ2 test assessed the significance of 2-phase and 4-phase imaging and operative findings. Results Twenty-seven patients had traditional four-dimensional computed tomography and 35 had modified 2-phase computed tomography. Effective radiation doses were 6.8 mSy for 2-phase and 14 mSv for 4-phase. Four-phase computed tomography had a sensitivity and positive predictive value of 93% and 96%, respectively. Two-phase computed tomography had a comparable sensitivity and positive predictive value of 97% and 94%, respectively. Eight patients with discordant imaging had an average parathyroid weight of 240 g compared with 1,300 g for all patients. Technical surgical success (90% for 4-phase computed tomography versus 91% 2-phase computed tomography) and normocalcemia rates at 6 months (88% for both) did not differ between computed tomography protocols. Computed tomography correctly predicted multiglandular disease and localization for reoperations in 88% and 90% of cases, respectively, with no difference by computed tomography protocol. Conclusion With regard to surgical outcomes and localization, 2-phase parathyroid computed tomography is equivalent to 4-phase for parathyroid localization, including small adenomas, reoperative cases, and multiglandular disease. Two-phase

  18. Spectral modulation interferometry for quantitative phase imaging

    PubMed Central

    Shang, Ruibo; Chen, Shichao; Li, Chengshuai; Zhu, Yizheng

    2015-01-01

    We propose a spectral-domain interferometric technique, termed spectral modulation interferometry (SMI), and present its application to high-sensitivity, high-speed, and speckle-free quantitative phase imaging. In SMI, one-dimensional complex field of an object is interferometrically modulated onto a broadband spectrum. Full-field phase and intensity images are obtained by scanning along the orthogonal direction. SMI integrates the high sensitivity of spectral-domain interferometry with the high speed of spectral modulation to quantify fast phase dynamics, and its dispersive and confocal nature eliminates laser speckles. The principle and implementation of SMI are discussed. Its performance is evaluated using static and dynamic objects. PMID:25780737

  19. On the relationship between intensity diffraction tomography and phase-contrast tomography

    NASA Astrophysics Data System (ADS)

    Anastasio, Mark A.; Shi, Daxin

    2004-10-01

    Diffraction tomography (DT) is a well-known method for reconstructing the complex-valued refractive index distribution of weakly scattering objects. A reconstruction theory of intensity DT (I-DT) has been proposed [Gbur and Wolf, JOSA A, 2002] that can accomplish such a reconstruction from knowledge of only the wavefield intensities on two different transverse planes at each tomographic view angle. In this work, we elucidate the relationship between I-DT and phase-contrast tomography and demonstrate that I-DT reconstruction theory contains some of the existing reconstruction algorithms for phase-contrast tomography as special cases.

  20. Quantitative flaw characterization with ultrasonic phased arrays

    NASA Astrophysics Data System (ADS)

    Engle, Brady John

    Ultrasonic nondestructive evaluation (NDE) is a critical diagnostic tool in many industries. It is used to characterize potentially dangerous flaws in critical components for aerospace, automotive, and energy applications. The use of phased array transducers allows for the extension of traditional techniques and the introduction of new methods for quantitative flaw characterization. An equivalent flaw sizing technique for use in time-of-flight diffraction setups is presented that provides an estimate of the size and orientation of isolated cracks, surface-breaking cracks, and volumetric flaws such as voids and inclusions. Experimental validation is provided for the isolated crack case. A quantitative imaging algorithm is developed that corrects for system effects and wave propagation, making the images formed directly related to the properties of the scatterer present. Simulated data is used to form images of cylindrical and spherical inclusions. The contributions of different signals to the image formation process are discussed and examples of the quantitative nature of the images are shown.

  1. Semiautomatic Software For Quantitative Analysis Of Cardiac Positron Tomography Studies

    NASA Astrophysics Data System (ADS)

    Ratib, Osman; Bidaut, Luc; Nienaber, Christoph; Krivokapich, Janine; Schelbert, Heinrich R.; Phelps, Michael E.

    1988-06-01

    In order to derive accurate values for true tissue radiotracers concentrations from gated positron emission tomography (PET) images of the heart, which are critical for quantifying noninvasively regional myocardial blood flow and metabolism, appropriate corrections for partial volume effect (PVE) and contamination from adjacent anatomical structures are required. We therefore developed an integrated software package for quantitative analysis of tomographic images which provides for such corrections. A semiautomatic edge detection technique outlines and partitions the myocardium into sectors. Myocardial wall thickness is measured on the images perpendicularly to the detected edges and used to correct for PVE. The programs automatically correct for radioactive decay, activity calibration and cross contaminations for both static and dynamic studies. Parameters derived with these programs include tracer concentrations and their changes over time. They are used for calculating regional metabolic rates and can be further displayed as color coded parametric images. The approach was validated for PET imaging in 11 dog experiments. 2D echocardiograms (Echo) were recorded simultaneously to validate the edge detection and wall thickness measurement techniques. After correction for PVE using automatic WT measurement, regional tissue tracer concentrations derived from PET images correlated well with true tissue concentrations as determined by well counting (r=0.98). These preliminary studies indicate that the developed automatic image analysis technique allows accurate and convenient evaluation of cardiac PET images for the measurement of both, regional tracer tissue concentrations as well as regional myocardial function.

  2. Concluding Report: Quantitative Tomography Simulations and Reconstruction Algorithms

    SciTech Connect

    Aufderheide, M B; Martz, H E; Slone, D M; Jackson, J A; Schach von Wittenau, A E; Goodman, D M; Logan, C M; Hall, J M

    2002-02-01

    In this report we describe the original goals and final achievements of this Laboratory Directed Research and Development project. The Quantitative was Tomography Simulations and Reconstruction Algorithms project (99-ERD-015) funded as a multi-directorate, three-year effort to advance the state of the art in radiographic simulation and tomographic reconstruction by improving simulation and including this simulation in the tomographic reconstruction process. Goals were to improve the accuracy of radiographic simulation, and to couple advanced radiographic simulation tools with a robust, many-variable optimization algorithm. In this project, we were able to demonstrate accuracy in X-Ray simulation at the 2% level, which is an improvement of roughly a factor of 5 in accuracy, and we have successfully coupled our simulation tools with the CCG (Constrained Conjugate Gradient) optimization algorithm, allowing reconstructions that include spectral effects and blurring in the reconstructions. Another result of the project was the assembly of a low-scatter X-Ray imaging facility for use in nondestructive evaluation applications. We conclude with a discussion of future work.

  3. Limited-view multi-source quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Gao, Hao; Feng, Jing; Song, Liang

    2015-06-01

    A limited-view scheme is proposed for multi-source quantitative photoacoustic tomography (MS-QPAT), in which the acoustic measurements following each optical illumination are acquired on the partial boundary near the optical source instead of the entire boundary, namely the limited-view MS-QPAT. The proposed limited-view scheme has an improved signal-to-noise ratio when the data are measured near the optical source, and reduces the acquisition time of the imaging system with a single or limited-view acoustic detector. A limited-view MS-QPAT example is to acquire 4{}^\\circ acoustic data following each of 90 optical illuminations, in contrast to 360{}^\\circ acoustic data for each of 90 optical illuminations under the conventional MS-QPAT setting. However, due to the incomplete data, the initial acoustic pressure can no longer be stably reconstructed that serves as an intermediate step in the conventional two-step reconstruction that first reconstructs the initial acoustic pressure and then the optical coefficients. Therefore the direct reconstruction of optical coefficients is considered using the coupled opto-acoustic forward model. The reconstruction algorithm is based on the quasi-Newton method, i.e. limited-memory BFGS with efficient adjoint computations of objective function gradients, and the sparsity-regularized formulation is also considered with tensor framelet sparsity transform and solved by the alternating direction method of multipliers.

  4. Quantitative Tomography of Organic Photovoltaic Blends at the Nanoscale.

    PubMed

    Pfannmöller, M; Heidari, H; Nanson, L; Lozman, O R; Chrapa, M; Offermans, T; Nisato, G; Bals, S

    2015-10-14

    The success of semiconducting organic materials has enabled green technologies for electronics, lighting, and photovoltaics. However, when blended together, these materials have also raised novel fundamental questions with respect to electronic, optical, and thermodynamic properties. This is particularly important for organic photovoltaic cells based on the bulk heterojunction. Here, the distribution of nanoscale domains plays a crucial role depending on the specific device structure. Hence, correlation of the aforementioned properties requires 3D nanoscale imaging of materials domains, which are embedded in a multilayer device. Such visualization has so far been elusive due to lack of contrast, insufficient signal, or resolution limits. In this Letter, we introduce spectral scanning transmission electron tomography for reconstruction of entire volume plasmon spectra from rod-shaped specimens. We provide 3D structural correlations and compositional mapping at a resolution of approximately 7 nm within advanced organic photovoltaic tandem cells. Novel insights that are obtained from quantitative 3D analyses reveal that efficiency loss upon thermal annealing can be attributed to subtle, fundamental blend properties. These results are invaluable in guiding the design and optimization of future devices in plastic electronics applications and provide an empirical basis for modeling and simulation of organic solar cells.

  5. Quantitative Tomography of Organic Photovoltaic Blends at the Nanoscale.

    PubMed

    Pfannmöller, M; Heidari, H; Nanson, L; Lozman, O R; Chrapa, M; Offermans, T; Nisato, G; Bals, S

    2015-10-14

    The success of semiconducting organic materials has enabled green technologies for electronics, lighting, and photovoltaics. However, when blended together, these materials have also raised novel fundamental questions with respect to electronic, optical, and thermodynamic properties. This is particularly important for organic photovoltaic cells based on the bulk heterojunction. Here, the distribution of nanoscale domains plays a crucial role depending on the specific device structure. Hence, correlation of the aforementioned properties requires 3D nanoscale imaging of materials domains, which are embedded in a multilayer device. Such visualization has so far been elusive due to lack of contrast, insufficient signal, or resolution limits. In this Letter, we introduce spectral scanning transmission electron tomography for reconstruction of entire volume plasmon spectra from rod-shaped specimens. We provide 3D structural correlations and compositional mapping at a resolution of approximately 7 nm within advanced organic photovoltaic tandem cells. Novel insights that are obtained from quantitative 3D analyses reveal that efficiency loss upon thermal annealing can be attributed to subtle, fundamental blend properties. These results are invaluable in guiding the design and optimization of future devices in plastic electronics applications and provide an empirical basis for modeling and simulation of organic solar cells. PMID:26390367

  6. Quantitative Phase Microscopy: how to make phase data meaningful

    PubMed Central

    Goldstein, Goldie; Creath, Katherine

    2014-01-01

    The continued development of hardware and associated image processing techniques for quantitative phase microscopy has allowed superior phase data to be acquired that readily shows dynamic optical volume changes and enables particle tracking. Recent efforts have focused on tying phase data and associated metrics to cell morphology. One challenge in measuring biological objects using interferometrically obtained phase information is achieving consistent phase unwrapping and -dimensions and correct for temporal discrepanices using a temporal unwrapping procedure. The residual background shape due to mean value fluctuations and residual tilts can be removed automatically using a simple object characterization algorithm. Once the phase data are processed consistently, it is then possible to characterize biological samples such as myocytes and myoblasts in terms of their size, texture and optical volume and track those features dynamically. By observing optical volume dynamically it is possible to determine the presence of objects such as vesicles within myoblasts even when they are co-located with other objects. Quantitative phase microscopy provides a label-free mechanism to characterize living cells and their morphology in dynamic environments, however it is critical to connect the measured phase to important biological function for this measurement modality to prove useful to a broader scientific community. In order to do so, results must be highly consistent and require little to no user manipulation to achieve high quality nynerical results that can be combined with other imaging modalities. PMID:25309099

  7. Quantitative phase imaging with partially coherent illumination.

    PubMed

    Nguyen, T H; Edwards, C; Goddard, L L; Popescu, G

    2014-10-01

    In this Letter, we formulate a mathematical model for predicting experimental outcomes in quantitative phase imaging (QPI) when the illumination field is partially spatially coherent. We derive formulae that apply to QPI and discuss expected results for two classes of QPI experiments: common path and traditional interferometry, under varying degrees of spatial coherence. In particular, our results describe the physical relationship between the spatial coherence of the illuminating field and the halo effect, which is well known in phase-contrast microscopy. We performed experiments relevant to this common situation and found that our theory is in excellent agreement with the data. With this new understanding of the effects of spatial coherence, our formulae offer an avenue for removing halo artifacts from phase images. PMID:25360915

  8. Quantitative Computed Tomography Protocols Affect Material Mapping and Quantitative Computed Tomography-Based Finite-Element Analysis Predicted Stiffness.

    PubMed

    Giambini, Hugo; Dragomir-Daescu, Dan; Nassr, Ahmad; Yaszemski, Michael J; Zhao, Chunfeng

    2016-09-01

    Quantitative computed tomography-based finite-element analysis (QCT/FEA) has become increasingly popular in an attempt to understand and possibly reduce vertebral fracture risk. It is known that scanning acquisition settings affect Hounsfield units (HU) of the CT voxels. Material properties assignments in QCT/FEA, relating HU to Young's modulus, are performed by applying empirical equations. The purpose of this study was to evaluate the effect of QCT scanning protocols on predicted stiffness values from finite-element models. One fresh frozen cadaveric torso and a QCT calibration phantom were scanned six times varying voltage and current and reconstructed to obtain a total of 12 sets of images. Five vertebrae from the torso were experimentally tested to obtain stiffness values. QCT/FEA models of the five vertebrae were developed for the 12 image data resulting in a total of 60 models. Predicted stiffness was compared to the experimental values. The highest percent difference in stiffness was approximately 480% (80 kVp, 110 mAs, U70), while the lowest outcome was ∼1% (80 kVp, 110 mAs, U30). There was a clear distinction between reconstruction kernels in predicted outcomes, whereas voltage did not present a clear influence on results. The potential of QCT/FEA as an improvement to conventional fracture risk prediction tools is well established. However, it is important to establish research protocols that can lead to results that can be translated to the clinical setting. PMID:27428281

  9. Bone morphometry and mineral density measurement using quantitative computed tomography

    SciTech Connect

    Jacobson, D.R.

    1991-01-01

    Application of computed tomography (CT) to the study of bone structure and density was explored and developed. A review of bone mineral densitometry (BMD) methodology and general principles of quantitative CT (QCT) are presented. A method for QCT of the spine was developed using a flexible tissue equivalent reference placed adjacent to the patient. A methodology for the development and production of tissue equivalent materials is also presented. Patient equivalent phantoms were used to characterize the method, and phantom studies were performed at five clinical sites. A protocol is defined for measuring the inside diameter of the lumbar pedicular canal. Data generated from this study has proven invaluable in the planning for lumbar fusion surgery when screws are to be used for immobilization. Pedicular canal data from 33 patients is presented. QCT was also used to quantify several parameters of the femoral shaft for use in hip replacement surgical planning. Parameters studied include inside diameter, BMD, endosteal BMD and proximal shaft morphology. The structure and trabecular BMD of the proximal femur was extensively studied using QCT. A large variation was found in the fat content of marrow within the proximal femur, and phantom studies were performed to quantify the effect of fat on trabecular QCT BMD. Cadaveric trabecular bone samples with marrow were analyzed physically to determine water, fat, non-fat soft tissue, and ash content. Multiple thin-slice CT studies were performed on cadaveric femurs. A structural model of the proximal femur was developed in which the structural support is provided primarily by trabecular bone. This model may have profound implications in the study of femoral fractures and prosthetic hardware design.

  10. Quantitative phase imaging with programmable illumination

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Edwards, Chris; Goddard, Lynford L.; Popescu, Gabriel

    2015-03-01

    Even with the recent rapid advances in the field of microscopy, non-laser light sources used for light microscopy have not been developing significantly. Most current optical microscopy systems use halogen bulbs as their light sources to provide a white-light illumination. Due to the confined shapes and finite filament size of the bulbs, little room is available for modification in the light source, which prevents further advances in microscopy. By contrast, commercial projectors provide a high power output that is comparable to the halogen lamps while allowing for great flexibility in patterning the illumination. In addition to their high brightness, the illumination can be patterned to have arbitrary spatial and spectral distributions. Therefore, commercial projectors can be adopted as a flexible light source to an optical microscope by careful alignment to the existing optical path. In this study, we employed a commercial projector source to a quantitative phase imaging system called spatial light interference microscopy (SLIM), which is an outside module for an existing phase contrast (PC) microscope. By replacing the ring illumination of PC with a ring-shaped pattern projected onto the condenser plane, we were able to recover the same result as the original SLIM. Furthermore, the ring illumination is replaced with multiple dots aligned along the same ring to minimize the overlap between the scattered and unscattered fields. This new method minimizes the halo artifact of the imaging system, which allows for a halo-free high-resolution quantitative phase microscopy system.

  11. Assessment of patient selection criteria for quantitative imaging with respiratory-gated positron emission tomography.

    PubMed

    Bowen, Stephen R; Pierce, Larry A; Alessio, Adam M; Liu, Chi; Wollenweber, Scott D; Stearns, Charles W; Kinahan, Paul E

    2014-07-01

    The objective of this investigation was to propose techniques for determining which patients are likely to benefit from quantitative respiratory-gated imaging by correlating respiratory patterns to changes in positron emission tomography (PET) metrics. Twenty-six lung and liver cancer patients underwent PET/computed tomography exams with recorded chest/abdominal displacements. Static and adaptive amplitude-gated [[Formula: see text

  12. Swept source quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Zhu, Yizheng; Chen, Shichao

    2016-03-01

    Holographic phase microscopy has seen rapid growth in the past two decades. Numerous schemes have been proposed and commercial products are now available. Since most systems are laser based, speckle noise and other non-signal interference in the system have been problematic, limiting the technique's phase sensitivity, image quality and the ability for accurate quantitative analysis. Low coherence source-based HPM have also been proposed to mitigate this issue, but often with increased system complexity and reduced implementation flexibility. Here, we demonstrate a swept-source HPM technique, which acquires on-axis holograms while continuously scanning the laser through a range of wavelengths. This technique is capable of identifying interference from various sources and effectively isolating sample interference, therefore minimizing unwanted signals and achieving high spatial and temporal sensitivity across the entire field of view. The ability of acquiring spectral interferogram for each pixel also make it possible to implement spectral shaping, which can further suppress interference side-lobes and improve sensitivity. Additionally, when coupled with a spectral modulation technique, such interference spectrum will permit spectroscopic measurement of phase-related properties of the sample. We will introduce the principle of the system, discuss its theoretical sensitivity bound, and present its application to phase imaging of live cells.

  13. Image reconstruction with noise and error modelling in quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Tarvainen, Tanja; Pulkkinen, Aki; Cox, Ben T.; Kaipio, Jari P.; Arridge, Simon R.

    2016-03-01

    Quantitative photoacoustic tomography is an emerging imaging technique aimed at estimating the optical parameters inside tissue from photoacoustic images. The method proceeds from photoacoustic tomography by taking the estimated initial pressure distributions as data and estimating the absolute values of the optical parameters. Therefore, both the data and the noise of the second (optical) inverse problem are affected by the method applied to solve the first (acoustic) inverse problem. In this work, the Bayesian approach for quantitative photoacoustic tomography is taken. Modelling of noise and errors and incorporating their statistics into the solution of the inverse problem are investigated.

  14. Development of neutron tomography and phase contrast imaging technique

    SciTech Connect

    Kashyap, Y. S.; Agrawal, Ashish; Sarkar, P. S.; Shukla, Mayank; Sinha, Amar

    2013-02-05

    This paper presents design and development of a state of art neutron imaging technique at CIRUS reactor with special reference for techniques adopted for tomography and phase contrast imaging applications. Different components of the beamline such as collimator, shielding, sample manipulator, digital imaging system were designed keeping in mind the requirements of data acquisition time and resolution. The collimator was designed in such a way that conventional and phase contrast imaging can be done using same collimator housing. We have done characterization of fuel pins, study of hydride blisters in pressure tubes hydrogen based cells, two phase flow visualization, and online study of locomotive parts etc. using neutron tomography and radiography technique. We have also done some studies using neutron phase contrast imaging technique on this beamline.

  15. Beam Tomography in Longitudinal Phase Space

    NASA Astrophysics Data System (ADS)

    Mane, V.; Wei, J.; Peggs, S.

    1997-05-01

    Longitudinal particle motion in circular accelerators is typically monitored by one dimensional (1-D) profiles. Adiabatic particle motion in 2-D phase space can be reconstructed with tomographic techniques, using 1-D profiles. In this paper, we discuss a filtered backprojection algorithm, with a high pass ramp or Hann filter, for phase space reconstruction. The algorithm uses several projections of the beam at equally spaced angles over half a synchrotron period. A computer program RADON has been developed to process digitized mountain range data and do the phase space reconstruction for the AGS, and later for Relativistic Heavy Ion Collider (RHIC). Analysis has been performed to determine the sensitivity to machine parameters and data acquisition errors. During the Sextant test of RHIC in early 1997, this program has been successfully employed to reconstruct the motion of Au^77+ beam in the AGS.

  16. Phase retrieval tomography in the presence of noise

    NASA Astrophysics Data System (ADS)

    Arhatari, B. D.; Gates, W. P.; Eshtiaghi, N.; Peele, A. G.

    2010-02-01

    We describe the use of single-plane phase retrieval tomography using a laboratory-based x-ray source, under conditions where the retrieval is not formally valid, to present images of the internal structure of an Aerosil granule and a hydrated bentonite gel. The technique provides phase images for samples that interact weakly with the x-ray beam. As the method is less affected by noise than an alternative two-plane phase retrieval method that is otherwise formally valid, object structure can be observed that would not otherwise be seen. We demonstrate our results for phase imaging in tomographic measurements.

  17. Lower mantle tomography and phase change mapping

    NASA Astrophysics Data System (ADS)

    Sun, Daoyuan; Helmberger, Don

    2008-10-01

    A lower mantle S wave triplication (Scd) has been recognized for many years and appears to be explained by the recently discovered perovskite (PV) to postperovskite (PPV) phase change. Seismic observations of Scd display (1) rapid changes in strength and timing relative to S and ScS and (2) early arrivals beneath fast lower mantle regions. While the latter feature can be explained by a Clapeyron slope (γ) of 6 MPa/K and a velocity jump of 1.5% when corrected by tomographic predictions, it does not explain the first feature. Here, we expand on this mapping approach by attempting a new parameterization that requires a sample of D" near the ScS bounce point (δVS) where the phase height (hph) and velocity jump (β) are functions of (δVS). These parameters are determined by modeling dense record sections collected from USArray and PASSCAL data where Grand's tomographic model is the most detailed in D" structure beneath Central America. We also address the range of γ to generate new global models of the phase boundary and associated temperature variation. We conclude that a γ near 9 MPa/K is most satisfactory but requires β to be nonuniform with a range from about 1.0 to 4.0% with some slow region samples requiring the largest values. Moreover, the edges of the supposed buckled slabs delimitated by both P and S waves display very rapid changes in phase boundary heights producing Scd multipathing. These features can explain the unstable nature of the Scd phase with easy detection to no detection commonly observed. The fine structure at the base of the mantle beneath these edges contains particularly strong reflections indicative of local ultralow velocity zones, which are predicted in some dynamic models.

  18. Reconstruction methods for phase-contrast tomography

    SciTech Connect

    Raven, C.

    1997-02-01

    Phase contrast imaging with coherent x-rays can be distinguished in outline imaging and holography, depending on the wavelength {lambda}, the object size d and the object-to-detector distance r. When r << d{sup 2}{lambda}, phase contrast occurs only in regions where the refractive index fastly changes, i.e. at interfaces and edges in the sample. With increasing object-to-detector distance we come in the area of holographic imaging. The image contrast outside the shadow region of the object is due to interference of the direct, undiffracted beam and a beam diffracted by the object, or, in terms of holography, the interference of a reference wave with the object wave. Both, outline imaging and holography, offer the possibility to obtain three dimensional information of the sample in conjunction with a tomographic technique. But the data treatment and the kind of information one can obtain from the reconstruction is different.

  19. Quantitative phase-amplitude microscopy. III. The effects of noise.

    PubMed

    Paganin, D; Barty, A; McMahon, P J; Nugent, K A

    2004-04-01

    We explore the effect of noise on images obtained using quantitative phase-amplitude microscopy - a new microscopy technique based on the determination of phase from the intensity evolution of propagating radiation. We compare the predictions with experimental results and also propose an approach that allows good-quality quantitative phase retrieval to be obtained even for very noisy data.

  20. Lensless transport-of-intensity phase microscopy and tomography with a color LED matrix

    NASA Astrophysics Data System (ADS)

    Zuo, Chao; Sun, Jiasong; Zhang, Jialin; Hu, Yan; Chen, Qian

    2015-07-01

    We demonstrate lens-less quantitative phase microscopy and diffraction tomography based on a compact on-chip platform, using only a CMOS image sensor and a programmable color LED array. Based on multi-wavelength transport-of- intensity phase retrieval and multi-angle illumination diffraction tomography, this platform offers high quality, depth resolved images with a lateral resolution of ˜3.7μm and an axial resolution of ˜5μm, over wide large imaging FOV of 24mm2. The resolution and FOV can be further improved by using a larger image sensors with small pixels straightforwardly. This compact, low-cost, robust, portable platform with a decent imaging performance may offer a cost-effective tool for telemedicine needs, or for reducing health care costs for point-of-care diagnostics in resource-limited environments.

  1. Quantitative shear wave imaging optical coherence tomography for noncontact mechanical characterization of myocardium

    NASA Astrophysics Data System (ADS)

    Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

    2015-03-01

    Optical coherence elastography (OCE) is an emerging low-coherence imaging technique that provides noninvasive assessment of tissue biomechanics with high spatial resolution. Among various OCE methods, the capability of quantitative measurement of tissue elasticity is of great importance for tissue characterization and pathology detection across different samples. Here we report a quantitative OCE technique, termed quantitative shear wave imaging optical coherence tomography (Q-SWI-OCT), which enables noncontact measurement of tissue Young's modulus based on the ultra-fast imaging of the shear wave propagation inside the sample. A focused air-puff device is used to interrogate the tissue with a low-pressure short-duration air stream that stimulates a localized displacement with the scale at micron level. The propagation of this tissue deformation in the form of shear wave is captured by a phase-sensitive OCT system running with the scan of the M-mode imaging over the path of the wave propagation. The temporal characteristics of the shear wave is quantified based on the cross-correlation of the tissue deformation profiles at all the measurement locations, and linear regression is utilized to fit the data plotted in the domain of time delay versus wave propagation distance. The wave group velocity is thus calculated, which results in the quantitative measurement of the Young's modulus. As the feasibility demonstration, experiments are performed on tissuemimicking phantoms with different agar concentrations and the quantified elasticity values with Q-SWI-OCT agree well with the uniaxial compression tests. For functional characterization of myocardium with this OCE technique, we perform our pilot experiments on ex vivo mouse cardiac muscle tissues with two studies, including 1) elasticity difference of cardiac muscle under relaxation and contract conditions and 2) mechanical heterogeneity of the heart introduced by the muscle fiber orientation. Our results suggest the

  2. Development of a prototype gantry system for preclinical x-ray phase-contrast computed tomography

    SciTech Connect

    Tapfer, Arne; Bech, Martin; Pauwels, Bart; Liu Xuan; Bruyndonckx, Peter; Sasov, Alexander; Kenntner, Johannes; Mohr, Juergen; Walter, Marco; Schulz, Joachim; Pfeiffer, Franz

    2011-11-15

    Purpose: To explore the potential of grating-based x-ray phase-contrast imaging for clinical applications, a first compact gantry system was developed. It is designed such that it can be implemented into an in-vivo small-animal phase-contrast computed tomography (PC-CT) scanner. The purpose of the present study is to assess the accuracy and quantitativeness of the described gantry in both absorption and phase-contrast. Methods: A phantom, containing six chemically well-defined liquids, was constructed. A tomography scan with cone-beam reconstruction of this phantom was performed yielding the spatial distribution of the linear attenuation coefficient {mu} and decrement {delta} of the complex refractive index. Theoretical values of {mu} and {delta} were calculated for each liquid from tabulated data and compared with the experimentally measured values. Additionally, a color-fused image representation is proposed to display the complementary absorption and phase-contrast information in a single image. Results: Experimental and calculated data of the phantom agree well confirming the quantitativeness and accuracy of the reconstructed spatial distributions of {mu} and {delta}. The proposed color-fused image representation, which combines the complementary absorption and phase information, considerably helps in distinguishing the individual substances. Conclusions: The concept of grating-based phase-contrast computed tomography (CT) can be implemented into a compact, cone-beam geometry gantry setup. The authors believe that this work represents an important milestone in translating phase-contrast x-ray imaging from previous proof-of-principle experiments to first preclinical biomedical imaging applications on small-animal models.

  3. Quantitative evaluation of regularized phase retrieval algorithms on bone scaffolds seeded with bone cells

    NASA Astrophysics Data System (ADS)

    Weber, L.; Langer, M.; Tavella, S.; Ruggiu, A.; Peyrin, F.

    2016-05-01

    In the field of regenerative medicine, there has been a growing interest in studying the combination of bone scaffolds and cells that can maximize newly formed bone. In-line phase-contrast x-ray tomography was used to image porous bone scaffolds (Skelite©), seeded with bone forming cells. This technique allows the quantification of both mineralized and soft tissue, unlike with classical x-ray micro-computed tomography. Phase contrast images were acquired at four distances. The reconstruction is typically performed in two successive steps: phase retrieval and tomographic reconstruction. In this work, different regularization methods were applied to the phase retrieval process. The application of a priori terms for heterogeneous objects enables quantitative 3D imaging of not only bone morphology, mineralization, and soft tissue formation, but also cells trapped in the pre-bone matrix. A statistical study was performed to derive statistically significant information on the different culture conditions.

  4. Cumulative phase delay imaging for contrast-enhanced ultrasound tomography

    NASA Astrophysics Data System (ADS)

    Demi, Libertario; van Sloun, Ruud J. G.; Wijkstra, Hessel; Mischi, Massimo

    2015-11-01

    Standard dynamic-contrast enhanced ultrasound (DCE-US) imaging detects and estimates ultrasound-contrast-agent (UCA) concentration based on the amplitude of the nonlinear (harmonic) components generated during ultrasound (US) propagation through UCAs. However, harmonic components generation is not specific to UCAs, as it also occurs for US propagating through tissue. Moreover, nonlinear artifacts affect standard DCE-US imaging, causing contrast to tissue ratio reduction, and resulting in possible misclassification of tissue and misinterpretation of UCA concentration. Furthermore, no contrast-specific modality exists for DCE-US tomography; in particular speed-of-sound changes due to UCAs are well within those caused by different tissue types. Recently, a new marker for UCAs has been introduced. A cumulative phase delay (CPD) between the second harmonic and fundamental component is in fact observable for US propagating through UCAs, and is absent in tissue. In this paper, tomographic US images based on CPD are for the first time presented and compared to speed-of-sound US tomography. Results show the applicability of this marker for contrast specific US imaging, with cumulative phase delay imaging (CPDI) showing superior capabilities in detecting and localizing UCA, as compared to speed-of-sound US tomography. Cavities (filled with UCA) which were down to 1 mm in diameter were clearly detectable. Moreover, CPDI is free of the above mentioned nonlinear artifacts. These results open important possibilities to DCE-US tomography, with potential applications to breast imaging for cancer localization.

  5. Theory of Fourier phase within the framework of Fourier-domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Uttam, Shikhar; Liu, Yang

    2016-03-01

    Fourier phase in Fourier-domain optical coherence tomography (FD-OCT) has been shown to estimate the sub- resolution change in the optical depth location of a strong interface in refractive index profile of a sample using spectral-domain phase microscopy (SDPM), a derivative of FD-OCT. From first principles we show that in general Fourier phase not only estimates this sub-resolution change but also the mean spatial frequency of the coherence-gated refractive index, and both SDPM and depth-resolved spatial-domain low-coherence quantitative phase microscopy (dr-SLQPM) are special cases of this general theory. We also show that for spectral source with infinite bandwidth Fourier phase is zero. We provide analytical expressions and numerical simulations to support our results.

  6. Quantitative simultaneous positron emission tomography and magnetic resonance imaging

    PubMed Central

    Ouyang, Jinsong; Petibon, Yoann; Huang, Chuan; Reese, Timothy G.; Kolnick, Aleksandra L.; El Fakhri, Georges

    2014-01-01

    Abstract. Simultaneous positron emission tomography and magnetic resonance imaging (PET-MR) is an innovative and promising imaging modality that is generating substantial interest in the medical imaging community, while offering many challenges and opportunities. In this study, we investigated whether MR surface coils need to be accounted for in PET attenuation correction. Furthermore, we integrated motion correction, attenuation correction, and point spread function modeling into a single PET reconstruction framework. We applied our reconstruction framework to in vivo animal and patient PET-MR studies. We have demonstrated that our approach greatly improved PET image quality. PMID:26158055

  7. Comparison of different numerical treatments for x-ray phase tomography of soft tissue from differential phase projections

    NASA Astrophysics Data System (ADS)

    Pelliccia, Daniele; Vaz, Raquel; Svalbe, Imants; Morgan, Kaye S.; Marathe, Shashidhara; Xiao, Xianghui; Assoufid, Lahsen; Anderson, Rebecca A.; Topczewski, Jacek; Bryson-Richardson, Robert J.

    2015-04-01

    X-ray imaging of soft tissue is made difficult by their low absorbance. The use of x-ray phase imaging and tomography can significantly enhance the detection of these tissues and several approaches have been proposed to this end. Methods such as analyzer-based imaging or grating interferometry produce differential phase projections that can be used to reconstruct the 3D distribution of the sample refractive index. We report on the quantitative comparison of three different methods to obtain x-ray phase tomography with filtered back-projection from differential phase projections in the presence of noise. The three procedures represent different numerical approaches to solve the same mathematical problem, namely phase retrieval and filtered back-projection. It is found that obtaining individual phase projections and subsequently applying a conventional filtered back-projection algorithm produces the best results for noisy experimental data, when compared with other procedures based on the Hilbert transform. The algorithms are tested on simulated phantom data with added noise and the predictions are confirmed by experimental data acquired using a grating interferometer. The experiment is performed on unstained adult zebrafish, an important model organism for biomedical studies. The method optimization described here allows resolution of weak soft tissue features, such as muscle fibers.

  8. Cell death monitoring using quantitative optical coherence tomography methods

    NASA Astrophysics Data System (ADS)

    Farhat, Golnaz; Yang, Victor X. D.; Kolios, Michael C.; Czarnota, Gregory J.

    2011-03-01

    Cell death is characterized by a series of predictable morphological changes, which modify the light scattering properties of cells. We present a multi-parametric approach to detecting changes in subcellular morphology related to cell death using optical coherence tomography (OCT). Optical coherence tomography data were acquired from acute myeloid leukemia (AML) cells undergoing apoptosis over a period of 48 hours. Integrated backscatter (IB) and spectral slope (SS) were computed from OCT backscatter spectra and statistical parameters were extracted from a generalized gamma (GG) distribution fit to OCT signal intensity histograms. The IB increased by 2-fold over 48 hours with significant increases observed as early as 4 hours. The SS increased in steepness by 2.5-fold with significant changes at 12 hours, while the GG parameters were sensitive to apoptotic changes at 24 to 48 hours. Histology slides indicated nuclear condensation and fragmentation at 24 hours, suggesting the late scattering changes could be related to nuclear structure. A second series of measurements from AML cells treated with cisplatin, colchicine or ionizing radiation suggested that the GG parameters could potentially differentiate between modes of cell death. Distinct cellular morphology was observed in histology slides obtained from cells treated under each condition.

  9. Quantitative analysis of pulmonary ventilation scans with N-13 nitrogen gas and positron computed tomography

    SciTech Connect

    Senda, M.; Murata, K.; Itoh, H.; Yonekura, Y.; Saji, H.; Torizuka, K.

    1985-05-01

    The authors developed a quantitative method for the analysis of pulmonary ventilation studies using N-13 labeled nitrogen gas and positron computed tomography (PCT). The subject inhales N-13 nitrogen gas diluted with oxygen gas in a closed circuit. When the count rate comes up to the equilibrium in 2 or 4 minutes, the equilibrium phase scan (EQ) is performed for 3 min. Then the radioactive gas is washed out by the room air, during which the washout phase scan (WO) is performed for 5 min. Because nitrogen gas is almost insoluble in blood or tissue, the activity of the alveolus can be described with single compartment model if the dead space is ignored. The authors integrated the equation during the scanning period of EQ or WO, expressed the pixel count in each scan with V and T, and solved the equations simultaneously to obtain V and T. In clinical studies, poorly ventilated regions, which had decreased counts in EQ images, showed normal value in V images. Fibrotic regions showed normal T and decreased V. The authors method yields not only the distribution of alveolar volume which they cannot evaluate in EQ images, but also more accurate regional T values than Stewart-Hamilton method. Thus it is useful for the evaluation of regional pulmonary ventilatory function.

  10. Quantitative computed tomography for spinal mineral assessment: current status

    NASA Technical Reports Server (NTRS)

    Genant, H. K.; Cann, C. E.; Ettinger, B.; Gordan, G. S.; Kolb, F. O.; Reiser, U.; Arnaud, C. D.

    1985-01-01

    Quantitative CT (QCT) is an established method for the noninvasive assessment of bone mineral content in the vertebral spongiosum and other anatomic locations. The potential strengths of QCT relative to dual photon absorptiometry (DPA) are its capability for precise three-dimensional anatomic localization providing a direct density measurement and its capability for spatial separation of highly responsive cancellous bone from less responsive cortical bone. The extraction of this quantitative information from the CT image, however, requires sophisticated calibration and positioning techniques and careful technical monitoring.

  11. 3D quantitative phase imaging of neural networks using WDT

    NASA Astrophysics Data System (ADS)

    Kim, Taewoo; Liu, S. C.; Iyer, Raj; Gillette, Martha U.; Popescu, Gabriel

    2015-03-01

    White-light diffraction tomography (WDT) is a recently developed 3D imaging technique based on a quantitative phase imaging system called spatial light interference microscopy (SLIM). The technique has achieved a sub-micron resolution in all three directions with high sensitivity granted by the low-coherence of a white-light source. Demonstrations of the technique on single cell imaging have been presented previously; however, imaging on any larger sample, including a cluster of cells, has not been demonstrated using the technique. Neurons in an animal body form a highly complex and spatially organized 3D structure, which can be characterized by neuronal networks or circuits. Currently, the most common method of studying the 3D structure of neuron networks is by using a confocal fluorescence microscope, which requires fluorescence tagging with either transient membrane dyes or after fixation of the cells. Therefore, studies on neurons are often limited to samples that are chemically treated and/or dead. WDT presents a solution for imaging live neuron networks with a high spatial and temporal resolution, because it is a 3D imaging method that is label-free and non-invasive. Using this method, a mouse or rat hippocampal neuron culture and a mouse dorsal root ganglion (DRG) neuron culture have been imaged in order to see the extension of processes between the cells in 3D. Furthermore, the tomogram is compared with a confocal fluorescence image in order to investigate the 3D structure at synapses.

  12. Whole-cell phase contrast imaging at the nanoscale using Fresnel Coherent Diffractive Imaging Tomography

    NASA Astrophysics Data System (ADS)

    Jones, Michael W. M.; van Riessen, Grant A.; Abbey, Brian; Putkunz, Corey T.; Junker, Mark D.; Balaur, Eugeniu; Vine, David J.; McNulty, Ian; Chen, Bo; Arhatari, Benedicta D.; Frankland, Sarah; Nugent, Keith A.; Tilley, Leann; Peele, Andrew G.

    2013-07-01

    X-ray tomography can provide structural information of whole cells in close to their native state. Radiation-induced damage, however, imposes a practical limit to image resolution, and as such, a choice between damage, image contrast, and image resolution must be made. New coherent diffractive imaging techniques, such Fresnel Coherent Diffractive Imaging (FCDI), allows quantitative phase information with exceptional dose efficiency, high contrast, and nano-scale resolution. Here we present three-dimensional quantitative images of a whole eukaryotic cell by FCDI at a spatial resolution below 70 nm with sufficient phase contrast to distinguish major cellular components. From our data, we estimate that the minimum dose required for a similar resolution is close to that predicted by the Rose criterion, considerably below accepted estimates of the maximum dose a frozen-hydrated cell can tolerate. Based on the dose efficiency, contrast, and resolution achieved, we expect this technique will find immediate applications in tomographic cellular characterisation.

  13. Split-spectrum phase-gradient optical coherence tomography angiography.

    PubMed

    Liu, Gangjun; Jia, Yali; Pechauer, Alex D; Chandwani, Rahul; Huang, David

    2016-08-01

    A phase gradient angiography (PGA) method is proposed for optical coherence tomography (OCT). This method allows the use of phase information to map the microvasculature in tissue without the correction of bulk motion and laser trigger jitter induced phase artifacts. PGA can also be combined with the amplitude/intensity to improve the performance. Split-spectrum technique can further increase the signal to noise ratio by more than two times. In-vivo imaging of human retinal circulation is shown with a 70 kHz, 840 nm spectral domain OCT system and a 200 kHz, 1050 nm swept source OCT system. Four different OCT angiography methods are compared. The best performance was achieved with split-spectrum amplitude and phase-gradient angiography. PMID:27570689

  14. Split-spectrum phase-gradient optical coherence tomography angiography

    PubMed Central

    Liu, Gangjun; Jia, Yali; Pechauer, Alex D.; Chandwani, Rahul; Huang, David

    2016-01-01

    A phase gradient angiography (PGA) method is proposed for optical coherence tomography (OCT). This method allows the use of phase information to map the microvasculature in tissue without the correction of bulk motion and laser trigger jitter induced phase artifacts. PGA can also be combined with the amplitude/intensity to improve the performance. Split-spectrum technique can further increase the signal to noise ratio by more than two times. In-vivo imaging of human retinal circulation is shown with a 70 kHz, 840 nm spectral domain OCT system and a 200 kHz, 1050 nm swept source OCT system. Four different OCT angiography methods are compared. The best performance was achieved with split-spectrum amplitude and phase-gradient angiography. PMID:27570689

  15. Quantitative Computed Tomography and Image Analysis for Advanced Muscle Assessment

    PubMed Central

    Edmunds, Kyle Joseph; Gíslason, Magnus K.; Arnadottir, Iris D.; Marcante, Andrea; Piccione, Francesco; Gargiulo, Paolo

    2016-01-01

    Medical imaging is of particular interest in the field of translational myology, as extant literature describes the utilization of a wide variety of techniques to non-invasively recapitulate and quantity various internal and external tissue morphologies. In the clinical context, medical imaging remains a vital tool for diagnostics and investigative assessment. This review outlines the results from several investigations on the use of computed tomography (CT) and image analysis techniques to assess muscle conditions and degenerative process due to aging or pathological conditions. Herein, we detail the acquisition of spiral CT images and the use of advanced image analysis tools to characterize muscles in 2D and 3D. Results from these studies recapitulate changes in tissue composition within muscles, as visualized by the association of tissue types to specified Hounsfield Unit (HU) values for fat, loose connective tissue or atrophic muscle, and normal muscle, including fascia and tendon. We show how results from these analyses can be presented as both average HU values and compositions with respect to total muscle volumes, demonstrating the reliability of these tools to monitor, assess and characterize muscle degeneration. PMID:27478562

  16. Quantitative phase-sensitive imaging in a transmission electron microscope

    PubMed

    Bajt; Barty; Nugent; McCartney; Wall; Paganin

    2000-05-01

    This paper presents a new technique for forming quantitative phase and amplitude electron images applicable to a conventional transmission electron microscope. With magnetised cobalt microstructures used as a test object, we use electron holography to obtain an independent measurement of the phase shift. After a suitable calibration of the microscope, we obtain quantitative agreement of the phase shift imposed on the 200 keV electrons passing through the sample.

  17. HAADF-STEM atom counting in atom probe tomography specimens: Towards quantitative correlative microscopy.

    PubMed

    Lefebvre, W; Hernandez-Maldonado, D; Moyon, F; Cuvilly, F; Vaudolon, C; Shinde, D; Vurpillot, F

    2015-12-01

    The geometry of atom probe tomography tips strongly differs from standard scanning transmission electron microscopy foils. Whereas the later are rather flat and thin (<20 nm), tips display a curved surface and a significantly larger thickness. As far as a correlative approach aims at analysing the same specimen by both techniques, it is mandatory to explore the limits and advantages imposed by the particular geometry of atom probe tomography specimens. Based on simulations (electron probe propagation and image simulations), the possibility to apply quantitative high angle annular dark field scanning transmission electron microscopy to of atom probe tomography specimens has been tested. The influence of electron probe convergence and the benefice of deconvolution of electron probe point spread function electron have been established. Atom counting in atom probe tomography specimens is for the first time reported in this present work. It is demonstrated that, based on single projections of high angle annular dark field imaging, significant quantitative information can be used as additional input for refining the data obtained by correlative analysis of the specimen in APT, therefore opening new perspectives in the field of atomic scale tomography.

  18. High-resolution x-ray phase tomography

    NASA Astrophysics Data System (ADS)

    Peele, Andrew G.; Thomas, C. David L.; Clement, John G.; Arhatari, Benedicta D.; Hannah, Kevin M.; Doshi, Chandni; Putkunz, Corey T.; Clark, Jesse N.

    2010-09-01

    X-ray tomography is a workhorse tool of non-destructive imaging. It is used to probe three-dimensional structures across a wide range of length scales for objects that offer good absorption contrast to x-rays. In recent years extremely high resolution imaging (on the order of tens of nanometres) has become possible due to technological advances in x-ray optics. At the same time the requirement for strong absorption contrast has been relaxed thanks to the advent of new experimental and algorithmic techniques in phase imaging. Advances in both resolution and phase imaging can be combined to image biological samples at the sub-cellular level. I will report on recent advances in our work including improvements to the current approaches in extracting phase information at high resolution from measurements of the diffracted intensity from a sample. I will also discuss our current experimental status.

  19. Experimental comparison of grating- and propagation-based hard X-ray phase tomography of soft tissue

    NASA Astrophysics Data System (ADS)

    Lang, S.; Zanette, I.; Dominietto, M.; Langer, M.; Rack, A.; Schulz, G.; Le Duc, G.; David, C.; Mohr, J.; Pfeiffer, F.; Müller, B.; Weitkamp, T.

    2014-10-01

    When imaging soft tissues with hard X-rays, phase contrast is often preferred over conventional attenuation contrast due its superior sensitivity. However, it is unclear which of the numerous phase tomography methods yields the optimized results at given experimental conditions. Therefore, we quantitatively compared the three phase tomography methods implemented at the beamline ID19 of the European Synchrotron Radiation Facility: X-ray grating interferometry (XGI), and propagation-based phase tomography, i.e., single-distance phase retrieval (SDPR) and holotomography (HT), using cancerous tissue from a mouse model and an entire heart of a rat. We show that for both specimens, the spatial resolution derived from the characteristic morphological features is about a factor of two better for HT and SDPR compared to XGI, whereas the XGI data generally exhibit much better contrast-to-noise ratios for the anatomical features. Moreover, XGI excels in fidelity of the density measurements, and is also more robust against low-frequency artifacts than HT, but it might suffer from phase-wrapping artifacts. Thus, we can regard the three phase tomography methods discussed as complementary. The application will decide which spatial and density resolutions are desired, for the imaging task and dose requirements, and, in addition, the applicant must choose between the complexity of the experimental setup and the one of data processing.

  20. Experimental comparison of grating- and propagation-based hard X-ray phase tomography of soft tissue

    SciTech Connect

    Lang, S.; Schulz, G.; Müller, B.; Zanette, I.; Dominietto, M.; Langer, M.; Rack, A.; Le Duc, G.; David, C.; Mohr, J.; Pfeiffer, F.; Weitkamp, T.

    2014-10-21

    When imaging soft tissues with hard X-rays, phase contrast is often preferred over conventional attenuation contrast due its superior sensitivity. However, it is unclear which of the numerous phase tomography methods yields the optimized results at given experimental conditions. Therefore, we quantitatively compared the three phase tomography methods implemented at the beamline ID19 of the European Synchrotron Radiation Facility: X-ray grating interferometry (XGI), and propagation-based phase tomography, i.e., single-distance phase retrieval (SDPR) and holotomography (HT), using cancerous tissue from a mouse model and an entire heart of a rat. We show that for both specimens, the spatial resolution derived from the characteristic morphological features is about a factor of two better for HT and SDPR compared to XGI, whereas the XGI data generally exhibit much better contrast-to-noise ratios for the anatomical features. Moreover, XGI excels in fidelity of the density measurements, and is also more robust against low-frequency artifacts than HT, but it might suffer from phase-wrapping artifacts. Thus, we can regard the three phase tomography methods discussed as complementary. The application will decide which spatial and density resolutions are desired, for the imaging task and dose requirements, and, in addition, the applicant must choose between the complexity of the experimental setup and the one of data processing.

  1. Treatment modification of yttrium-90 radioembolization based on quantitative positron emission tomography/CT imaging.

    PubMed

    Chang, Ted T; Bourgeois, Austin C; Balius, Anastasia M; Pasciak, Alexander S

    2013-03-01

    Treatment activity for yttrium-90 ((90)Y) radioembolization when calculated by using the manufacturer-recommended technique is only partially patient-specific and may result in a subtumoricidal dose in some patients. The authors describe the use of quantitative (90)Y positron emission tomography/computed tomography as a tool to provide patient-specific optimization of treatment activity and evaluate this new method in a patient who previously received traditional (90)Y radioembolization. The modified treatment resulted in a 40-Gy increase in absorbed dose to tumor and complete resolution of disease in the treated area within 3 months.

  2. Phase-contrast tomography with low-intensity beams

    SciTech Connect

    Rehacek, J.; Hradil, Z.; Zawisky, M.; Dubus, F.; Bonse, U.

    2005-02-01

    In newly developed neutron phase tomography, wave properties of neutrons are exploited for the nondestructive testing of the internal structure of matter. We show how limitations due to small available intensities of present neutron sources can be overcome by using an advanced maximum-likelihood reconstruction algorithm. Unlike the standard filtered back-projection, the developed procedure gives reasonable results also when used on very noisy data or data consisting of only a few measured projections. This is demonstrated by means of simulations and also experimentally. The proposed method leads to considerably shorter measuring times and/or increased precision.

  3. The potential optical coherence tomography in tooth bleaching quantitative assessment

    NASA Astrophysics Data System (ADS)

    Ni, Y. R.; Guo, Z. Y.; Shu, S. Y.; Zeng, C. C.; Zhong, H. Q.; Chen, B. L.; Liu, Z. M.; Bao, Y.

    2011-12-01

    In this paper, we report the outcomes from a pilot study on using OCT functional imaging method to evaluate and quantify color alteration in the human teeth in vitro. The image formations of the dental tissues without and with treatment 35% hydrogen peroxide were obtained by an OCT system at a 1310 nm central wavelength. One parameter for the quantification of optical properties from OCT measurements is introduced in our study: attenuate coefficient (μ). And the attenuate coefficient have significant decrease ( p < 0.001) in dentine as well as a significant increase ( p < 0.001) in enamel was observed during tooth bleaching process. From the experimental results, it is found that attenuate coefficient could be useful to assess color alteration of the human tooth samples. OCT has a potential to become an effective tool for the assessment tooth bleaching. And our experiment offer a now method to evaluate color change in visible region by quantitative analysis of the infrared region information from OCT.

  4. Sensitivity of quantitative photoacoustic tomography inversion schemes to experimental uncertainty

    NASA Astrophysics Data System (ADS)

    Fonseca, Martina; Saratoon, Teedah; Zeqiri, Bajram; Beard, Paul; Cox, Ben

    2016-03-01

    The ability to accurately quantify chromophore concentration from photoacoustic images would have a major impact on pre-clinical and clinical imaging. Recent years have seen significant advances in the theoretical understanding of quantitative photoacoustic imaging and in the development of model-based inversion strategies that overcome issues such as non-uniqueness and non-linearity. Nevertheless, their full in vivo implementation has not successfully been achieved, partially because experimental uncertainties complicate the transition. In this study, a sensitivity analysis is performed to assess the impact on accuracy of having uncertainty in critical experimental parameters such as scattering, beam diameter, beam position and calibration factor. This study was performed using two virtual phantoms, at one illumination and four optical wavelengths. The model-based inversion was applied in 3 variants - one just inverting for chromophores and two others further inverting for either a scaling factor or the scatterer concentration. The performance of these model-based inversions is also compared to linear unmixing strategies - with and without fluence correction. The results show that experimental uncertainties in a priori fixed parameters - especially calibration factor and scatterer concentration - significantly affect accuracy of model-based inversions and therefore measures to ameliorate this uncertainty should be considered. Including a scaling parameter in the inversion appears to improve quantification estimates. Furthermore, even with realistic levels of experimental uncertainty in model-based input parameters, they outperform linear unmixing approaches. If parameter uncertainty is large and has significant impact on accuracy, the parameter can be included as an unknown in model-based schemes.

  5. Quantitation of the human basal ganglia with Positron Emission Tomography

    SciTech Connect

    Bendriem, B.; Dewey, S.L.; Schlyer, D.J.; Wolf, A.P.; Volkow, N.D.

    1990-01-01

    The accurate measurement of the concentration of a radioisotope in small structures with PET requires a correction for quantitation loss due to the partial volume effect and the effect of scattered radiation. To evaluate errors associated with measures in the human basal ganglia (BG) we have built a unilateral model of the BG that we have inserted in a 20 cm cylinder. The recovery coefficient (RC = measured activity/true activity) for our BG phantom has been measured on a CTI tomograph (model 931-08/12) with different background concentrations (contrast) and at different axial locations in the gantry. The BG was visualized on 4 or 5 slices depending on its position in the gantry and on the contrast used. The RC was 0.75 with no background (contrast equal to 1.0). Increasing the relative radioactivity concentration in the background increased the RC from 0.75 to 2.00 when the contrast was {minus}0.7 (BG < Background). The RC was also affected by the size and the shape of the region of interest (ROI) used (RC from 0.75 to 0.67 with ROI size from 0.12 to 1.41 cm{sup 2}). These results show that accurate RC correction depends not only on the volume of the structure but also on its contrast with its surroundings as well as on the selection of the ROI. They also demonstrate that the higher the contrast the more sensitive to axial positioning PET measurements in the BG are. These data provide us with some information about the variability of PET measurements in small structure like the BG and we have proposed some strategies to improve the reproducibility. 18 refs., 3 figs., 5 tabs.

  6. Quantitative Assessment of Radionuclide Uptake and Positron Emission Tomography-computed Tomography Image Contrast

    PubMed Central

    Francis, Hasford; Amuasi, John Humphrey; Kwame, Kyere Augustine; Vangu, Mboyo Di Tamba

    2016-01-01

    Radionuclide uptake and contrast for positron emission tomography-computed tomography (PET-CT) images have been assessed in this study using NEMA image quality phantom filled with background activity concentration of 5.3 kBq/mL fluorodeoxyglucose (F-18 FDG). Spheres in the phantom were filled in turns with water to mimic cold lesions and FDG of higher activity concentrations to mimic tumor sites. Transaxial image slices were acquired on the PET-CT system and used for the evaluation of mean standard uptake value (SUVmean) and contrasts for varying sphere sizes at different activity concentrations of 10.6 kBq/mL, 21.2 kBq/mL, and 42.4 kBq/mL. For spheres of same sizes, SUVmean increased with increase in activity concentration. SUVmean was increased by 80.6%, 83.5%, 63.2%, 87.4%, and 63.2% when activity concentrations of spheres with a diameter of 1.3 cm, 1.7 cm, 2.2 cm, 2.8 cm, and 3.7 cm, respectively, were increased from 10.6 kBq/mL to 42.4 kBq/mL. Average percentage contrast between cold spheres (cold lesions) and background activity concentration was estimated to be 89.96% for the spheres. Average contrast for the spheres containing 10.6 kBq/mL, 21.2 kBq/mL, and 42.4 kBq/mL were found to be 110.92%, 134.48%, and 150.52%, respectively. The average background contrast variability was estimated to be 2.97% at 95% confidence interval (P < 0.05). PMID:27650938

  7. Quantitative Assessment of Radionuclide Uptake and Positron Emission Tomography-computed Tomography Image Contrast

    PubMed Central

    Francis, Hasford; Amuasi, John Humphrey; Kwame, Kyere Augustine; Vangu, Mboyo Di Tamba

    2016-01-01

    Radionuclide uptake and contrast for positron emission tomography-computed tomography (PET-CT) images have been assessed in this study using NEMA image quality phantom filled with background activity concentration of 5.3 kBq/mL fluorodeoxyglucose (F-18 FDG). Spheres in the phantom were filled in turns with water to mimic cold lesions and FDG of higher activity concentrations to mimic tumor sites. Transaxial image slices were acquired on the PET-CT system and used for the evaluation of mean standard uptake value (SUVmean) and contrasts for varying sphere sizes at different activity concentrations of 10.6 kBq/mL, 21.2 kBq/mL, and 42.4 kBq/mL. For spheres of same sizes, SUVmean increased with increase in activity concentration. SUVmean was increased by 80.6%, 83.5%, 63.2%, 87.4%, and 63.2% when activity concentrations of spheres with a diameter of 1.3 cm, 1.7 cm, 2.2 cm, 2.8 cm, and 3.7 cm, respectively, were increased from 10.6 kBq/mL to 42.4 kBq/mL. Average percentage contrast between cold spheres (cold lesions) and background activity concentration was estimated to be 89.96% for the spheres. Average contrast for the spheres containing 10.6 kBq/mL, 21.2 kBq/mL, and 42.4 kBq/mL were found to be 110.92%, 134.48%, and 150.52%, respectively. The average background contrast variability was estimated to be 2.97% at 95% confidence interval (P < 0.05).

  8. Quantitative Assessment of Radionuclide Uptake and Positron Emission Tomography-computed Tomography Image Contrast.

    PubMed

    Francis, Hasford; Amuasi, John Humphrey; Kwame, Kyere Augustine; Vangu, Mboyo Di Tamba

    2016-09-01

    Radionuclide uptake and contrast for positron emission tomography-computed tomography (PET-CT) images have been assessed in this study using NEMA image quality phantom filled with background activity concentration of 5.3 kBq/mL fluorodeoxyglucose (F-18 FDG). Spheres in the phantom were filled in turns with water to mimic cold lesions and FDG of higher activity concentrations to mimic tumor sites. Transaxial image slices were acquired on the PET-CT system and used for the evaluation of mean standard uptake value (SUVmean) and contrasts for varying sphere sizes at different activity concentrations of 10.6 kBq/mL, 21.2 kBq/mL, and 42.4 kBq/mL. For spheres of same sizes, SUVmean increased with increase in activity concentration. SUVmean was increased by 80.6%, 83.5%, 63.2%, 87.4%, and 63.2% when activity concentrations of spheres with a diameter of 1.3 cm, 1.7 cm, 2.2 cm, 2.8 cm, and 3.7 cm, respectively, were increased from 10.6 kBq/mL to 42.4 kBq/mL. Average percentage contrast between cold spheres (cold lesions) and background activity concentration was estimated to be 89.96% for the spheres. Average contrast for the spheres containing 10.6 kBq/mL, 21.2 kBq/mL, and 42.4 kBq/mL were found to be 110.92%, 134.48%, and 150.52%, respectively. The average background contrast variability was estimated to be 2.97% at 95% confidence interval (P < 0.05). PMID:27650938

  9. Phase resolved digital signal processing in optical coherence tomography

    NASA Astrophysics Data System (ADS)

    de Boer, Johannes F.; Tripathi, Renu; Park, Boris H.; Nassif, Nader

    2002-06-01

    We present phase resolved digital signal processing techniques for Optical Coherence Tomography to correct for the non Gaussian shape of source spectra and for Group Delay Dispersion (GDD). A broadband source centered at 820 nm was synthesized by combining the spectra of two superluminescent diodes to improve axial image resolution in an optical coherence tomography (OCT) system. Spectral shaping was used to reduce the side lobes (ringing) in the axial point spread function due to the non-Gaussian shape of the spectra. Images of onion cells taken with each individual source and the combined sources, respectively, show the improved resolution and quality enhancement in a turbid biological sample. An OCT system operating at 1310 nm was used to demonstrate that the broadening effect of group delay dispersion (GDD) on the coherence function could be eliminated completely by introducing a quadratic phase shift in the Fourier domain of the interferometric signal. The technique is demonstrated by images of human skin grafts with group delay dispersion mismatch between sample and reference arm before and after digital processing.

  10. Quantitative photoacoustic tomography: Recovery of optical absorption coefficient maps of heterogeneous media

    NASA Astrophysics Data System (ADS)

    Yuan, Zhen; Jiang, Huabei

    2006-06-01

    We report on experimental demonstration of photoacoustic tomography for reconstructing the optical absorption coefficient images of heterogeneous media. Photoacoustic images are obtained from a series of tissuelike phantom experiments using a finite element-based reconstruction algorithm coupled with a scanning photoacoustic imaging system. The experimental results show that optical absorption images can be quantitatively reconstructed when the photon diffusion model is coupled with the Helmholtz photoacoustic wave equation.

  11. Quantitative assessment of the retinal microvasculature using optical coherence tomography angiography

    NASA Astrophysics Data System (ADS)

    Chu, Zhongdi; Lin, Jason; Gao, Chen; Xin, Chen; Zhang, Qinqin; Chen, Chieh-Li; Roisman, Luis; Gregori, Giovanni; Rosenfeld, Philip J.; Wang, Ruikang K.

    2016-06-01

    Optical coherence tomography angiography (OCTA) is clinically useful for the qualitative assessment of the macular microvasculature. However, there is a need for comprehensive quantitative tools to help objectively analyze the OCT angiograms. Few studies have reported the use of a single quantitative index to describe vessel density in OCT angiograms. In this study, we introduce a five-index quantitative analysis of OCT angiograms in an attempt to detect and assess vascular abnormalities from multiple perspectives. The indices include vessel area density, vessel skeleton density, vessel diameter index, vessel perimeter index, and vessel complexity index. We show the usefulness of the proposed indices with five illustrative cases. Repeatability is tested on both a healthy case and a stable diseased case, giving interclass coefficients smaller than 0.031. The results demonstrate that our proposed quantitative analysis may be useful as a complement to conventional OCTA for the diagnosis of disease and monitoring of treatment.

  12. Quantitative phase-shifting DIC using programmable spatial light modulators

    NASA Astrophysics Data System (ADS)

    Nguyen, Tan H.; Edwards, Chris; Goddard, Lynford L.; Popescu, Gabriel

    2015-03-01

    A quantitative phase-shifting Differential Interference Contrast (DIC) system is built using a programmable spatial light modulator (SLM). Our system offers halo-free phase gradient images with low illumination coherence and very good axial sectioning. Results are presented for standard polystyrene micro-beads and live cells.

  13. Quantitative phase imaging using grating-based quadrature phase interferometer

    NASA Astrophysics Data System (ADS)

    Wu, Jigang; Yaqoob, Zahid; Heng, Xin; Cui, Xiquan; Yang, Changhuei

    2007-02-01

    In this paper, we report the use of holographic gratings, which act as the free-space equivalent of the 3x3 fiber-optic coupler, to perform full field phase imaging. By recording two harmonically-related gratings in the same holographic plate, we are able to obtain nontrivial phase shift between different output ports of the gratings-based Mach-Zehnder interferometer. The phase difference can be adjusted by changing the relative phase of the recording beams when recording the hologram. We have built a Mach-Zehnder interferometer using harmonically-related holographic gratings with 600 and 1200 lines/mm spacing. Two CCD cameras at the output ports of the gratings-based Mach-Zehnder interferometer are used to record the full-field quadrature interferograms, which are subsequently processed to reconstruct the phase image. The imaging system has ~12X magnification with ~420μmx315μm field-of-view. To demonstrate the capability of our system, we have successfully performed phase imaging of a pure phase object and a paramecium caudatum.

  14. X-ray computed tomography of wood-adhesive bondlines: Attenuation and phase-contrast effects

    DOE PAGESBeta

    Paris, Jesse L.; Kamke, Frederick A.; Xiao, Xianghui

    2015-07-29

    Microscale X-ray computed tomography (XCT) is discussed as a technique for identifying 3D adhesive distribution in wood-adhesive bondlines. Visualization and material segmentation of the adhesives from the surrounding cellular structures require sufficient gray-scale contrast in the reconstructed XCT data. Commercial wood-adhesive polymers have similar chemical characteristics and density to wood cell wall polymers and therefore do not provide good XCT attenuation contrast in their native form. Here, three different adhesive types, namely phenol formaldehyde, polymeric diphenylmethane diisocyanate, and a hybrid polyvinyl acetate, are tagged with iodine such that they yield sufficient X-ray attenuation contrast. However, phase-contrast effects at material edgesmore » complicate image quality and segmentation in XCT data reconstructed with conventional filtered backprojection absorption contrast algorithms. A quantitative phase retrieval algorithm, which isolates and removes the phase-contrast effect, was demonstrated. The paper discusses and illustrates the balance between material X-ray attenuation and phase-contrast effects in all quantitative XCT analyses of wood-adhesive bondlines.« less

  15. X-ray computed tomography of wood-adhesive bondlines: Attenuation and phase-contrast effects

    SciTech Connect

    Paris, Jesse L.; Kamke, Frederick A.; Xiao, Xianghui

    2015-07-29

    Microscale X-ray computed tomography (XCT) is discussed as a technique for identifying 3D adhesive distribution in wood-adhesive bondlines. Visualization and material segmentation of the adhesives from the surrounding cellular structures require sufficient gray-scale contrast in the reconstructed XCT data. Commercial wood-adhesive polymers have similar chemical characteristics and density to wood cell wall polymers and therefore do not provide good XCT attenuation contrast in their native form. Here, three different adhesive types, namely phenol formaldehyde, polymeric diphenylmethane diisocyanate, and a hybrid polyvinyl acetate, are tagged with iodine such that they yield sufficient X-ray attenuation contrast. However, phase-contrast effects at material edges complicate image quality and segmentation in XCT data reconstructed with conventional filtered backprojection absorption contrast algorithms. A quantitative phase retrieval algorithm, which isolates and removes the phase-contrast effect, was demonstrated. The paper discusses and illustrates the balance between material X-ray attenuation and phase-contrast effects in all quantitative XCT analyses of wood-adhesive bondlines.

  16. Respiratory gating in positron emission tomography: A quantitative comparison of different gating schemes

    SciTech Connect

    Dawood, Mohammad; Buether, Florian; Lang, Norbert; Schober, Otmar; Schaefers, Klaus P

    2007-07-15

    Respiratory gating is used for reducing the effects of breathing motion in a wide range of applications from radiotherapy treatment to diagnostical imaging. Different methods are feasible for respiratory gating. In this study seven gating methods were developed and tested on positron emission tomography (PET) listmode data. The results of seven patient studies were compared quantitatively with respect to motion and noise. (1) Equal and (2) variable time-based gating methods use only the time information of the breathing cycle to define respiratory gates. (3) Equal and (4) variable amplitude-based gating approaches utilize the amplitude of the respiratory signal. (5) Cycle-based amplitude gating is a combination of time and amplitude-based techniques. A baseline correction was applied to methods (3) and (4) resulting in two new approaches: Baseline corrected (6) equal and (7) variable amplitude-based gating. Listmode PET data from seven patients were acquired together with a respiratory signal. Images were reconstructed applying the seven gating methods. Two parameters were used to quantify the results: Motion was measured as the displacement of the heart due to respiration and noise was defined as the standard deviation of pixel intensities in a background region. The amplitude-based approaches (3) and (4) were superior to the time-based methods (1) and (2). The improvement in capturing the motion was more than 30% (up to 130%) in all subjects. The variable time (2) and amplitude (4) methods had a more uniform noise distribution among all respiratory gates compared to equal time (1) and amplitude (3) methods. Baseline correction did not improve the results. Out of seven different respiratory gating approaches, the variable amplitude method (4) captures the respiratory motion best while keeping a constant noise level among all respiratory phases.

  17. Frequency domain optoacoustic tomography using amplitude and phase

    PubMed Central

    Mohajerani, Pouyan; Kellnberger, Stephan; Ntziachristos, Vasilis

    2014-01-01

    We introduce optoacoustic tomographic imaging using intensity modulated light sources and collecting amplitude and phase information in the frequency domain. Imaging is performed at multiple modulation frequencies. The forward modeling uses the Green's function solution to the pressure wave equation in frequency domain and the resulting inverse problem is solved using regularized least squares minimization. We study the effect of the number of frequencies and of the bandwidth employed on the image quality achieved. The possibility of employing an all-frequency domain optoacoustic imaging for experimental measurements is studied as a function of noise. We conclude that frequency domain optoacoustic tomography may evolve to a practical experimental method using light intensity modulated sources, with advantages over time-domain optoacoustics. PMID:25431755

  18. Helical X-ray phase-contrast computed tomography without phase stepping

    PubMed Central

    Marschner, M.; Willner, M.; Potdevin, G.; Fehringer, A.; Noël, P. B.; Pfeiffer, F.; Herzen, J.

    2016-01-01

    X-ray phase-contrast computed tomography (PCCT) using grating interferometry provides enhanced soft-tissue contrast. The possibility to use standard polychromatic laboratory sources enables an implementation into a clinical setting. Thus, PCCT has gained significant attention in recent years. However, phase-contrast CT scans still require significantly increased measurement times in comparison to conventional attenuation-based CT imaging. This is mainly due to a time-consuming stepping of a grating, which is necessary for an accurate retrieval of the phase information. In this paper, we demonstrate a novel scan technique, which directly allows the determination of the phase signal without a phase-stepping procedure. The presented work is based on moiré fringe scanning, which allows fast data acquisition in radiographic applications such as mammography or in-line product analysis. Here, we demonstrate its extension to tomography enabling a continuous helical sample rotation as routinely performed in clinical CT systems. Compared to standard phase-stepping techniques, the proposed helical fringe-scanning procedure enables faster measurements, an extended field of view and relaxes the stability requirements of the system, since the gratings remain stationary. Finally, our approach exceeds previously introduced methods by not relying on spatial interpolation to acquire the phase-contrast signal. PMID:27052368

  19. Helical X-ray phase-contrast computed tomography without phase stepping

    NASA Astrophysics Data System (ADS)

    Marschner, M.; Willner, M.; Potdevin, G.; Fehringer, A.; Noël, P. B.; Pfeiffer, F.; Herzen, J.

    2016-04-01

    X-ray phase-contrast computed tomography (PCCT) using grating interferometry provides enhanced soft-tissue contrast. The possibility to use standard polychromatic laboratory sources enables an implementation into a clinical setting. Thus, PCCT has gained significant attention in recent years. However, phase-contrast CT scans still require significantly increased measurement times in comparison to conventional attenuation-based CT imaging. This is mainly due to a time-consuming stepping of a grating, which is necessary for an accurate retrieval of the phase information. In this paper, we demonstrate a novel scan technique, which directly allows the determination of the phase signal without a phase-stepping procedure. The presented work is based on moiré fringe scanning, which allows fast data acquisition in radiographic applications such as mammography or in-line product analysis. Here, we demonstrate its extension to tomography enabling a continuous helical sample rotation as routinely performed in clinical CT systems. Compared to standard phase-stepping techniques, the proposed helical fringe-scanning procedure enables faster measurements, an extended field of view and relaxes the stability requirements of the system, since the gratings remain stationary. Finally, our approach exceeds previously introduced methods by not relying on spatial interpolation to acquire the phase-contrast signal.

  20. Image segmentation of nanoscale Zernike phase contrast X-ray computed tomography images

    SciTech Connect

    Kumar, Arjun S.; Mandal, Pratiti; Zhang, Yongjie; Litster, Shawn

    2015-05-14

    Zernike phase contrast is a useful technique for nanoscale X-ray computed tomography (CT) imaging of materials with a low X-ray absorption coefficient. It enhances the image contrast by phase shifting X-ray waves to create changes in amplitude. However, it creates artifacts that hinder the use of traditional image segmentation techniques. We propose an image restoration method that models the X-ray phase contrast optics and the three-dimensional image reconstruction method. We generate artifact-free images through an optimization problem that inverts this model. Though similar approaches have been used for Zernike phase contrast in visible light microscopy, this optimization employs an effective edge detection method tailored to handle Zernike phase contrast artifacts. We characterize this optics-based restoration method by removing the artifacts in and thresholding multiple Zernike phase contrast X-ray CT images to produce segmented results that are consistent with the physical specimens. We quantitatively evaluate and compare our method to other segmentation techniques to demonstrate its high accuracy.

  1. Low-dose phase contrast tomography with conventional x-ray sources

    SciTech Connect

    Hagen, C. K. Endrizzi, M.; Diemoz, P. C.; Olivo, A.; Munro, P. R. T.

    2014-07-15

    Purpose: The edge illumination (EI) x-ray phase contrast imaging (XPCi) method has been recently further developed to perform tomographic and, thus, volumetric imaging. In this paper, the first tomographic EI XPCi images acquired with a conventional x-ray source at dose levels below that used for preclinical small animal imaging are presented. Methods: Two test objects, a biological sample and a custom-built phantom, were imaged with a laboratory-based EI XPCi setup in tomography mode. Tomographic maps that show the phase shift and attenuating properties of the object were reconstructed, and analyzed in terms of signal-to-noise ratio and quantitative accuracy. Dose measurements using thermoluminescence devices were performed. Results: The obtained images demonstrate that phase based imaging methods can provide superior results compared to attenuation based modalities for weakly attenuating samples also in 3D. Moreover, and, most importantly, they demonstrate the feasibility of low-dose imaging. In addition, the experimental results can be considered quantitative within the constraints imposed by polychromaticity. Conclusions: The results, together with the method's dose efficiency and compatibility with conventional x-ray sources, indicate that tomographic EI XPCi can become an important tool for the routine imaging of biomedical samples.

  2. Quantitative computed tomography of the liver in juvenile green sea turtles (Chelonia mydas).

    PubMed

    Bonelli, Marília de Albuquerque; de Oliveira, Daniel Capucho; Costa, Lorena Adão Vescovi Séllos; Forattini, Jannine Garcia; Júnior, João Luiz Rossi; Leite, Flaviana Lima Guião; Costa, Fabiano Séllos

    2013-06-01

    Quantitative computed tomography (QCT) is a highly sensitive, applicable technique for determining the x-ray attenuation of organs. This technique reveals great precision in the detection of alterations in the x-ray attenuation of hepatic parenchyma, although the lack of studies establishing normal values limits its application in wild animals. The objective of this study was to establish mean hepatic attenuation values in four healthy juvenile sea turtles (Chelonia mydas) using QCT. Helical computed tomography scans were performed and regions of interest selected in the liver after multi-planar reconstruction images were obtained. The mean attenuation value for the hepatic parenchyma in these four turtles was 60.09 +/- 5.3 standard deviation Hounsfield units. Determining normal x-ray attenuation values of the liver increases knowledge of the computed tomographic anatomy of this species and may be useful in the investigation of hepatic diseases.

  3. Quantitative breast tissue characterization using grating-based x-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Willner, M.; Herzen, J.; Grandl, S.; Auweter, S.; Mayr, D.; Hipp, A.; Chabior, M.; Sarapata, A.; Achterhold, K.; Zanette, I.; Weitkamp, T.; Sztrókay, A.; Hellerhoff, K.; Reiser, M.; Pfeiffer, F.

    2014-04-01

    X-ray phase-contrast imaging has received growing interest in recent years due to its high capability in visualizing soft tissue. Breast imaging became the focus of particular attention as it is considered the most promising candidate for a first clinical application of this contrast modality. In this study, we investigate quantitative breast tissue characterization using grating-based phase-contrast computed tomography (CT) at conventional polychromatic x-ray sources. Different breast specimens have been scanned at a laboratory phase-contrast imaging setup and were correlated to histopathology. Ascertained tumor types include phylloides tumor, fibroadenoma and infiltrating lobular carcinoma. Identified tissue types comprising adipose, fibroglandular and tumor tissue have been analyzed in terms of phase-contrast Hounsfield units and are compared to high-quality, high-resolution data obtained with monochromatic synchrotron radiation, as well as calculated values based on tabulated tissue properties. The results give a good impression of the method’s prospects and limitations for potential tumor detection and the associated demands on such a phase-contrast breast CT system. Furthermore, the evaluated quantitative tissue values serve as a reference for simulations and the design of dedicated phantoms for phase-contrast mammography.

  4. X-ray phase contrast tomography by tracking near field speckle.

    PubMed

    Wang, Hongchang; Berujon, Sebastien; Herzen, Julia; Atwood, Robert; Laundy, David; Hipp, Alexander; Sawhney, Kawal

    2015-01-01

    X-ray imaging techniques that capture variations in the x-ray phase can yield higher contrast images with lower x-ray dose than is possible with conventional absorption radiography. However, the extraction of phase information is often more difficult than the extraction of absorption information and requires a more sophisticated experimental arrangement. We here report a method for three-dimensional (3D) X-ray phase contrast computed tomography (CT) which gives quantitative volumetric information on the real part of the refractive index. The method is based on the recently developed X-ray speckle tracking technique in which the displacement of near field speckle is tracked using a digital image correlation algorithm. In addition to differential phase contrast projection images, the method allows the dark-field images to be simultaneously extracted. After reconstruction, compared to conventional absorption CT images, the 3D phase CT images show greatly enhanced contrast. This new imaging method has advantages compared to other X-ray imaging methods in simplicity of experimental arrangement, speed of measurement and relative insensitivity to beam movements. These features make the technique an attractive candidate for material imaging such as in-vivo imaging of biological systems containing soft tissue.

  5. X-ray phase contrast tomography by tracking near field speckle

    NASA Astrophysics Data System (ADS)

    Wang, Hongchang; Berujon, Sebastien; Herzen, Julia; Atwood, Robert; Laundy, David; Hipp, Alexander; Sawhney, Kawal

    2015-03-01

    X-ray imaging techniques that capture variations in the x-ray phase can yield higher contrast images with lower x-ray dose than is possible with conventional absorption radiography. However, the extraction of phase information is often more difficult than the extraction of absorption information and requires a more sophisticated experimental arrangement. We here report a method for three-dimensional (3D) X-ray phase contrast computed tomography (CT) which gives quantitative volumetric information on the real part of the refractive index. The method is based on the recently developed X-ray speckle tracking technique in which the displacement of near field speckle is tracked using a digital image correlation algorithm. In addition to differential phase contrast projection images, the method allows the dark-field images to be simultaneously extracted. After reconstruction, compared to conventional absorption CT images, the 3D phase CT images show greatly enhanced contrast. This new imaging method has advantages compared to other X-ray imaging methods in simplicity of experimental arrangement, speed of measurement and relative insensitivity to beam movements. These features make the technique an attractive candidate for material imaging such as in-vivo imaging of biological systems containing soft tissue.

  6. Full range complex spectral domain optical coherence tomography without additional phase shifters.

    PubMed

    Baumann, Bernhard; Pircher, Michael; Götzinger, Erich; Hitzenberger, Christoph K

    2007-10-01

    We demonstrate a new full range complex spectral domain optical coherence tomography (FRC SD-OCT) method. Other than FRC SD-OCT systems reported in literature, which employed devices such as electro-/acousto optic modulators or piezo-driven mirrors providing the phase modulations necessary for retrieval of the complex-valued signal, the system presented works without any additional phase shifting device. The required phase shift is introduced by the galvanometer scanner used for transversally scanning the sample beam. By means of a slight displacement of the probe beam with respect to the scanning mirror's pivot axis, the sample arm length and thus the phase is continuously modulated as the beam is scanned in lateral direction. From such modulated spectral data, the complex-valued data yielding a twofold increase of accessible depth range can be calculated using an algorithm based on the Hilbert transform. To demonstrate the performance of our method quantitative measurements of the suppression of mirror images as a function of induced phase shift were performed. In order to validate the FRC SD-OCT technique for high-speed imaging of biological tissue, we present full-range images of the human anterior chamber in vivo. PMID:19550607

  7. Direct quantitative tomographic reconstruction for weakly absorbing homogeneous phase objects

    NASA Astrophysics Data System (ADS)

    Arhatari, B. D.; De Carlo, F.; Peele, A. G.

    2007-05-01

    We examine a direct filtered back projection approach that is suitable for the reconstruction of weakly absorbing homogeneous phase objects. Like recent similar approaches this method needs only one intensity image in each projection without the requirement for an intermediate step of phase retrieval. We tested the method using simulation and experimental results. Simulation results show good quantitative reconstruction which includes the correct refractive index value and distribution of the sample. However, experimental result still indicates the presence of artifacts.

  8. Quantitative evaluation of a single-distance phase-retrieval method applied on in-line phase-contrast images of a mouse lung

    PubMed Central

    Mohammadi, Sara; Larsson, Emanuel; Alves, Frauke; Dal Monego, Simeone; Biffi, Stefania; Garrovo, Chiara; Lorenzon, Andrea; Tromba, Giuliana; Dullin, Christian

    2014-01-01

    Propagation-based X-ray phase-contrast computed tomography (PBI) has already proven its potential in a great variety of soft-tissue-related applications including lung imaging. However, the strong edge enhancement, caused by the phase effects, often hampers image segmentation and therefore the quantitative analysis of data sets. Here, the benefits of applying single-distance phase retrieval prior to the three-dimensional reconstruction (PhR) are discussed and quantified compared with three-dimensional reconstructions of conventional PBI data sets in terms of contrast-to-noise ratio (CNR) and preservation of image features. The PhR data sets show more than a tenfold higher CNR and only minor blurring of the edges when compared with PBI in a predominately absorption-based set-up. Accordingly, phase retrieval increases the sensitivity and provides more functionality in computed tomography imaging. PMID:24971975

  9. A fast-converging iterative method for X-ray in-line phase contrast tomography

    SciTech Connect

    Vo, Nghia T.; Breese, Mark B. H.; Atwood, Robert C.; Drakopoulos, Michael; Moser, Herbert O.; Lee, Peter D.

    2012-11-26

    X-ray in-line phase contrast tomography holds great promise for the quantitative analysis of soft materials. However, its applications have been limited, so far, by the fact that direct methods based on the transport-of-intensity equation and the contrast transfer function are sensitive to noise and applicable only to limited types of samples. Here, we propose an iterative method based on the Gerchberg-Saxton algorithm (R. W. Gerchberg and W. O. Saxton, Optik 35, 237 (1972)), but overcoming its slow convergence by an acceleration technique, named random signed feedback, which shows an excellent performance, both in numerical simulation and tomographic experiment, of discriminating various polymers even when using 53 keV synchrotron X-rays.

  10. Volumetric monitoring of aqueous two phase system droplets using time-lapse optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Lee, J.; Bathany, C.; Ahn, Y.; Takayama, S.; Jung, W.

    2016-02-01

    We present a volumetric monitoring method to observe the morphological changes of aqueous two phase system (ATPS) droplets in a microfluidic system. Our method is based on time-lapse optical coherence tomography (OCT) which allows the study of the dynamics of ATPS droplets while visualizing their 3D structures and providing quantitative information on the droplets. In this study, we monitored the process of rehydration and deformation of an ATPS droplet in a microfluidic system and quantified the changes of its volume and velocity under both static and dynamic fluid conditions. Our results indicate that time-lapse OCT is a very promising tool to evaluate the unprecedented features of droplet-based microfluidics.

  11. A quantitative method based on total relative change for dynamic electrical impedance tomography.

    PubMed

    You, Fusheng; Shi, Xuetao; Dong, Xiuzhen; Fu, Feng; Liu, Ruigang; Shuai, Wanjun; Li, Zheng

    2008-03-01

    We proposed a new method based on total relative change (TRC) from measured boundary voltages to quantify the volume changes of fluid during electrical impedance tomography (EIT) monitoring. The results showed that TRC linearly correlated with the volume of infused saline solution into a phantom, and the slope of TRC changes was approximately linear with the infusion speed. A inserted copper tube at different positions did not affect TRC significantly. The linear relationship between TRC and volume change indicates that TRC could be a good quantitative index for dynamic EIT.

  12. Quantitative polarization and flow evaluation of choroid and sclera by multifunctional Jones matrix optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Sugiyama, S.; Hong, Y.-J.; Kasaragod, D.; Makita, S.; Miura, M.; Ikuno, Y.; Yasuno, Y.

    2016-03-01

    Quantitative evaluation of optical properties of choroid and sclera are performed by multifunctional optical coherence tomography. Five normal eyes, five glaucoma eyes and one choroidal atrophy eye are examined. The refractive error was found to be correlated with choroidal birefringence, polarization uniformity, and flow in addition to scleral birefringence among normal eyes. The significant differences were observed between the normal and the glaucoma eyes, as for choroidal polarization uniformity, flow and scleral birefringence. An automatic segmentation algorithm of retinal pigment epithelium and chorioscleral interface based on multifunctional signals is also presented.

  13. Quantitative evaluation of phase processing approaches in susceptibility weighted imaging

    NASA Astrophysics Data System (ADS)

    Li, Ningzhi; Wang, Wen-Tung; Sati, Pascal; Pham, Dzung L.; Butman, John A.

    2012-03-01

    Susceptibility weighted imaging (SWI) takes advantage of the local variation in susceptibility between different tissues to enable highly detailed visualization of the cerebral venous system and sensitive detection of intracranial hemorrhages. Thus, it has been increasingly used in magnetic resonance imaging studies of traumatic brain injury as well as other intracranial pathologies. In SWI, magnitude information is combined with phase information to enhance the susceptibility induced image contrast. Because of global susceptibility variations across the image, the rate of phase accumulation varies widely across the image resulting in phase wrapping artifacts that interfere with the local assessment of phase variation. Homodyne filtering is a common approach to eliminate this global phase variation. However, filter size requires careful selection in order to preserve image contrast and avoid errors resulting from residual phase wraps. An alternative approach is to apply phase unwrapping prior to high pass filtering. A suitable phase unwrapping algorithm guarantees no residual phase wraps but additional computational steps are required. In this work, we quantitatively evaluate these two phase processing approaches on both simulated and real data using different filters and cutoff frequencies. Our analysis leads to an improved understanding of the relationship between phase wraps, susceptibility effects, and acquisition parameters. Although homodyne filtering approaches are faster and more straightforward, phase unwrapping approaches perform more accurately in a wider variety of acquisition scenarios.

  14. Quantitative Phase Microscopy of Live Biological Cell Dynamics

    NASA Astrophysics Data System (ADS)

    Shaked, Natan T.; Wax, Adam

    2010-04-01

    Interferometric phase microscopy of biological cell dynamics has the potential to provide a label-free quantitative tool for cell biology, as well as for medical diagnosis and monitoring. The current state of the art of this field, the open questions, and specific solutions developed in our laboratory will be presented.

  15. Noise texture and signal detectability in propagation-based x-ray phase-contrast tomography

    SciTech Connect

    Chou, Cheng-Ying; Anastasio, Mark A.

    2010-01-15

    Purpose: X-ray phase-contrast tomography (PCT) is a rapidly emerging imaging modality for reconstructing estimates of an object's three-dimensional x-ray refractive index distribution. Unlike conventional x-ray computed tomography methods, the statistical properties of the reconstructed images in PCT remain unexplored. The purpose of this work is to quantitatively investigate noise propagation in PCT image reconstruction. Methods: The authors derived explicit expressions for the autocovariance of the reconstructed absorption and refractive index images to characterize noise texture and understand how the noise properties are influenced by the imaging geometry. Concepts from statistical detection theory were employed to understand how the imaging geometry-dependent statistical properties affect the signal detection performance in a signal-known-exactly/background-known-exactly task. Results: The analytical formulas for the phase and absorption autocovariance functions were implemented numerically and compared to the corresponding empirical values, and excellent agreement was found. They observed that the reconstructed refractive images are highly spatially correlated, while the absorption images are not. The numerical results confirm that the strength of the covariance is scaled by the detector spacing. Signal detection studies were conducted, employing a numerical observer. The detection performance was found to monotonically increase as the detector-plane spacing was increased. Conclusions: The authors have conducted the first quantitative investigation of noise propagation in PCT image reconstruction. The reconstructed refractive images were found to be highly spatially correlated, while absorption images were not. This is due to the presence of a Fourier space singularity in the reconstruction formula for the refraction images. The statistical analysis may facilitate the use of task-based image quality measures to further develop and optimize this emerging

  16. 4D x-ray phase contrast tomography for repeatable motion of biological samples

    NASA Astrophysics Data System (ADS)

    Hoshino, Masato; Uesugi, Kentaro; Yagi, Naoto

    2016-09-01

    X-ray phase contrast tomography based on a grating interferometer was applied to fast and dynamic measurements of biological samples. To achieve this, the scanning procedure in the tomographic scan was improved. A triangle-shaped voltage signal from a waveform generator to a Piezo stage was used for the fast phase stepping in the grating interferometer. In addition, an optical fiber coupled x-ray scientific CMOS camera was used to achieve fast and highly efficient image acquisitions. These optimizations made it possible to perform an x-ray phase contrast tomographic measurement within an 8 min scan with density resolution of 2.4 mg/cm3. A maximum volume size of 13 × 13 × 6 mm3 was obtained with a single tomographic measurement with a voxel size of 6.5 μm. The scanning procedure using the triangle wave was applied to four-dimensional measurements in which highly sensitive three-dimensional x-ray imaging and a time-resolved dynamic measurement of biological samples were combined. A fresh tendon in the tail of a rat was measured under a uniaxial stretching and releasing condition. To maintain the freshness of the sample during four-dimensional phase contrast tomography, the temperature of the bathing liquid of the sample was kept below 10° using a simple cooling system. The time-resolved deformation of the tendon and each fascicle was measured with a temporal resolution of 5.7 Hz. Evaluations of cross-sectional area size, length of the axis, and mass density in the fascicle during a stretching process provided a basis for quantitative analysis of the deformation of tendon fascicle.

  17. Quantitative phase-amplitude microscopy I: optical microscopy.

    PubMed

    Barone-Nugent, E D; Barty, A; Nugent, K A

    2002-06-01

    In this paper, the application of a new optical microscopy method (quantitative phase-amplitude microscopy) to biological imaging is explored, and the issue of resolution and image quality is examined. The paper begins by presenting a theoretical analysis of the method using the optical transfer function formalism of Streibl (1985). The effect of coherence on the formation of the phase image is explored, and it is shown that the resolution of the method is not compromised over that of a conventional bright-field image. It is shown that the signal-to-noise ratio of the phase recovery, however, does depend on the degree of coherence in the illumination. Streibl (1985) notes that partially coherent image formation is a non-linear process because of the intermingling of amplitude and phase information. The work presented here shows that the quantitative phase-amplitude microscopy method acts to linearize the image formation process, and that the phase and amplitude information is properly described using a transfer function analysis. The theoretical conclusions are tested experimentally using an optical microscope and the theoretical deductions are confirmed. Samples for microscopy influence both the phase and amplitude of the light wave and it is demonstrated that the new phase recovery method can separate the amplitude and phase information, something not possible using traditional phase microscopy. In the case of a coherent wave, knowledge of the phase and amplitude constitutes complete information that can be used to emulate other forms of microscopy. This capacity is demonstrated by recovering the phase of a sample and using the data to emulate a differential interference contrast image.

  18. Concentration measurement of injected gaseous fuel using quantitative schlieren and optical tomography

    NASA Astrophysics Data System (ADS)

    Iffa, E. D.; Aziz, A. R. A.; Malik, A. S.

    2010-06-01

    In this paper, the quantitative schlieren method is extended to measure the concentration field of an injected gaseous fuel along several planes perpendicular to the jet axis. Background Oriented Schlieren (BOS) is used as a quantitative flow field concentration measurement based on the deflection made by features in the background pattern. The flow field which is located between the camera and the background pattern varies the intensity value of the background points in the transfer medium. The Optical flow algorithm, which is used to measure the deflection vectors in the background due to the change in index of refraction, is modified to consider the change in intensity of the background image. Optical tomography served as a tool to extract the index of refraction of the gaseous field. Mole fraction values at differentplanes perpendicular to the jet axis are obtained and displayed.

  19. Quantitative three-dimensional photoacoustic tomography of the finger joints: an in vivo study

    NASA Astrophysics Data System (ADS)

    Sun, Yao; Sobel, Eric; Jiang, Huabei

    2009-11-01

    We present for the first time in vivo full three-dimensional (3-D) photoacoustic tomography (PAT) of the distal interphalangeal joint in a human subject. Both absorbed energy density and absorption coefficient images of the joint are quantitatively obtained using our finite-element-based photoacoustic image reconstruction algorithm coupled with the photon diffusion equation. The results show that major anatomical features in the joint along with the side arteries can be imaged with a 1-MHz transducer in a spherical scanning geometry. In addition, the cartilages associated with the joint can be quantitatively differentiated from the phalanx. This in vivo study suggests that the 3-D PAT method described has the potential to be used for early diagnosis of joint diseases such as osteoarthritis and rheumatoid arthritis.

  20. Experimental assessment of bone mineral density using quantitative computed tomography in holstein dairy cows

    PubMed Central

    MAETANI, Ayami; ITOH, Megumi; NISHIHARA, Kahori; AOKI, Takahiro; OHTANI, Masayuki; SHIBANO, Kenichi; KAYANO, Mitsunori; YAMADA, Kazutaka

    2016-01-01

    The aim of this study was to assess the measurement of bone mineral density (BMD) by quantitative computed tomography (QCT), comparing the relationships of BMD between QCT and dual-energy X-ray absorptiometry (DXA) and between QCT and radiographic absorptiometry (RA) in the metacarpal bone of Holstein dairy cows (n=27). A significant positive correlation was found between QCT and DXA measurements (r=0.70, P<0.01), and a significant correlation was found between QCT and RA measurements (r=0.50, P<0.01). We conclude that QCT provides quantitative evaluation of BMD in dairy cows, because BMD measured by QCT showed positive correlations with BMD measured by the two conventional methods: DXA and RA. PMID:27075115

  1. Quantitative photoacoustic tomography by stochastic search: direct recovery of the optical absorption field.

    PubMed

    Venugopal, Mamatha; van Es, Peter; Manohar, Srirang; Roy, Debasish; Vasu, Ram Mohan

    2016-09-15

    We present, perhaps for the first time, a stochastic search algorithm in quantitative photoacoustic tomography (QPAT) for a one-step recovery of the optical absorption map from time-resolved photoacoustic signals. Such a direct recovery is free of the numerical inaccuracies inherent in conventional two-step approaches that depend on an accurate estimation of the absorbed energy distribution. The absorption profile parameterized as a vector stochastic process is additively updated over time recursions so as to drive the measurement-prediction misfit to a zero-mean white noise. The derivative-free additive update is a welcome departure from the conventional gradient-based methods requiring evaluation of Jacobians at every recursion. The quantitative accuracy of the recovered absorption map from both numerical and experimental data is good with an overall error of less than 10%.

  2. Quantitative photoacoustic tomography by stochastic search: direct recovery of the optical absorption field.

    PubMed

    Venugopal, Mamatha; van Es, Peter; Manohar, Srirang; Roy, Debasish; Vasu, Ram Mohan

    2016-09-15

    We present, perhaps for the first time, a stochastic search algorithm in quantitative photoacoustic tomography (QPAT) for a one-step recovery of the optical absorption map from time-resolved photoacoustic signals. Such a direct recovery is free of the numerical inaccuracies inherent in conventional two-step approaches that depend on an accurate estimation of the absorbed energy distribution. The absorption profile parameterized as a vector stochastic process is additively updated over time recursions so as to drive the measurement-prediction misfit to a zero-mean white noise. The derivative-free additive update is a welcome departure from the conventional gradient-based methods requiring evaluation of Jacobians at every recursion. The quantitative accuracy of the recovered absorption map from both numerical and experimental data is good with an overall error of less than 10%. PMID:27628357

  3. Shear wave elastography using phase sensitive optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Song, Shaozhen; Huang, Zhihong; Nguyen, Thu-Mai; Wong, Emily Y.; Arnal, Bastien; O'Donnell, Matthew; Wang, Ruikang K.

    2014-03-01

    Optical coherence tomography (OCT) provides high spatial resolution and sensitivity that are ideal for imaging the cornea and lens. Quantifying the biomechanical properties of these tissues could add clinically valuable information. Thus, we propose a dynamic elastography method combining OCT detection and a mechanical actuator to map the shear modulus of soft tissues. We used a piezoelectric actuator driven in the kHz range and we used phase-sensitive OCT (PhS-OCT) to track the resulting shear waves at an equivalent frame rate of 47 kHz. We mapped the shear wave speed of anesthetized mice cornea using monochromatic excitations. We found a significant difference between a group of knock-out (3.92 +/- 0.35 m/s, N=4) and wild-type mice (5.04 +/- 0.51 m/s, N=3). These preliminary results demonstrate the feasibility of using PhS-OCT to perform in vivo shear wave elastography of the cornea. We then implemented a shear pulse compression approach on ex vivo human cornea. For that purpose, frequency- modulated excitations were used and the resulting displacement field was digitally compressed in a short broadband pulse with a 7 dB gain in signal-to-noise ratio (SNR).

  4. Quantitative cell imaging using single beam phase retrieval method

    NASA Astrophysics Data System (ADS)

    Anand, Arun; Chhaniwal, Vani; Javidi, Bahram

    2011-06-01

    Quantitative three-dimensional imaging of cells can provide important information about their morphology as well as their dynamics, which will be useful in studying their behavior under various conditions. There are several microscopic techniques to image unstained, semi-transparent specimens, by converting the phase information into intensity information. But most of the quantitative phase contrast imaging techniques is realized either by using interference of the object wavefront with a known reference beam or using phase shifting interferometry. A two-beam interferometric method is challenging to implement especially with low coherent sources and it also requires a fine adjustment of beams to achieve high contrast fringes. In this letter, the development of a single beam phase retrieval microscopy technique for quantitative phase contrast imaging of cells using multiple intensity samplings of a volume speckle field in the axial direction is described. Single beam illumination with multiple intensity samplings provides fast convergence and a unique solution of the object wavefront. Three-dimensional thickness profiles of different cells such as red blood cells and onion skin cells were reconstructed using this technique with an axial resolution of the order of several nanometers.

  5. Whole-cell phase contrast imaging at the nanoscale using Fresnel Coherent Diffractive Imaging Tomography

    PubMed Central

    Jones, Michael W. M.; van Riessen, Grant A.; Abbey, Brian; Putkunz, Corey T.; Junker, Mark D.; Balaur, Eugeniu; Vine, David J.; McNulty, Ian; Chen, Bo; Arhatari, Benedicta D.; Frankland, Sarah; Nugent, Keith A.; Tilley, Leann; Peele, Andrew G.

    2013-01-01

    X-ray tomography can provide structural information of whole cells in close to their native state. Radiation-induced damage, however, imposes a practical limit to image resolution, and as such, a choice between damage, image contrast, and image resolution must be made. New coherent diffractive imaging techniques, such Fresnel Coherent Diffractive Imaging (FCDI), allows quantitative phase information with exceptional dose efficiency, high contrast, and nano-scale resolution. Here we present three-dimensional quantitative images of a whole eukaryotic cell by FCDI at a spatial resolution below 70 nm with sufficient phase contrast to distinguish major cellular components. From our data, we estimate that the minimum dose required for a similar resolution is close to that predicted by the Rose criterion, considerably below accepted estimates of the maximum dose a frozen-hydrated cell can tolerate. Based on the dose efficiency, contrast, and resolution achieved, we expect this technique will find immediate applications in tomographic cellular characterisation. PMID:23887204

  6. Non-interferometric quantitative phase imaging of yeast cells

    NASA Astrophysics Data System (ADS)

    Poola, Praveen K.; Pandiyan, Vimal Prabhu; John, Renu

    2015-12-01

    Real-time imaging of live cells is quite difficult without the addition of external contrast agents. Various methods for quantitative phase imaging of living cells have been proposed like digital holographic microscopy and diffraction phase microscopy. In this paper, we report theoretical and experimental results of quantitative phase imaging of live yeast cells with nanometric precision using transport of intensity equations (TIE). We demonstrate nanometric depth sensitivity in imaging live yeast cells using this technique. This technique being noninterferometric, does not need any coherent light sources and images can be captured through a regular bright-field microscope. This real-time imaging technique would deliver the depth or 3-D volume information of cells and is highly promising in real-time digital pathology applications, screening of pathogens and staging of diseases like malaria as it does not need any preprocessing of samples.

  7. Quantitative Analysis of Intraventricular Dyssynchrony Using Wall Thickness by Multidetector Computed Tomography

    PubMed Central

    Truong, Quynh A.; Singh, Jagmeet P.; Cannon, Christopher P.; Sarwar, Ammar; Nasir, Khurram; Auricchio, Angelo; Faletra, Francesco F.; Sorgente, Antonio; Conca, Cristina; Moccetti, Tiziano; Handschumacher, Mark; Brady, Thomas J.; Hoffmann, Udo

    2009-01-01

    OBJECTIVES We sought to determine the feasibility of cardiac computed tomography (CT) to detect significant differences in the extent of left ventricular dyssynchrony in heart failure (HF) patients with wide QRS, HF patients with narrow QRS, and age-matched controls. BACKGROUND The degree of mechanical dyssynchrony has been suggested as a predictor of response to cardiac resynchronization therapy. There have been no published reports of dyssynchrony assessment with the use of CT. METHODS Thirty-eight subjects underwent electrocardiogram-gated contrast-enhanced 64-slice multidetector CT. The left ventricular endocardial and epicardial boundaries were delineated from short-axis images reconstructed at 10% phase increments of the cardiac cycle. Global and segmental CT dyssynchrony metrics that used changes in wall thickness, wall motion, and volume over time were assessed for reproducibility. We defined a global metric using changes in wall thickness as the dyssynchrony index (DI). RESULTS The DI was the most reproducible metric (interobserver and intraobserver intraclass correlation coefficients ≥0.94, p < 0.0001) and was used to determine differences between the 3 groups: HF-wide QRS group (ejection fraction [EF] 22 ± 8%, QRS 163 ± 28 ms), HF-narrow QRS (EF 26 ± 7%, QRS 96 ± 11 ms), and age-matched control subjects (EF 64 ± 5%, QRS 87 ± 9 ms). Mean DI was significantly different between the 3 groups (HF-wide QRS: 152 ± 44 ms, HF-narrow QRS: 121 ± 58 ms, and control subjects: 65 ± 12 ms; p < 0.0001) and greater in the HF-wide QRS (p < 0.0001) and HF-narrow QRS (p = 0.005) groups compared with control subjects. We found that DI had a good correlation with 2-dimensional (r = 0.65, p = 0.012) and 3-dimensional (r = 0.68, p = 0.008) echocardiographic dyssynchrony. CONCLUSIONS Quantitative assessment of global CT-derived DI, based on changes in wall thickness over time, is highly reproducible and renders significant differences between subjects most likely to

  8. Phase Space Tomography: A Simple, Portable and Accurate Technique to Map Phase Spaces of Beams with Space Charge

    SciTech Connect

    Stratakis, D.; Kishek, R. A.; Bernal, S.; Walter, M.; Haber, I.; Fiorito, R.; Thangaraj, J. C. T.; Quinn, B.; Reiser, M.; O'Shea, P. G.; Li, H.

    2006-11-27

    In order to understand the charged particle dynamics, e.g. the halo formation, emittance growth, x-y energy transfer and coupling, knowledge of the actual phase space is needed. Other the past decade there is an increasing number of articles who use tomography to map the beam phase space and measure the beam emittance. These studies where performed at high energy facilities where the effect of space charge was neglible and therefore not considered in the analysis. This work extends the tomography technique to beams with space charge. In order to simplify the analysis linear forces where assumed. By carefully modeling the tomography process using the particle-in-cell code WARP we test the validity of our assumptions and the accuracy of the reconstructed phase space. Finally, we report experimental results of phase space mapping at the University of Maryland Electron Ring (UMER) using tomography.

  9. Quantitative computed tomography of vertebral spongiosa: a sensitive method for detecting early bone loss after oophorectomy

    SciTech Connect

    Genant, H.K.; Cann, C.E.; Ettinger, B.; Gordan, G.S.

    1982-11-01

    The bone mineral loss was assessed serially in 37 premenopausal women for 24 months after oophorectomy and the dose-response for conjugated estrogen therapy in preventing this loss was determined. Spinal cancellous bone was measured by quantitative computed tomography and measurement of appendicular cortical bone by radial photon absorptiometry and metacarpal radiogrammetry. For the placebo and low-dose treatment groups, the mean annual bone mineral losses were 7% to 9% from the vertebral spongiosum and 1% to 3% from the peripheral cortex. The correlation between axial and appendicular loss was weak, precluding a reliable estimate of spinal loss from peripheral measurements. For the maximal-dose group (0.6 mg/d), the mean annual bone mineral losses were less than 0.5% from the axial and appendicular sites, and were not significant. The results indicate that spinal quantitative computed tomography provides a highly sensitive measurement of bone mineral loss after oophorectomy, that bone mineral loss is five- to sevenfold greater from the spinal spongiosum than from the appendicular cortex, and that conjugated estrogen in doses of less than 0.6 mg/d are inadequate to prevent the vertebral mineral loss.

  10. Objective interpretation of induced polarization tomography using a quantitative approach for the investigation of periglacial environments

    NASA Astrophysics Data System (ADS)

    Banville, David Roy; Fortier, Richard; Dupuis, Christian

    2016-07-01

    The objective interpretation of induced polarization tomography for applications in periglacial environments is sometimes challenging using smoothness-regularized least square inversion because strong resistivity contrasts are often present. Ambiguities arise from the regularization process which smooths the contrast between layers and from artifacts created by the inversion. In periglacial environments, where frozen and thawed ground can coexist with large resistivity contrasts, such artefacts are often found in the models of electrical resistivity. To assess reliable cryohydrogeological models from the inversion of induced polarization tomography, quantitative interpretation criteria are needed. The present work describes a methodology based on forward-inverse modeling to build a cryohydrogeological model from induced polarization data and prior information using the resistivity and chargeability gradients to map transitions between adjacent layers. This methodology is tested on field-data acquired over a coarse grained aquifer within a glaciomarine deposit and ice-rich permafrost mounds within marine sediments. Delineation of the permafrost base is achieved despite the presence of an inversion artefact. The results of the interpretation are used to further constrain the inversion in order to map the ice-content based on the resistivity model and an empirical relationship. The proposed methodology provides a way to extract quantitative information even in difficult environmental settings.

  11. Noninterferometric quantitative phase imaging with soft x rays.

    PubMed

    Allman, B E; McMahon, P J; Tiller, J B; Nugent, K A; Paganin, D; Barty, A

    2000-10-01

    We demonstrate quantitative noninterferometric x-ray phase-amplitude measurement. We present results from two experimental geometries. The first geometry uses x rays diverging from a point source to produce high-resolution holograms of submicrometer-sized objects. The measured phase of the projected image agrees with the geometrically determined phase to within +/-7%. The second geometry uses a direct imaging microscope setup that allows the formation of a magnified image with a zone-plate lens. Here a direct measure of the object phase is made and agrees with that of the magnified object to better than +/-10%. In both cases the accuracy of the phase is limited by the pixel resolution.

  12. High-sensitivity quantitative phase microcopy (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Zhou, Renjie; Kuang, Cuifang; Hosseini, Poorya; Chowdhary, Ravi; Yaqoob, Zahid; So, Peter T. C.

    2016-03-01

    In the past decade, various quantitative phase microscopy (QPM) techniques have emerged, driven by the need to study biological samples non-invasively. However, the fundamental limit for phase noise is scarcely discussed in the literature. In a typically off-axis phase microscope system, the phase noise is limited to a few milliradians using a moderate camera. Common-path QPMs offer much reduced phase noise compared to typical Mach-Zehnder-based systems. However, further scaling down the phase noise becomes difficult. Here we propose a high-sensitivity common-path QPM that promises to reduce the phase noise by a factor of 10 (assuming the mechanical noise is negligible). This is achieved by a specifically designed signal filter, leaving only the subtle phase fluctuations coming from the dynamics sample scattering. By working at photon shot-noise limited detection, we can magnify the subtle phase contrast which is proportional to the camera well depth. We expect this system to have the height sensitivity similar to an atomic force microcopy, while measuring biological structures with a full field of view in a single-shot. We plan to use this system to study cell dynamics, particularly lamellipodial height fluctuations as well as stiffer cell membrane fluctuations.

  13. In-line x-ray phase-contrast tomography and diffraction-contrast tomography study of the ferrite-cementite microstructure in steel

    NASA Astrophysics Data System (ADS)

    Kostenko, Alexander; Sharma, Hemant; Dere, E. Gözde; King, Andrew; Ludwig, Wolfgang; Van Oel, Wim; Offerman, S. Erik; Stallinga, Sjoerd; Vliet, Lucas J. van

    2012-05-01

    This work presents the development of a non-destructive imaging technique for the investigation of the microstructure of cementite grains embedded in a ferrite matrix of medium-carbon steel. The measurements were carried out at the material science beamline of the European Synchrotron Radiation Facility (ESRF) ID11. It was shown that in-line X-ray phase-contrast tomography (PCT) can be used for the detection of cementite grains of several microns in size. X-ray PCT of the cementite structure can be achieved by either a `single distance' or a `multiple distance' acquisition protocol. The latter permits quantitative phase retrieval. A second imaging technique, X-ray diffraction-contrast tomography (DCT), was employed to obtain information about the shapes and crystallographic orientations of the distinct ferrite grains surrounding the cementite structures. The initial results demonstrate the feasibility of determining the geometry of the cementite grains after the austenite-ferrite phase-transformation in a non-destructive manner. The results obtained with PCT and DCT are verified with ex-situ optical microscopy studies of the same specimen.

  14. Spatiotemporal Characterization of a Fibrin Clot Using Quantitative Phase Imaging

    PubMed Central

    Gannavarpu, Rajshekhar; Bhaduri, Basanta; Tangella, Krishnarao; Popescu, Gabriel

    2014-01-01

    Studying the dynamics of fibrin clot formation and its morphology is an important problem in biology and has significant impact for several scientific and clinical applications. We present a label-free technique based on quantitative phase imaging to address this problem. Using quantitative phase information, we characterized fibrin polymerization in real-time and present a mathematical model describing the transition from liquid to gel state. By exploiting the inherent optical sectioning capability of our instrument, we measured the three-dimensional structure of the fibrin clot. From this data, we evaluated the fractal nature of the fibrin network and extracted the fractal dimension. Our non-invasive and speckle-free approach analyzes the clotting process without the need for external contrast agents. PMID:25386701

  15. Biomechanical cell analysis using quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wax, Adam; Park, Han Sang; Eldridge, William J.

    2016-03-01

    Quantitative phase imaging provides nanometer scale sensitivity and has been previously used to study spectral and temporal characteristics of individual cells in vitro, especially red blood cells. Here we extend this work to study the mechanical responses of individual cells due to the influence of external stimuli. Cell stiffness may be characterized by analyzing the inherent thermal fluctuations of cells but by applying external stimuli, additional information can be obtained. The time dependent response of cells due to external shear stress is examined with high speed quantitative phase imaging and found to exhibit characteristics that relate to their stiffness. However, analysis beyond the cellular scale also reveals internal organization of the cell and its modulation due to pathologic processes such as carcinogenesis. Further studies with microfluidic platforms point the way for using this approach in high throughput assays.

  16. Quantitative phase retrieval with arbitrary pupil and illumination

    DOE PAGESBeta

    Claus, Rene A.; Naulleau, Patrick P.; Neureuther, Andrew R.; Waller, Laura

    2015-10-02

    We present a general algorithm for combining measurements taken under various illumination and imaging conditions to quantitatively extract the amplitude and phase of an object wave. The algorithm uses the weak object transfer function, which incorporates arbitrary pupil functions and partially coherent illumination. The approach is extended beyond the weak object regime using an iterative algorithm. Finally, we demonstrate the method on measurements of Extreme Ultraviolet Lithography (EUV) multilayer mask defects taken in an EUV zone plate microscope with both a standard zone plate lens and a zone plate implementing Zernike phase contrast.

  17. Semiconductor defect metrology using laser-based quantitative phase imaging

    NASA Astrophysics Data System (ADS)

    Zhou, Renjie; Edwards, Chris; Popescu, Gabriel; Goddard, Lynford

    2015-03-01

    A highly sensitive laser-based quantitative phase imaging tool, using an epi-illumination diffraction phase microscope, has been developed for silicon wafer defect inspection. The first system used a 532 nm solid-state laser and detected 20 nm by 100 nm by 110 nm defects in a 22 nm node patterned silicon wafer. The second system, using a 405 nm diode laser, is more sensitive and has enabled detection of 15 nm by 90 nm by 35 nm defects in a 9 nm node densely patterned silicon wafer. In addition to imaging, wafer scanning and image-post processing are also crucial for defect detection.

  18. Quantitative phase retrieval with arbitrary pupil and illumination.

    PubMed

    Claus, Rene A; Naulleau, Patrick P; Neureuther, Andrew R; Waller, Laura

    2015-10-01

    We present a general algorithm for combining measurements taken under various illumination and imaging conditions to quantitatively extract the amplitude and phase of an object wave. The algorithm uses the weak object transfer function, which incorporates arbitrary pupil functions and partially coherent illumination. The approach is extended beyond the weak object regime using an iterative algorithm. We demonstrate the method on measurements of Extreme Ultraviolet Lithography (EUV) multilayer mask defects taken in an EUV zone plate microscope with both a standard zone plate lens and a zone plate implementing Zernike phase contrast. PMID:26480180

  19. Quantitative appraisal for noise reduction in digital holographic phase imaging.

    PubMed

    Montresor, Silvio; Picart, Pascal

    2016-06-27

    This paper discusses on a quantitative comparison of the performances of different advanced algorithms for phase data de-noising. In order to quantify the performances, several criteria are proposed: the gain in the signal-to-noise ratio, the Q index, the standard deviation of the phase error, and the signal to distortion ratio. The proposed methodology to investigate de-noising algorithms is based on the use of a realistic simulation of noise-corrupted phase data. A database including 25 fringe patterns divided into 5 patterns and 5 different signal-to-noise ratios was generated to evaluate the selected de-noising algorithms. A total of 34 algorithms divided into different families were evaluated. Quantitative appraisal leads to ranking within the considered criteria. A fairly good correlation between the signal-to-noise ratio gain and the quality index has been observed. There exists an anti-correlation between the phase error and the quality index which indicates that the phase errors are mainly structural distortions in the fringe pattern. Experimental results are thoroughly discussed in the paper. PMID:27410587

  20. Regularized iterative integration combined with non-linear diffusion filtering for phase-contrast x-ray computed tomography.

    PubMed

    Burger, Karin; Koehler, Thomas; Chabior, Michael; Allner, Sebastian; Marschner, Mathias; Fehringer, Andreas; Willner, Marian; Pfeiffer, Franz; Noël, Peter

    2014-12-29

    Phase-contrast x-ray computed tomography has a high potential to become clinically implemented because of its complementarity to conventional absorption-contrast.In this study, we investigate noise-reducing but resolution-preserving analytical reconstruction methods to improve differential phase-contrast imaging. We apply the non-linear Perona-Malik filter on phase-contrast data prior or post filtered backprojected reconstruction. Secondly, the Hilbert kernel is replaced by regularized iterative integration followed by ramp filtered backprojection as used for absorption-contrast imaging. Combining the Perona-Malik filter with this integration algorithm allows to successfully reveal relevant sample features, quantitatively confirmed by significantly increased structural similarity indices and contrast-to-noise ratios. With this concept, phase-contrast imaging can be performed at considerably lower dose.

  1. Accounting for filter bandwidth improves the quantitative accuracy of bioluminescence tomography.

    PubMed

    Taylor, Shelley L; Mason, Suzannah K G; Glinton, Sophie L; Cobbold, Mark; Dehghani, Hamid

    2015-09-01

    Bioluminescence imaging is a noninvasive technique whereby surface weighted images of luminescent probes within animals are used to characterize cell count and function. Traditionally, data are collected over the entire emission spectrum of the source using no filters and are used to evaluate cell count/function over the entire spectrum. Alternatively, multispectral data over several wavelengths can be incorporated to perform tomographic reconstruction of source location and intensity. However, bandpass filters used for multispectral data acquisition have a specific bandwidth, which is ignored in the reconstruction. In this work, ignoring the bandwidth is shown to introduce a dependence of the recovered source intensity on the bandwidth of the filters. A method of accounting for the bandwidth of filters used during multispectral data acquisition is presented and its efficacy in increasing the quantitative accuracy of bioluminescence tomography is demonstrated through simulation and experiment. It is demonstrated that while using filters with a large bandwidth can dramatically decrease the data acquisition time, if not accounted for, errors of up to 200% in quantitative accuracy are introduced in two-dimensional planar imaging, even after normalization. For tomographic imaging, the use of this method to account for filter bandwidth dramatically improves the quantitative accuracy. PMID:26325264

  2. Automated quantitative assessment of three-dimensional bioprinted hydrogel scaffolds using optical coherence tomography

    PubMed Central

    Wang, Ling; Xu, Mingen; Zhang, LieLie; Zhou, QingQing; Luo, Li

    2016-01-01

    Reconstructing and quantitatively assessing the internal architecture of opaque three-dimensional (3D) bioprinted hydrogel scaffolds is difficult but vital to the improvement of 3D bioprinting techniques and to the fabrication of functional engineered tissues. In this study, swept-source optical coherence tomography was applied to acquire high-resolution images of hydrogel scaffolds. Novel 3D gelatin/alginate hydrogel scaffolds with six different representative architectures were fabricated using our 3D bioprinting system. Both the scaffold material networks and the interconnected flow channel networks were reconstructed through volume rendering and binarisation processing to provide a 3D volumetric view. An image analysis algorithm was developed based on the automatic selection of the spatially-isolated region-of–interest. Via this algorithm, the spatially-resolved morphological parameters including pore size, pore shape, strut size, surface area, porosity, and interconnectivity were quantified precisely. Fabrication defects and differences between the designed and as-produced scaffolds were clearly identified in both 2D and 3D; the locations and dimensions of each of the fabrication defects were also defined. It concludes that this method will be a key tool for non-destructive and quantitative characterization, design optimisation and fabrication refinement of 3D bioprinted hydrogel scaffolds. Furthermore, this method enables investigation into the quantitative relationship between scaffold structure and biological outcome. PMID:27231597

  3. Accounting for filter bandwidth improves the quantitative accuracy of bioluminescence tomography

    NASA Astrophysics Data System (ADS)

    Taylor, Shelley L.; Mason, Suzannah K. G.; Glinton, Sophie L.; Cobbold, Mark; Dehghani, Hamid

    2015-09-01

    Bioluminescence imaging is a noninvasive technique whereby surface weighted images of luminescent probes within animals are used to characterize cell count and function. Traditionally, data are collected over the entire emission spectrum of the source using no filters and are used to evaluate cell count/function over the entire spectrum. Alternatively, multispectral data over several wavelengths can be incorporated to perform tomographic reconstruction of source location and intensity. However, bandpass filters used for multispectral data acquisition have a specific bandwidth, which is ignored in the reconstruction. In this work, ignoring the bandwidth is shown to introduce a dependence of the recovered source intensity on the bandwidth of the filters. A method of accounting for the bandwidth of filters used during multispectral data acquisition is presented and its efficacy in increasing the quantitative accuracy of bioluminescence tomography is demonstrated through simulation and experiment. It is demonstrated that while using filters with a large bandwidth can dramatically decrease the data acquisition time, if not accounted for, errors of up to 200% in quantitative accuracy are introduced in two-dimensional planar imaging, even after normalization. For tomographic imaging, the use of this method to account for filter bandwidth dramatically improves the quantitative accuracy.

  4. Experimental investigation of bone mineral density in Thoroughbreds using quantitative computed tomography

    PubMed Central

    YAMADA, Kazutaka; SATO, Fumio; HIGUCHI, Tohru; NISHIHARA, Kaori; KAYANO, Mitsunori; SASAKI, Naoki; NAMBO, Yasuo

    2015-01-01

    ABSTRACT Bone mineral density (BMD) is one of the indications of the strength and health. BMD measured by quantitative computed tomography (QCT) was compared with that measured by dual energy X-ray absorptiometry (DXA) and radiographic bone aluminum equivalence (RBAE). Limbs were removed from horses that had been euthanized for reasons not associated with this study. Sixteen limbs (left and right metacarpals and metatarsals) from 4 horses were used to compare BMD as measured by QCT with those measured by DXA and RBAE. There was a strong correlation between BMD values measured by QCT and those measured by DXA (R2=0.85); correlation was also observed between values obtained by QCT and those obtained by RBAE (R2=0.61). To investigate changes in BMD with age, 37 right metacarpal bones, including 7 from horses euthanized because of fracture were examined by QCT. The BMD value of samples from horses dramatically increased until 2 years of age and then plateaued, a pattern similar to the growth curve. The BMD values of bone samples from horses euthanized because of fracture were within the population range, and samples of morbid fracture were not included. The relationship between BMD and age provides a reference for further quantitative studies of bone development and remodeling. Quantitative measurement of BMD using QCT may have great potential for the evaluation of bone biology for breeding and rearing management. PMID:26435681

  5. Experimental investigation of bone mineral density in Thoroughbreds using quantitative computed tomography.

    PubMed

    Yamada, Kazutaka; Sato, Fumio; Higuchi, Tohru; Nishihara, Kaori; Kayano, Mitsunori; Sasaki, Naoki; Nambo, Yasuo

    2015-01-01

    Bone mineral density (BMD) is one of the indications of the strength and health. BMD measured by quantitative computed tomography (QCT) was compared with that measured by dual energy X-ray absorptiometry (DXA) and radiographic bone aluminum equivalence (RBAE). Limbs were removed from horses that had been euthanized for reasons not associated with this study. Sixteen limbs (left and right metacarpals and metatarsals) from 4 horses were used to compare BMD as measured by QCT with those measured by DXA and RBAE. There was a strong correlation between BMD values measured by QCT and those measured by DXA (R(2)=0.85); correlation was also observed between values obtained by QCT and those obtained by RBAE (R(2)=0.61). To investigate changes in BMD with age, 37 right metacarpal bones, including 7 from horses euthanized because of fracture were examined by QCT. The BMD value of samples from horses dramatically increased until 2 years of age and then plateaued, a pattern similar to the growth curve. The BMD values of bone samples from horses euthanized because of fracture were within the population range, and samples of morbid fracture were not included. The relationship between BMD and age provides a reference for further quantitative studies of bone development and remodeling. Quantitative measurement of BMD using QCT may have great potential for the evaluation of bone biology for breeding and rearing management. PMID:26435681

  6. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    NASA Astrophysics Data System (ADS)

    Beasley, D. G.; Alves, L. C.; Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C.; Le Trequesser, Q.; Marques, A. C.; Seznec, H.; da Silva, R. C.

    2014-07-01

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans - a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

  7. Swept source optical coherence tomography for quantitative and qualitative assessment of dental composite restorations

    NASA Astrophysics Data System (ADS)

    Sadr, Alireza; Shimada, Yasushi; Mayoral, Juan Ricardo; Hariri, Ilnaz; Bakhsh, Turki A.; Sumi, Yasunori; Tagami, Junji

    2011-03-01

    The aim of this work was to explore the utility of swept-source optical coherence tomography (SS-OCT) for quantitative evaluation of dental composite restorations. The system (Santec, Japan) with a center wavelength of around 1300 nm and axial resolution of 12 μm was used to record data during and after placement of light-cured composites. The Fresnel phenomenon at the interfacial defects resulted in brighter areas indicating gaps as small as a few micrometers. The gap extension at the interface was quantified and compared to the observation by confocal laser scanning microscope after trimming the specimen to the same cross-section. Also, video imaging of the composite during polymerization could provide information about real-time kinetics of contraction stress and resulting gaps, distinguishing them from those gaps resulting from poor adaptation of composite to the cavity prior to polymerization. Some samples were also subjected to a high resolution microfocus X-ray computed tomography (μCT) assessment; it was found that differentiation of smaller gaps from the radiolucent bonding layer was difficult with 3D μCT. Finally, a clinical imaging example using a newly developed dental SS-OCT system with an intra-oral scanning probe (Panasonic Healthcare, Japan) is presented. SS-OCT is a unique tool for clinical assessment and laboratory research on resin-based dental restorations. Supported by GCOE at TMDU and NCGG.

  8. Evaluation of dental enamel caries assessment using Quantitative Light Induced Fluorescence and Optical Coherence Tomography.

    PubMed

    Maia, Ana Marly Araújo; de Freitas, Anderson Zanardi; de L Campello, Sergio; Gomes, Anderson Stevens Leônidas; Karlsson, Lena

    2016-06-01

    An in vitro study of morphological alterations between sound dental structure and artificially induced white spot lesions in human teeth, was performed through the loss of fluorescence by Quantitative Light-Induced Fluorescence (QLF) and the alterations of the light attenuation coefficient by Optical Coherence Tomography (OCT). To analyze the OCT images using a commercially available system, a special algorithm was applied, whereas the QLF images were analyzed using the software available in the commercial system employed. When analyzing the sound region against white spot lesions region by QLF, a reduction in the fluorescence intensity was observed, whilst an increase of light attenuation by the OCT system occurred. Comparison of the percentage of alteration between optical properties of sound and artificial enamel caries regions showed that OCT processed images through the attenuation of light enhanced the tooth optical alterations more than fluorescence detected by QLF System. QLF versus OCT imaging of enamel caries: a photonics assessment.

  9. Changes in bone structure of Corriedale sheep with inherited rickets: a peripheral quantitative computed tomography assessment.

    PubMed

    Dittmer, Keren E; Firth, Elwyn C; Thompson, Keith G; Marshall, Jonathan C; Blair, Hugh T

    2011-03-01

    An inherited skeletal disease with gross and microscopic features of rickets has been diagnosed in Corriedale sheep in New Zealand. The aim of this study was to quantify the changes present in tibia from sheep with inherited rickets using peripheral quantitative computed tomography. In affected sheep, scans in the proximal tibia, where metaphysis becomes diaphysis, showed significantly greater trabecular bone mineral content (BMC) and bone mineral density (BMD). The sheep with inherited rickets had significantly greater BMC and bone area in the mid-diaphysis of the proximal tibia compared to control sheep. However, BMD in the mid-diaphysis was significantly less in affected sheep than in controls, due to the greater cortical area and lower voxel density values in affected sheep. From this it was concluded that the increased strain on under-mineralised bone in sheep with inherited rickets led to increased bone mass in an attempt to improve bone strength.

  10. Diagnosis of breast cancer biopsies using quantitative phase imaging

    NASA Astrophysics Data System (ADS)

    Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel

    2015-03-01

    The standard practice in the histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope. The pathologist looks at certain morphological features, visible under the stain, to diagnose whether a tumor is benign or malignant. This determination is made based on qualitative inspection making it subject to investigator bias. Furthermore, since this method requires a microscopic examination by the pathologist it suffers from low throughput. A quantitative, label-free and high throughput method for detection of these morphological features from images of tissue biopsies is, hence, highly desirable as it would assist the pathologist in making a quicker and more accurate diagnosis of cancers. We present here preliminary results showing the potential of using quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated optical path length maps of unstained breast tissue biopsies using Spatial Light Interference Microscopy (SLIM). As a first step towards diagnosis based on quantitative phase imaging, we carried out a qualitative evaluation of the imaging resolution and contrast of our label-free phase images. These images were shown to two pathologists who marked the tumors present in tissue as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on H&E stained tissue images and the number of agreements were counted. In our experiment, the agreement between SLIM and H&E based diagnosis was measured to be 88%. Our preliminary results demonstrate the potential and promise of SLIM for a push in the future towards quantitative, label-free and high throughput diagnosis.

  11. Application of gamma-densitometry tomography to determine phase spatial variation in two-phase and three-phase bubbly flows

    SciTech Connect

    Torczynski, J.R.; Adkins, D.R.; Shollenberger, K.A.; O`Hern, T.J.

    1995-12-31

    Gamma-densitometry tomography is applied to two-phase and three-phase bubbly flows. Spatially resolved measurements of the phase volume fractions are presented for air-water and air-water-sand experiments at various airflow rates. For the conditions examined, the presence of the solid particulate phase had only a minimal effect on the gas volume fraction spatial variation.

  12. High-speed X-ray phase tomography with Talbot interferometer and fringe scanning method

    SciTech Connect

    Kibayashi, Shunsuke; Harasse, Sebastien; Yashiro, Wataru; Momose, Atsushi

    2012-07-31

    High-speed X-ray phase tomography based on the Fourier-transform method has been demonstrated with an X-ray Talbot interferometer using white synchrotron radiation. We report the experimental results of high-speed X-ray phase tomography with fringe-scanning method instead of Fourier-transform method to improve spatial resolution without a considerable increase of scan time. To apply fringe-scanning method to high speed tomography, we tested a scan that is a synchronous combination of one-way continuous movements of the sample rotation and the grating displacement. When this scanning method was combined with X-ray phase tomography, we were able to obtain a scan time of 5 s. A comparison of the image quality derived with the conventional approach and with the proposed approach using the fringe-scanning method showed that the latter had better spatial resolution.

  13. Quantitative phase measurement for wafer-level optics

    NASA Astrophysics Data System (ADS)

    Qu, Weijuan; Wen, Yongfu; Wang, Zhaomin; Yang, Fang; Huang, Lei; Zuo, Chao

    2015-07-01

    Wafer-level-optics now is widely used in smart phone camera, mobile video conferencing or in medical equipment that require tiny cameras. Extracting quantitative phase information has received increased interest in order to quantify the quality of manufactured wafer-level-optics, detect defective devices before packaging, and provide feedback for manufacturing process control, all at the wafer-level for high-throughput microfabrication. We demonstrate two phase imaging methods, digital holographic microscopy (DHM) and Transport-of-Intensity Equation (TIE) to measure the phase of the wafer-level lenses. DHM is a laser-based interferometric method based on interference of two wavefronts. It can perform a phase measurement in a single shot. While a minimum of two measurements of the spatial intensity of the optical wave in closely spaced planes perpendicular to the direction of propagation are needed to do the direct phase retrieval by solving a second-order differential equation, i.e., with a non-iterative deterministic algorithm from intensity measurements using the Transport-of-Intensity Equation (TIE). But TIE is a non-interferometric method, thus can be applied to partial-coherence light. We demonstrated the capability and disability for the two phase measurement methods for wafer-level optics inspection.

  14. Quantitative measurement of ultrasound pressure field by optical phase contrast method and acoustic holography

    NASA Astrophysics Data System (ADS)

    Oyama, Seiji; Yasuda, Jun; Hanayama, Hiroki; Yoshizawa, Shin; Umemura, Shin-ichiro

    2016-07-01

    A fast and accurate measurement of an ultrasound field with various exposure sequences is necessary to ensure the efficacy and safety of various ultrasound applications in medicine. The most common method used to measure an ultrasound pressure field, that is, hydrophone scanning, requires a long scanning time and potentially disturbs the field. This may limit the efficiency of developing applications of ultrasound. In this study, an optical phase contrast method enabling fast and noninterfering measurements is proposed. In this method, the modulated phase of light caused by the focused ultrasound pressure field is measured. Then, a computed tomography (CT) algorithm used to quantitatively reconstruct a three-dimensional (3D) pressure field is applied. For a high-intensity focused ultrasound field, a new approach that combines the optical phase contrast method and acoustic holography was attempted. First, the optical measurement of focused ultrasound was rapidly performed over the field near a transducer. Second, the nonlinear propagation of the measured ultrasound was simulated. The result of the new approach agreed well with that of the measurement using a hydrophone and was improved from that of the phase contrast method alone with phase unwrapping.

  15. Rapid quantitative phase imaging for partially coherent light microscopy.

    PubMed

    Rodrigo, José A; Alieva, Tatiana

    2014-06-01

    Partially coherent light provides promising advantages for imaging applications. In contrast to its completely coherent counterpart, it prevents image degradation due to speckle noise and decreases cross-talk among the imaged objects. These facts make attractive the partially coherent illumination for accurate quantitative imaging in microscopy. In this work, we present a non-interferometric technique and system for quantitative phase imaging with simultaneous determination of the spatial coherence properties of the sample illumination. Its performance is experimentally demonstrated in several examples underlining the benefits of partial coherence for practical imagining applications. The programmable optical setup comprises an electrically tunable lens and sCMOS camera that allows for high-speed measurement in the millisecond range.

  16. Quantitative phase-field modeling for boiling phenomena.

    PubMed

    Badillo, Arnoldo

    2012-10-01

    A phase-field model is developed for quantitative simulation of bubble growth in the diffusion-controlled regime. The model accounts for phase change and surface tension effects at the liquid-vapor interface of pure substances with large property contrast. The derivation of the model follows a two-fluid approach, where the diffuse interface is assumed to have an internal microstructure, defined by a sharp interface. Despite the fact that phases within the diffuse interface are considered to have their own velocities and pressures, an averaging procedure at the atomic scale, allows for expressing all the constitutive equations in terms of mixture quantities. From the averaging procedure and asymptotic analysis of the model, nonconventional terms appear in the energy and phase-field equations to compensate for the variation of the properties across the diffuse interface. Without these new terms, no convergence towards the sharp-interface model can be attained. The asymptotic analysis also revealed a very small thermal capillary length for real fluids, such as water, that makes impossible for conventional phase-field models to capture bubble growth in the millimeter range size. For instance, important phenomena such as bubble growth and detachment from a hot surface could not be simulated due to the large number of grids points required to resolve all the scales. Since the shape of the liquid-vapor interface is primarily controlled by the effects of an isotropic surface energy (surface tension), a solution involving the elimination of the curvature from the phase-field equation is devised. The elimination of the curvature from the phase-field equation changes the length scale dominating the phase change from the thermal capillary length to the thickness of the thermal boundary layer, which is several orders of magnitude larger. A detailed analysis of the phase-field equation revealed that a split of this equation into two independent parts is possible for system sizes

  17. Single beam Fourier transform digital holographic quantitative phase microscopy

    SciTech Connect

    Anand, A. Chhaniwal, V. K.; Mahajan, S.; Trivedi, V.; Faridian, A.; Pedrini, G.; Osten, W.; Dubey, S. K.; Javidi, B.

    2014-03-10

    Quantitative phase contrast microscopy reveals thickness or height information of a biological or technical micro-object under investigation. The information obtained from this process provides a means to study their dynamics. Digital holographic (DH) microscopy is one of the most used, state of the art single-shot quantitative techniques for three dimensional imaging of living cells. Conventional off axis DH microscopy directly provides phase contrast images of the objects. However, this process requires two separate beams and their ratio adjustment for high contrast interference fringes. Also the use of two separate beams may make the system more vulnerable to vibrations. Single beam techniques can overcome these hurdles while remaining compact as well. Here, we describe the development of a single beam DH microscope providing whole field imaging of micro-objects. A hologram of the magnified object projected on to a diffuser co-located with a pinhole is recorded with the use of a commercially available diode laser and an arrayed sensor. A Fourier transform of the recorded hologram directly yields the complex amplitude at the image plane. The method proposed was investigated using various phase objects. It was also used to image the dynamics of human red blood cells in which sub-micrometer level thickness variation were measurable.

  18. Quantitative elastography of skin and skin lesion using phase-sensitive OCT (PhS-OCT) and surface wave method

    NASA Astrophysics Data System (ADS)

    Li, Chunhui; Guan, Guangying; Huang, Zhihong; Wang, Ruikang

    2012-01-01

    This paper presents the combination of phase sensitive optical coherence tomography (PhS-OCT) imaging system and surface wave method to achieve quantitative evaluation and elastography of the mechanical properties of in vivo human skin. PhS-OCT measures the surface acoustic waves (SAWs) generated by impulse stimulation from a home-made shaker, and provide the B-frame images for the sample. The surface wave phase velocity dispersion curves were calculated, from which the elasticity of different skin layers were determined. The combination of phase velocities from adjacent two locations generates a quantitative elastography of sample. The experimental results agree well with theoretical expectations and may offer potential use in clinical situations.

  19. Bilateral filtering using the full noise covariance matrix applied to x-ray phase-contrast computed tomography

    NASA Astrophysics Data System (ADS)

    Allner, S.; Koehler, T.; Fehringer, A.; Birnbacher, L.; Willner, M.; Pfeiffer, F.; Noël, P. B.

    2016-05-01

    The purpose of this work is to develop an image-based de-noising algorithm that exploits complementary information and noise statistics from multi-modal images, as they emerge in x-ray tomography techniques, for instance grating-based phase-contrast CT and spectral CT. Among the noise reduction methods, image-based de-noising is one popular approach and the so-called bilateral filter is a well known algorithm for edge-preserving filtering. We developed a generalization of the bilateral filter for the case where the imaging system provides two or more perfectly aligned images. The proposed generalization is statistically motivated and takes the full second order noise statistics of these images into account. In particular, it includes a noise correlation between the images and spatial noise correlation within the same image. The novel generalized three-dimensional bilateral filter is applied to the attenuation and phase images created with filtered backprojection reconstructions from grating-based phase-contrast tomography. In comparison to established bilateral filters, we obtain improved noise reduction and at the same time a better preservation of edges in the images on the examples of a simulated soft-tissue phantom, a human cerebellum and a human artery sample. The applied full noise covariance is determined via cross-correlation of the image noise. The filter results yield an improved feature recovery based on enhanced noise suppression and edge preservation as shown here on the example of attenuation and phase images captured with grating-based phase-contrast computed tomography. This is supported by quantitative image analysis. Without being bound to phase-contrast imaging, this generalized filter is applicable to any kind of noise-afflicted image data with or without noise correlation. Therefore, it can be utilized in various imaging applications and fields.

  20. Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

    NASA Astrophysics Data System (ADS)

    Favicchio, Rosy; Psycharakis, Stylianos; Schönig, Kai; Bartsch, Dusan; Mamalaki, Clio; Papamatheakis, Joseph; Ripoll, Jorge; Zacharakis, Giannis

    2016-02-01

    Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture.

  1. Electrical impedance tomography-based sensing skin for quantitative imaging of damage in concrete

    NASA Astrophysics Data System (ADS)

    Hallaji, Milad; Seppänen, Aku; Pour-Ghaz, Mohammad

    2014-08-01

    This paper outlines the development of a large-area sensing skin for damage detection in concrete structures. The developed sensing skin consists of a thin layer of electrically conductive copper paint that is applied to the surface of the concrete. Cracking of the concrete substrate results in the rupture of the sensing skin, decreasing its electrical conductivity locally. The decrease in conductivity is detected with electrical impedance tomography (EIT) imaging. In previous works, electrically based sensing skins have provided only qualitative information on the damage on the substrate surface. In this paper, we study whether quantitative imaging of the damage is possible. We utilize application-specific models and computational methods in the image reconstruction, including a total variation (TV) prior model for the damage and an approximate correction of the modeling errors caused by the inhomogeneity of the painted sensing skin. The developed damage detection method is tested experimentally by applying the sensing skin to polymeric substrates and a reinforced concrete beam under four-point bending. In all test cases, the EIT-based sensing skin provides quantitative information on cracks and/or other damages on the substrate surface: featuring a very low conductivity in the damage locations, and a reliable indication of the lengths and shapes of the cracks. The results strongly support the applicability of the painted EIT-based sensing skin for damage detection in reinforced concrete elements and other substrates.

  2. Quantitative evaluation of optical coherence tomography signal enhancement with gold nanoshells.

    PubMed

    Agrawal, Anant; Huang, Stanley; Wei Haw Lin, Alex; Lee, Min-Ho; Barton, Jennifer K; Drezek, Rebekah A; Pfefer, T Joshua

    2006-01-01

    Nanoshell-enhanced optical coherence tomography (OCT) is a novel technique with the potential for molecular imaging and improved disease detection. However, optimization of this approach will require a quantitative understanding of the influence of nanoshell parameters on detected OCT signals. In this study, OCT was performed at 1310 nm in water and turbid tissue-simulating phantoms to which nanoshells were added. The effect of nanoshell concentration, core diameter, and shell thickness on signal enhancement was characterized. Experimental results indicated trends that were consistent with predicted optical properties-a monotonic increase in signal intensity and attenuation with increasing shell and core size. Threshold concentrations for a 2-dB OCT signal intensity gain were determined for several nanoshell geometries. For the most highly backscattering nanoshells tested-291-nm core diameter, 25-nm shell thickness-a concentration of 10(9) nanoshells/mL was needed to produce this signal increase. Based on these results, we discuss various practical considerations for optimizing nanoshell-enhanced OCT. Quantitative experimental data presented here will facilitate optimization of OCT-based diagnostics and may also be relevant to other reflectance-based approaches as well. PMID:16965149

  3. Quantitative analysis on PUVA-induced skin photodamages using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhai, Juan; Guo, Zhouyi; Liu, Zhiming; Xiong, Honglian; Zeng, Changchun; Jin, Ying

    2009-08-01

    Psoralen plus ultraviolet A radiation (PUVA) therapy is a very important clinical treatment of skin diseases such as vitiligo and psoriasis, but associated with an increased risk of skin photodamages especially photoaging. Since skin biopsy alters the original skin morphology and always requires an iatrogenic trauma, optical coherence tomography (OCT) appears to be a promising technique to study skin damage in vivo. In this study, the Balb/c mice had 8-methoxypsralen (8-MOP) treatment prior to UVA radiation was used as PUVA-induced photo-damaged modal. The OCT imaging of photo-damaged group (modal) and normal group (control) in vivo was obtained of mice dorsal skin at 0, 24, 48, 72 hours after irradiation respectively. And then the results were quantitatively analyzed combined with histological information. The experimental results showed that, PUVA-induced photo-damaged skin had an increase in epidermal thickness (ET), a reduction of attenuation coefficient in OCT images signal, and an increase in brightness of the epidermis layer compared with the control group. In conclusion, noninvasive high-resolution imaging techniques such as OCT may be a promising tool for photobiological studies aimed at assessing photo-damage and repair processes in vivo. It can be used to quantitative analysis of changes in photo-damaged skin, such as the ET and collagen in dermis, provides a theoretical basis for treatment and prevention of skin photodamages.

  4. Evaluation of static and dynamic perfusion cardiac computed tomography for quantitation and classification tasks.

    PubMed

    Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R; La Riviere, Patrick J; Alessio, Adam M

    2016-04-01

    Cardiac computed tomography (CT) acquisitions for perfusion assessment can be performed in a dynamic or static mode. Either method may be used for a variety of clinical tasks, including (1) stratifying patients into categories of ischemia and (2) using a quantitative myocardial blood flow (MBF) estimate to evaluate disease severity. In this simulation study, we compare method performance on these classification and quantification tasks for matched radiation dose levels and for different flow states, patient sizes, and injected contrast levels. Under conditions simulated, the dynamic method has low bias in MBF estimates (0 to [Formula: see text]) compared to linearly interpreted static assessment (0.45 to [Formula: see text]), making it more suitable for quantitative estimation. At matched radiation dose levels, receiver operating characteristic analysis demonstrated that the static method, with its high bias but generally lower variance, had superior performance ([Formula: see text]) in stratifying patients, especially for larger patients and lower contrast doses [area under the curve [Formula: see text] to 96 versus 0.86]. We also demonstrate that static assessment with a correctly tuned exponential relationship between the apparent CT number and MBF has superior quantification performance to static assessment with a linear relationship and to dynamic assessment. However, tuning the exponential relationship to the patient and scan characteristics will likely prove challenging. This study demonstrates that the selection and optimization of static or dynamic acquisition modes should depend on the specific clinical task.

  5. System for quantitative analysis of coronary calcification via electron-beam computed tomography

    NASA Astrophysics Data System (ADS)

    Reed, Judd E.; Rumberger, John A.; Davitt, Patrick J.; Kaufman, R. B.; Sheedy, Patrick F., II

    1994-05-01

    Electron beam computed tomography (EBCT) has provided a new tool for identification and possible quantification of coronary arterial plaque calcium. EBCT is the only imaging modality currently available which generates images of the spatial, temporal, and contrast resolution required for the identification of small foci of calcium and the potential for accurate quantification of calcium. Meanwhile, interest in quantification of coronary arterial calcium via EBCT and its correlation with severity of coronary atherosclerosis is increasing. Data remain inconclusive, but it appears that the reproducibility of quantitative grading of the extent of calcification by EBCT may be limited, in part, by the arbitrary nature of the scoring algorithm employed within the analysis tools currently provided by the EBCT manufacturer. It has not been possible to objectively determine optimum values for minimum plaque area and brightness threshold or to quantitatively determine whether single optimal values even exist. Also, although the current system tabulates the score, area, and mean attenuation for each plaque, the locations of the plaques are not reported.

  6. Quantitative Diagnosis of Colorectal Polyps by Spectral Domain Optical Coherence Tomography

    PubMed Central

    Wang, Chen; Zhang, Qinqin; Wu, Xiaojing; Tang, Tao; Liu, Hong; Zhu, S. W.; Gao, Bruce Z.; Yuan, X.-C.

    2014-01-01

    The principal aim of this study is to investigate the scattering coefficient of colorectal polyp tissues using an optical coherence tomography (OCT) technique. It combines the existing scattering coefficient model and spectral domain OCT to achieve method of early diagnosis of colorectal polyp in hospitals. Seventeen patients were studied, and a total of 1456 data points were extracted by curve-fitting the OCT signals into a confocal single-backscattering model. The results show that the mean scattering coefficient value for colorectal polyps is 1.91 mm−1 (std: ±0.54 mm−1), which is between the values for normal and malignant tissues. In addition, we studied the difference between adenomatous polyps (n = 15) and inflammatory polyps (n = 2) quantitatively and found that the adenomatous tissues had lower scattering coefficients than the inflammatory ones. The quantitative measurements confirmed that OCT can be used in primary diagnosis to compensate for the deficiencies in methods of pathological diagnosis, with a great potential for early diagnosis of tissues. PMID:24818145

  7. Volumetric quantitative computed tomography measurement precision for volumes and densities of tarsal and metatarsal bones.

    PubMed

    Commean, Paul K; Kennedy, Jared A; Bahow, Karen A; Hildebolt, Charles F; Liu, Lu; Smith, Kirk E; Hastings, Mary K; Ju, Tao; Prior, Fred W; Sinacore, David R

    2011-01-01

    Diabetic foot diseases, such as ulcerations, infections, and neuropathic (Charcot's) arthropathy, are major complications of diabetes mellitus (DM) and peripheral neuropathy (PN) and may cause osteolysis (bone loss) in foot bones. The purposes of our study were to make computed tomography (CT) measurements of foot-bone volumes and densities and to determine measurement precision (percent coefficients of variation for root-mean-square standard deviations) and least significant changes (LSCs) in these percentages that could be considered biologically real with 95% confidence. Volumetric quantitative CT scans were performed and repeated on 10 young healthy subjects and 13 subjects with DM and PN. Two raters used the original- and repeat-scan data sets to make measurements of volumes and bone mineral densities (BMDs) of the tarsal and metatarsal bones of the 2 feet (24 bones). Precisions for the bones ranged from 0.1% to 0.9% for volume measurements and from 0.6% to 1.9% for BMD measurements. The LSCs ranged from 0.4% to 2.5% for volume measurements and from 1.5% to 5.4% for BMD measurements. Volumetric quantitative CT provides precise measurements of volume and BMD for metatarsal and tarsal bones, where diabetic foot diseases commonly occur.

  8. Quantitative phase imaging by single-shot Hilbert-Huang phase microscopy.

    PubMed

    Trusiak, Maciej; Mico, Vicente; Garcia, Javier; Patorski, Krzysztof

    2016-09-15

    We propose a novel single-shot Hilbert-Huang transform-based algorithm applied to digital holographic microscopy (DHM) for robust, fast, and accurate single-shot quantitative phase imaging in on-axis and off-axis configurations. Fringe pattern with possible defects and closed fringes are adaptively filtered and accurately phase demodulated using local fringe direction estimation. Experimental validation of the proposed techniques is presented as the DHM study of microbeads and red blood cells phase samples. Obtained results compare very favorably with the Fourier approach (off-axis) and temporal phase shifting (on-axis). PMID:27628393

  9. Differential phase microscope and micro-tomography with a Foucault knife-edge scanning filter

    NASA Astrophysics Data System (ADS)

    Watanabe, N.; Hashizume, J.; Goto, M.; Yamaguchi, M.; Tsujimura, T.; Aoki, S.

    2013-10-01

    An x-ray differential phase microscope with a Foucault knife-edge scanning filter was set up at the bending magnet source BL3C, Photon Factory. A reconstructed phase profile from the differential phase image of an aluminium wire at 5.36 keV was fairly good agreement with the numerical simulation. Phase tomography of a biological specimen, such as an Artemia cyst, could be successfully demonstrated.

  10. Three-phase material distribution measurements in a vertical flow using gamma-densitometry tomography and electrical-impedance tomography

    SciTech Connect

    GEORGE,DARIN L.; SHOLLENBERGER,KIM ANN; TORCZYNSKI,JOHN R.; O'HERN,TIMOTHY J.; CECCIO,S.L.

    2000-03-28

    Experiments are presented in which electrical-impedance tomography (EIT) and gamma-densitometry tomography (GDT) measurements were combined to simultaneously measure the solid, liquid, and gas radial distributions in a vertical three-phase flow. The experimental testbed was a 19.05-cm diameter bubble column in which gas is injected at the bottom and exits out the top while the liquid and solid phases recirculate. The gas phase was air and the liquid phase was deionized water with added electrolytes. Four different particle classes were investigated for the solid phase: 40--100 {micro}m and 120--200 {micro}m glass beads (2.41 g/cm{sup 3}), and 170--260 {micro}m and 200--700 {micro}m polystyrene beads (1.04 g/cm{sup 3}). Superficial gas velocities of 3 to 30 cm/s and solid volume fractions up to 0.30 were examined. For all experimental conditions investigated, the gas distribution showed only a weak dependence on both particle size and density. Average gas volume fraction as a function of superficial gas velocity can be described to within {+-} 0.04 by curve passing through the center of the data. For most cases the solid particle appeared to be radically uniformly dispersed in the liquid.

  11. Quantitative Phase Analysis by the Rietveld Method for Forensic Science.

    PubMed

    Deng, Fei; Lin, Xiaodong; He, Yonghong; Li, Shu; Zi, Run; Lai, Shijun

    2015-07-01

    Quantitative phase analysis (QPA) is helpful to determine the type attribute of the object because it could present the content of the constituents. QPA by Rietveld method requires neither measurement of calibration data nor the use of an internal standard; however, the approximate crystal structure of each phase in a mixture is necessary. In this study, 8 synthetic mixtures composed of potassium nitrate and sulfur were analyzed by Rietveld QPA method. The Rietveld refinement was accomplished with a material analysis using diffraction program and evaluated by three agreement indices. Results showed that Rietveld QPA yielded precise results, with errors generally less than 2.0% absolute. In addition, a criminal case which was broken successfully with the help of Rietveld QPA method was also introduced. This method will allow forensic investigators to acquire detailed information of the material evidence, which could point out the direction for case detection and court proceedings.

  12. Application of X-ray phase contrast micro-tomography to the identification of traditional Chinese medicines

    NASA Astrophysics Data System (ADS)

    Ye, L. L.; Xue, Y. L.; Ni, L. H.; Tan, H.; Wang, Y. D.; Xiao, T. Q.

    2013-07-01

    Nondestructive and in situ investigation to the characteristic microstructures are important to the identification of traditional Chinese medicines (TCMs), especially for precious specimens and samples with oil contains. X-ray phase contrast micro-tomography (XPCMT) could be a practical solution for this kind of investigation. Fructus Foeniculi, a fruit kind of TCMs, is selected as the test sample. Experimental results show that the characteristic microstructures of Fructus Foeniculi, including vittae, vascular bundles, embryo, endosperm and the mesocarp reticulate cells around the vittae can be clearly distinguished and the integrated dissepiments microstructure in the vittae was observed successfully. Especially, for the first time, with virtual slice technique, it can investigate the liquid contains inside the TCMs. The results show that the vittae filled with volatile oil in the oil chamber were observed with this nondestructive and in situ 3-dimensional imaging technique. Furthermore, taking the advantage of micro-computed tomography, we can obtain the characteristic microstructures' quantitative information of the volume in liquid state. The volume of the oil chambers and the volatile oil, which are contained inside the vittae, was quantitatively analyzed. Accordingly, it can calculate the volume ratio of the volatile oil easily and accurately. As a result, we could conclude that XPCMT could be a useful tool for the nondestructive identification and quantitative analysis to TCMs.

  13. Quantitative evaluation of benzodiazepine receptors in live Papio papio baboons using positron emission tomography

    SciTech Connect

    Brouillet, E.; Chavoix, C.; Khalili-Varasteh, M.; Bottlaender, M.; Hantraye, P.; Yorke, J.C.; Maziere, M. )

    1990-10-01

    The binding of the 11C-labeled benzodiazepine antagonist Ro 15-1788 (flumazenil) was measured in the neocortex of live Papio papio baboons by positron emission tomography. This allowed us to calculate in vivo (i.e., at physiological temperature, neurotransmitters concentrations, and ionic environment) the apparent density of available benzodiazepine receptors (B'max) and the dissociation constant of Ro 15-1788 (Kd). By coadministering increasing doses of unlabeled Ro 15-1788 with (11C)Ro 15-1788 and assuming that nonsaturable radioactivity indicated the free ligand concentration, we were able to obtain saturation isotherms. We showed that a state of quasiequilibrium was reached 50 min after the administration of the radioligand. Linear Scatchard plots allowed us to calculate B'max at 78 and 50 pmol/ml of cerebral tissue in the occipital and frontal cortices, respectively. In both these areas, Kd is on the order of 6 nM, with a Hill number very close to unity. This indicates that Ro 15-1788 binds in vivo with high affinity to an homogeneous population of saturable sites. A similar measurement was carried out on a naturally photosensitive P. papio baboon. Absolute values of B'max, Kd, and Hill number were similar to those of the control baboons. Although results concerning this baboon can only be considered as a case report, this similarity may suggest that its epileptic syndrome is not related to a large change in B'max or Kd, at least in occipital and frontal cortices. Our results showed that quantitative estimation by positron emission tomography of some characteristics of benzodiazepine receptors is possible in live baboons and may represent a supplementary tool for investigating further the molecular mechanisms of benzodiazepine receptor function in physiological and physiopathological conditions.

  14. Quantitative volumetric breast density estimation using phase contrast mammography

    NASA Astrophysics Data System (ADS)

    Wang, Zhentian; Hauser, Nik; Kubik-Huch, Rahel A.; D'Isidoro, Fabio; Stampanoni, Marco

    2015-05-01

    Phase contrast mammography using a grating interferometer is an emerging technology for breast imaging. It provides complementary information to the conventional absorption-based methods. Additional diagnostic values could be further obtained by retrieving quantitative information from the three physical signals (absorption, differential phase and small-angle scattering) yielded simultaneously. We report a non-parametric quantitative volumetric breast density estimation method by exploiting the ratio (dubbed the R value) of the absorption signal to the small-angle scattering signal. The R value is used to determine breast composition and the volumetric breast density (VBD) of the whole breast is obtained analytically by deducing the relationship between the R value and the pixel-wise breast density. The proposed method is tested by a phantom study and a group of 27 mastectomy samples. In the clinical evaluation, the estimated VBD values from both cranio-caudal (CC) and anterior-posterior (AP) views are compared with the ACR scores given by radiologists to the pre-surgical mammograms. The results show that the estimated VBD results using the proposed method are consistent with the pre-surgical ACR scores, indicating the effectiveness of this method in breast density estimation. A positive correlation is found between the estimated VBD and the diagnostic ACR score for both the CC view (p=0.033 ) and AP view (p=0.001 ). A linear regression between the results of the CC view and AP view showed a correlation coefficient γ = 0.77, which indicates the robustness of the proposed method and the quantitative character of the additional information obtained with our approach.

  15. Quantitative volumetric breast density estimation using phase contrast mammography.

    PubMed

    Wang, Zhentian; Hauser, Nik; Kubik-Huch, Rahel A; D'Isidoro, Fabio; Stampanoni, Marco

    2015-05-21

    Phase contrast mammography using a grating interferometer is an emerging technology for breast imaging. It provides complementary information to the conventional absorption-based methods. Additional diagnostic values could be further obtained by retrieving quantitative information from the three physical signals (absorption, differential phase and small-angle scattering) yielded simultaneously. We report a non-parametric quantitative volumetric breast density estimation method by exploiting the ratio (dubbed the R value) of the absorption signal to the small-angle scattering signal. The R value is used to determine breast composition and the volumetric breast density (VBD) of the whole breast is obtained analytically by deducing the relationship between the R value and the pixel-wise breast density. The proposed method is tested by a phantom study and a group of 27 mastectomy samples. In the clinical evaluation, the estimated VBD values from both cranio-caudal (CC) and anterior-posterior (AP) views are compared with the ACR scores given by radiologists to the pre-surgical mammograms. The results show that the estimated VBD results using the proposed method are consistent with the pre-surgical ACR scores, indicating the effectiveness of this method in breast density estimation. A positive correlation is found between the estimated VBD and the diagnostic ACR score for both the CC view (p = 0.033) and AP view (p = 0.001). A linear regression between the results of the CC view and AP view showed a correlation coefficient γ = 0.77, which indicates the robustness of the proposed method and the quantitative character of the additional information obtained with our approach.

  16. Volumetric characterization of human patellar cartilage matrix on phase contrast x-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Abidin, Anas Z.; Nagarajan, Mahesh B.; Checefsky, Walter A.; Coan, Paola; Diemoz, Paul C.; Hobbs, Susan K.; Huber, Markus B.; Wismüller, Axel

    2015-03-01

    Phase contrast X-ray computed tomography (PCI-CT) has recently emerged as a novel imaging technique that allows visualization of cartilage soft tissue, subsequent examination of chondrocyte patterns, and their correlation to osteoarthritis. Previous studies have shown that 2D texture features are effective at distinguishing between healthy and osteoarthritic regions of interest annotated in the radial zone of cartilage matrix on PCI-CT images. In this study, we further extend the texture analysis to 3D and investigate the ability of volumetric texture features at characterizing chondrocyte patterns in the cartilage matrix for purposes of classification. Here, we extracted volumetric texture features derived from Minkowski Functionals and gray-level co-occurrence matrices (GLCM) from 496 volumes of interest (VOI) annotated on PCI-CT images of human patellar cartilage specimens. The extracted features were then used in a machine-learning task involving support vector regression to classify ROIs as healthy or osteoarthritic. Classification performance was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). The best classification performance was observed with GLCM features correlation (AUC = 0.83 +/- 0.06) and homogeneity (AUC = 0.82 +/- 0.07), which significantly outperformed all Minkowski Functionals (p < 0.05). These results suggest that such quantitative analysis of chondrocyte patterns in human patellar cartilage matrix involving GLCM-derived statistical features can distinguish between healthy and osteoarthritic tissue with high accuracy.

  17. X-ray micro-beam techniques and phase contrast tomography applied to biomaterials

    NASA Astrophysics Data System (ADS)

    Fratini, Michela; Campi, Gaetano; Bukreeva, Inna; Pelliccia, Daniele; Burghammer, Manfred; Tromba, Giuliana; Cancedda, Ranieri; Mastrogiacomo, Maddalena; Cedola, Alessia

    2015-12-01

    A deeper comprehension of the biomineralization (BM) process is at the basis of tissue engineering and regenerative medicine developments. Several in-vivo and in-vitro studies were dedicated to this purpose via the application of 2D and 3D diagnostic techniques. Here, we develop a new methodology, based on different complementary experimental techniques (X-ray phase contrast tomography, micro-X-ray diffraction and micro-X-ray fluorescence scanning technique) coupled to new analytical tools. A qualitative and quantitative structural investigation, from the atomic to the micrometric length scale, is obtained for engineered bone tissues. The high spatial resolution achieved by X-ray scanning techniques allows us to monitor the bone formation at the first-formed mineral deposit at the organic-mineral interface within a porous scaffold. This work aims at providing a full comprehension of the morphology and functionality of the biomineralization process, which is of key importance for developing new drugs for preventing and healing bone diseases and for the development of bio-inspired materials.

  18. SU-D-210-03: Limited-View Multi-Source Quantitative Photoacoustic Tomography

    SciTech Connect

    Feng, J; Gao, H

    2015-06-15

    Purpose: This work is to investigate a novel limited-view multi-source acquisition scheme for the direct and simultaneous reconstruction of optical coefficients in quantitative photoacoustic tomography (QPAT), which has potentially improved signal-to-noise ratio and reduced data acquisition time. Methods: Conventional QPAT is often considered in two steps: first to reconstruct the initial acoustic pressure from the full-view ultrasonic data after each optical illumination, and then to quantitatively reconstruct optical coefficients (e.g., absorption and scattering coefficients) from the initial acoustic pressure, using multi-source or multi-wavelength scheme.Based on a novel limited-view multi-source scheme here, We have to consider the direct reconstruction of optical coefficients from the ultrasonic data, since the initial acoustic pressure can no longer be reconstructed as an intermediate variable due to the incomplete acoustic data in the proposed limited-view scheme. In this work, based on a coupled photo-acoustic forward model combining diffusion approximation and wave equation, we develop a limited-memory Quasi-Newton method (LBFGS) for image reconstruction that utilizes the adjoint forward problem for fast computation of gradients. Furthermore, the tensor framelet sparsity is utilized to improve the image reconstruction which is solved by Alternative Direction Method of Multipliers (ADMM). Results: The simulation was performed on a modified Shepp-Logan phantom to validate the feasibility of the proposed limited-view scheme and its corresponding image reconstruction algorithms. Conclusion: A limited-view multi-source QPAT scheme is proposed, i.e., the partial-view acoustic data acquisition accompanying each optical illumination, and then the simultaneous rotations of both optical sources and ultrasonic detectors for next optical illumination. Moreover, LBFGS and ADMM algorithms are developed for the direct reconstruction of optical coefficients from the

  19. Quantitative assessment of the stent/scaffold strut embedment analysis by optical coherence tomography.

    PubMed

    Sotomi, Yohei; Tateishi, Hiroki; Suwannasom, Pannipa; Dijkstra, Jouke; Eggermont, Jeroen; Liu, Shengnan; Tenekecioglu, Erhan; Zheng, Yaping; Abdelghani, Mohammad; Cavalcante, Rafael; de Winter, Robbert J; Wykrzykowska, Joanna J; Onuma, Yoshinobu; Serruys, Patrick W; Kimura, Takeshi

    2016-06-01

    The degree of stent/scaffold embedment could be a surrogate parameter of the vessel wall-stent/scaffold interaction and could have biological implications in the vascular response. We have developed a new specific software for the quantitative evaluation of embedment of struts by optical coherence tomography (OCT). In the present study, we described the algorithm of the embedment analysis and its reproducibility. The degree of embedment was evaluated as the ratio of the embedded part versus the whole strut height and subdivided into quartiles. The agreement and the inter- and intra-observer reproducibility were evaluated using the kappa and the interclass correlation coefficient (ICC). A total of 4 pullbacks of OCT images in 4 randomly selected coronary lesions with 3.0 × 18 mm devices [2 lesions with Absorb BVS and 2 lesions with XIENCE (both from Abbott Vascular, Santa Clara, CA, USA)] from Absorb Japan trial were evaluated by two investigators with QCU-CMS software version 4.69 (Leiden University Medical Center, Leiden, The Netherlands). Finally, 1481 polymeric struts in 174 cross-sections and 1415 metallic struts in 161 cross-sections were analyzed. Inter- and intra-observer reproducibility of quantitative measurements of embedment ratio and categorical assessment of embedment in Absorb BVS and XIENCE had excellent agreement with ICC ranging from 0.958 to 0.999 and kappa ranging from 0.850 to 0.980. The newly developed embedment software showed excellent reproducibility. Computer-assisted embedment analysis could be a feasible tool to assess the strut penetration into the vessel wall that could be a surrogate of acute injury caused by implantation of devices. PMID:26898315

  20. Simulation-based evaluation of the resolution and quantitative accuracy of temperature-modulated fluorescence tomography

    PubMed Central

    Lin, Yuting; Nouizi, Farouk; Kwong, Tiffany C.; Gulsen, Gultekin

    2016-01-01

    Conventional fluorescence tomography (FT) can recover the distribution of fluorescent agents within a highly scattering medium. However, poor spatial resolution remains its foremost limitation. Previously, we introduced a new fluorescence imaging technique termed “temperature-modulated fluorescence tomography” (TM-FT), which provides high-resolution images of fluorophore distribution. TM-FT is a multimodality technique that combines fluorescence imaging with focused ultrasound to locate thermo-sensitive fluorescence probes using a priori spatial information to drastically improve the resolution of conventional FT. In this paper, we present an extensive simulation study to evaluate the performance of the TM-FT technique on complex phantoms with multiple fluorescent targets of various sizes located at different depths. In addition, the performance of the TM-FT is tested in the presence of background fluorescence. The results obtained using our new method are systematically compared with those obtained with the conventional FT. Overall, TM-FT provides higher resolution and superior quantitative accuracy, making it an ideal candidate for in vivo preclinical and clinical imaging. For example, a 4 mm diameter inclusion positioned in the middle of a synthetic slab geometry phantom (D:40 mm × W :100 mm) is recovered as an elongated object in the conventional FT (x = 4.5 mm; y = 10.4 mm), while TM-FT recovers it successfully in both directions (x = 3.8 mm; y = 4.6 mm). As a result, the quantitative accuracy of the TM-FT is superior because it recovers the concentration of the agent with a 22% error, which is in contrast with the 83% error of the conventional FT. PMID:26368884

  1. Quantitative evaluation of knee subchondral bone mineral density using cone beam computed tomography.

    PubMed

    Turunen, Mikael J; Töyräs, Juha; Kokkonen, Harri T; Jurvelin, Jukka S

    2015-10-01

    Contrast agent enhanced cone beam computed tomography (CE-CBCT), a technique capable of high-resolution in vivo imaging with small radiation dose, has been applied successfully for clinical diagnostics of cartilage degeneration, i.e., osteoarthritis (OA). As an X-ray technique, CE-CBCT may also detect changes in mineral density of subchondral bone (volumetric bone mineral density, vBMD), known to be characteristic for OA. However, its feasibility for density measurements is not clear due to limited signal-to-noise ratio and contrast of CBCT images. In the present study, we created clinically applicable hydroxyapatite phantoms and determined vBMDs of cortical bone, trabecular bone, subchondral trabecular bone and subchondral plate of 10 cadaver (ex vivo) and 10 volunteer (in vivo) distal femora using a clinical CBCT scanner, and for reference, also using a conventional CT scanner. Our results indicated strong linear correlations between the vBMD values measured with the CT and CBCT scanners , however, absolute vBMD values were dependent on the scanner in use. Further, the differences between the vBMDs of cortical bone, trabecular bone and subchondral bone were similar and independent of the scanner. The present results indicate that vBMD values might not be directly comparable between different instruments. However, based on our present and previous results, we propose that, for OA diagnostics, clinical CBCT enables not only quantitative analysis of articular cartilage but also subchondral bone vBMD. Quantitative information on both cartilage and subchondral bone could be beneficial in OA diagnostics.

  2. Real-time quantitative phase imaging for cell studies

    NASA Astrophysics Data System (ADS)

    Pham, Hoa Vinh

    Most biological cells are not clearly visible with a bright field microscope. Several methods have been developed to improve contrast in cell imaging, including use of exogenous contrast agents such as fluorescence microscopy, as well as utilizing properties of light-specimen interaction for optics design, to reveal the endogenous contrast, such as phase contrast microscopy (PCM) and differential interference contrast (DIC) microscopy. Although PCM and DIC methods significantly improve the image contrast without the need for staining agents, they only provide qualitative information about the phase change induced by the cells as light passes through them. Quantitative phase imaging (QPI) has recently emerged as an effective imaging tool which provides not only better image contrast but also cell-induced phase shifts in the optical pathlength, thus allowing nanometer-scale measurements of structures and dynamics of the cells. Other important aspects of an imaging system are its imaging speed and throughput. High-throughput, high-speed, real-time quantitative phase imaging with high spatial and temporal sensitivity is highly desirable in many applications including applied physics and biomedicine. In this dissertation, to address this need, I discuss the development of such an imaging system that includes the white light diffraction phase microscopy (wDPM), a new optical imaging method, and image reconstruction/analysis algorithms using graphics processing units (GPUs). wDPM can measure optical pathlength changes at nanometer scale both spatially and temporally with single-shot image acquisition, enabling very fast imaging. I also exploit the broadband spectrum of white light used as the light source in wDPM to develop a system called spectroscopic diffraction phase microscopy (sDPM). This sDPM system allows QPI measurements at several wavelengths, which solves the problem of thickness and refractive index coupling in the phase shifts induced by the cell, and which

  3. Peripheral quantitative computed tomography in children and adolescents: the 2007 ISCD Pediatric Official Positions.

    PubMed

    Zemel, Babette; Bass, Shona; Binkley, Teresa; Ducher, Gaele; Macdonald, Heather; McKay, Heather; Moyer-Mileur, Laurie; Shepherd, John; Specker, Bonny; Ward, Kate; Hans, Didier

    2008-01-01

    Peripheral quantitative computed tomography (pQCT) has mainly been used as a research tool in children. To evaluate the clinical utility of pQCT and formulate recommendations for its use in children, the International Society of Clinical Densitometry (ISCD) convened a task force to review the literature and propose areas of consensus and future research. The types of pQCT technology available, the clinical application of pQCT for bone health assessment in children, the important elements to be included in a pQCT report, and quality control monitoring techniques were evaluated. The review revealed a lack of standardization of pQCT techniques, and a paucity of data regarding differences between pQCT manufacturers, models and software versions and their impact in pediatric assessment. Measurement sites varied across studies. Adequate reference data, a critical element for interpretation of pQCT results, were entirely lacking, although some comparative data on healthy children were available. The elements of the pQCT clinical report and quality control procedures are similar to those recommended for dual-energy X-ray absorptiometry. Future research is needed to establish evidence-based criteria for the selection of the measurement site, scan acquisition and analysis parameters, and outcome measures. Reference data that sufficiently characterize the normal range of variability in the population also need to be established.

  4. Assessing vertebral fracture risk on volumetric quantitative computed tomography by geometric characterization of trabecular bone structure

    NASA Astrophysics Data System (ADS)

    Checefsky, Walter A.; Abidin, Anas Z.; Nagarajan, Mahesh B.; Bauer, Jan S.; Baum, Thomas; Wismüller, Axel

    2016-03-01

    The current clinical standard for measuring Bone Mineral Density (BMD) is dual X-ray absorptiometry, however more recently BMD derived from volumetric quantitative computed tomography has been shown to demonstrate a high association with spinal fracture susceptibility. In this study, we propose a method of fracture risk assessment using structural properties of trabecular bone in spinal vertebrae. Experimental data was acquired via axial multi-detector CT (MDCT) from 12 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. Common image processing methods were used to annotate the trabecular compartment in the vertebral slices creating a circular region of interest (ROI) that excluded cortical bone for each slice. The pixels inside the ROI were converted to values indicative of BMD. High dimensional geometrical features were derived using the scaling index method (SIM) at different radii and scaling factors (SF). The mean BMD values within the ROI were then extracted and used in conjunction with a support vector machine to predict the failure load of the specimens. Prediction performance was measured using the root-mean-square error (RMSE) metric and determined that SIM combined with mean BMD features (RMSE = 0.82 +/- 0.37) outperformed MDCT-measured mean BMD (RMSE = 1.11 +/- 0.33) (p < 10-4). These results demonstrate that biomechanical strength prediction in vertebrae can be significantly improved through the use of SIM-derived texture features from trabecular bone.

  5. Physical bone changes in carragheenin-induced arthritis evaluated by quantitative computed tomography.

    PubMed

    Søballe, K; Pedersen, C M; Odgaard, A; Juhl, G I; Hansen, E S; Rasmussen, H B; Hvid, I; Bünger, C

    1991-01-01

    Repeated non-invasive measurements were performed in dogs of trabecular bone density (TBD), low density bone area (LDBA), and high density bone area (HDBA) in chronic arthritis using quantitative computed tomography (QCT). Unilateral chronic arthritis of the knee had been induced by weekly instillation of 2 ml carragheenin into the right knee joint for 12 weeks with the left knee serving as a control. CT scanning of the distal femoral condyles was performed in 12 mature dogs with chronic arthritis. Another 6 dogs underwent a longitudinal CT study starting immediately prior to induction of arthritis. During induction of arthritis TBD decreased (P less than 0.01), LDBA increased (P less than 0.05) and HDBA decreased (P less than 0.01) in the arthritic bone. Opposite changes were found on the control side, i.e. TBD increased (P less than 0.01), LDBA decreased (P less than 0.01) and HDBA increased (P less than 0.01). The chronic arthropathic bone showed 20% lower TBD (P less than 0.0001), greater LDBA (P less than 0.0001) and lower HDBA (P less than 0.0001) as compared with the control bone. Reproducibility tests of TBD showed a coefficient of variation of 0.8%. Indentation tests and histomorphometric analyses confirmed the bone density changes as measured by CT. PMID:1896875

  6. Quantitative optical coherence tomography of skin lesions induced by different ultraviolet B sources

    NASA Astrophysics Data System (ADS)

    Liu, Zhiming; Guo, Zhouyi; Zhuang, Zhengfei; Zhai, Juan; Xiong, Honglian; Zeng, Changchun

    2010-10-01

    Ultraviolet B (UVB) has been widely used in dermatological phototherapy. Narrowband UVB (NB-UVB), with a peak at 311 nm, is considered to be more effective than broadband UVB (BB-UVB). However, the safety of NB-UVB is controversial. In this study, we first introduced optical coherence tomography (OCT), a novel, non-invasive in vivo imaging technology, to assess the effect of NB-UVB and BB-UVB on skin. Balb/c mice dorsal skin was exposed with increasing UVB doses (1MED, 3MEDs and 5MEDs), and then OCT images of the tissues were obtained by an OCT system with 1310 nm central wavelength. Quantitative parameters (skin thickness, disruption of the entrance signal and correlation coefficient) were extracted from the OCT images. The data indicated that NB-UVB-induced skin lesions were similar to that of BB-UVB at 1MED or 3MEDs UVB. However, the skin tissues exposed with 5MEDs NB-UVB suffered from more lesions than BB-UVB. Furthermore, the persistence of skin inflammation in 3MEDs NB-UVB-induced skin tissues was much longer than that of BB-UVB (P = 0.004). In conclusion, optimized treatment time and frequency as well as close clinical monitoring should be undertaken to reduce the latent risk of NB-UVB phototherapy.

  7. Quantitative optical coherence tomography angiography of vascular abnormalities in the living human eye

    PubMed Central

    Jia, Yali; Bailey, Steven T.; Hwang, Thomas S.; McClintic, Scott M.; Pennesi, Mark E.; Flaxel, Christina J.; Lauer, Andreas K.; Wilson, David J.; Hornegger, Joachim; Fujimoto, James G.; Huang, David

    2015-01-01

    Retinal vascular diseases are important causes of vision loss. A detailed evaluation of the vascular abnormalities facilitates diagnosis and treatment in these diseases. Optical coherence tomography (OCT) angiography using the highly efficient split-spectrum amplitude decorrelation angiography algorithm offers an alternative to conventional dye-based retinal angiography. OCT angiography has several advantages, including 3D visualization of retinal and choroidal circulations (including the choriocapillaris) and avoidance of dye injection-related complications. Results from six illustrative cases are reported. In diabetic retinopathy, OCT angiography can detect neovascularization and quantify ischemia. In age-related macular degeneration, choroidal neovascularization can be observed without the obscuration of details caused by dye leakage in conventional angiography. Choriocapillaris dysfunction can be detected in the nonneovascular form of the disease, furthering our understanding of pathogenesis. In choroideremia, OCT's ability to show choroidal and retinal vascular dysfunction separately may be valuable in predicting progression and assessing treatment response. OCT angiography shows promise as a noninvasive alternative to dye-based angiography for highly detailed, in vivo, 3D, quantitative evaluation of retinal vascular abnormalities. PMID:25897021

  8. Quantitative assessment of cervical vertebral maturation using cone beam computed tomography in Korean girls.

    PubMed

    Byun, Bo-Ram; Kim, Yong-Il; Yamaguchi, Tetsutaro; Maki, Koutaro; Son, Woo-Sung

    2015-01-01

    This study was aimed to examine the correlation between skeletal maturation status and parameters from the odontoid process/body of the second vertebra and the bodies of third and fourth cervical vertebrae and simultaneously build multiple regression models to be able to estimate skeletal maturation status in Korean girls. Hand-wrist radiographs and cone beam computed tomography (CBCT) images were obtained from 74 Korean girls (6-18 years of age). CBCT-generated cervical vertebral maturation (CVM) was used to demarcate the odontoid process and the body of the second cervical vertebra, based on the dentocentral synchondrosis. Correlation coefficient analysis and multiple linear regression analysis were used for each parameter of the cervical vertebrae (P < 0.05). Forty-seven of 64 parameters from CBCT-generated CVM (independent variables) exhibited statistically significant correlations (P < 0.05). The multiple regression model with the greatest R (2) had six parameters (PH2/W2, UW2/W2, (OH+AH2)/LW2, UW3/LW3, D3, and H4/W4) as independent variables with a variance inflation factor (VIF) of <2. CBCT-generated CVM was able to include parameters from the second cervical vertebral body and odontoid process, respectively, for the multiple regression models. This suggests that quantitative analysis might be used to estimate skeletal maturation status.

  9. Noninvasive determination of bone stiffness for distraction osteogenesis by quantitative computed tomography scans.

    PubMed

    Harp, J H; Aronson, J; Hollis, M

    1994-04-01

    Apparent density of canine tibial specimens was correlated to measured quantitative computed tomography (QCT) numbers, and a conversion equation was derived. Finite element analysis models of canine tibiae were constructed using spatial coordinates of converted QCT data. Two QCT-derived finite elemental analysis models were constructed for a pair of matched tibiae: one lengthened 15% by distraction osteogenesis and one contralateral control. Two equations relating the modulus of elasticity to apparent density were used. These models were then verified mechanically by measuring strains of the two specimens under applied load. Equation I correlated best with measured strains in the less-dense regenerate bone of the distracted tibia (R2 = 0.914, p = 0.0028, n = 6); Equation II performed best in the denser control tibia (R2 = 0.820, p = 0.0129, n = 6). These results demonstrate that the stiffness of tubular bones, including cortical and heterogenous cancellous structure, can be accurately predicted by a noninvasive QCT scan.

  10. Noninvasive Quantitative Evaluation of the Dentin Layer during Dental Procedures Using Optical Coherence Tomography

    PubMed Central

    Sinescu, Cosmin; Negrutiu, Meda Lavinia; Bradu, Adrian; Duma, Virgil-Florin; Podoleanu, Adrian Gh.

    2015-01-01

    A routine cavity preparation of a tooth may lead to opening the pulp chamber. The present study evaluates quantitatively, in real time, for the first time to the best of our knowledge, the drilled cavities during dental procedures. An established noninvasive imaging technique, Optical Coherence Tomography (OCT), is used. The main scope is to prevent accidental openings of the dental pulp chamber. Six teeth with dental cavities have been used in this ex vivo study. The real time assessment of the distances between the bottom of the drilled cavities and the top of the pulp chamber was performed using an own assembled OCT system. The evaluation of the remaining dentin thickness (RDT) allowed for the positioning of the drilling tools in the cavities in relation to the pulp horns. Estimations of the safe and of the critical RDT were made; for the latter, the opening of the pulp chamber becomes unavoidable. Also, by following the fractures that can occur when the extent of the decay is too large, the dentist can decide upon the right therapy to follow, endodontic or conventional filling. The study demonstrates the usefulness of OCT imaging in guiding such evaluations during dental procedures. PMID:26078779

  11. Micro/Nano-Computed Tomography Technology for Quantitative Dynamic, Multi-scale Imaging of Morphogenesis

    PubMed Central

    Gregg, Chelsea L.; Recknagel, Andrew K.; Butcher, Jonathan T.

    2015-01-01

    Tissue morphogenesis and embryonic development are dynamic events challenging to quantify, especially considering the intricate events that happen simultaneously in different locations and time. Micro-, and more recently nano-computed tomography (micro/nanoCT), has been used for the past 15 years to characterize large 3D fields of tortuous geometries at high spatial resolution. We and others have advanced micro/nanoCT imaging strategies for quantifying tissue and organ level fate changes throughout morphogenesis. Exogenous soft tissue contrast media enables visualization of vascular lumens and tissues via extravasation. Furthermore, the emergence of antigen specific tissue contrast enables direct quantitative visualization of protein and mRNA expression. Micro-CT X-ray doses appear to be non-embryotoxic, enabling longitudinal imaging studies in live embryos. In this paper we present established soft tissue contrast protocols for obtaining high quality micro/nanoCT images and the image processing techniques useful for quantifying anatomical and physiological information from the datasets. PMID:25245686

  12. Light fluence correction for quantitative determination of tissue absorption coefficient using multi-spectral optoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Brochu, Frederic M.; Joseph, James; Tomaszewski, Michal; Bohndiek, Sarah E.

    2015-07-01

    MultiSpectral Optoacoustic Tomography (MSOT) is a fast developing imaging modality, combining the high resolution and penetration depth of ultrasound with the excellent contrast from optical imaging of tissue. Absorption and scattering of the near infrared excitation light modulates the spectral profile of light as it propagates deep into biological tissue, meaning the images obtained provide only qualitative insight into the distribution of tissue chromophores. The goal of this work is to accurately recover the spectral profile of excitation light by modelling light fluence in the data reconstruction, to enable quantitative imaging. We worked with a commercial small animal MSOT scanner and developed our light fluence correction for its' cylindrical geometry. Optoacoustic image reconstruction pinpoints the sources of acoustic waves detected by the transducers and returns the initial pressure amplitude at these points. This pressure is the product of the dimensionless Grüneisen parameter, the absorption coefficient and the light fluence. Under the condition of constant Grüneisen parameter and well modelled light fluence, there is a linear relationship between the initial pressure amplitude measured in the optoacoustic image and the absorption coefficient. We were able to reproduce this linear relationship in different physical regions of an agarose gel phantom containing targets of known optical absorption coefficient, demonstrating that our light fluence model was working. We also demonstrate promising results of light fluence correction effects on in vivo data.

  13. Micro/nano-computed tomography technology for quantitative dynamic, multi-scale imaging of morphogenesis.

    PubMed

    Gregg, Chelsea L; Recknagel, Andrew K; Butcher, Jonathan T

    2015-01-01

    Tissue morphogenesis and embryonic development are dynamic events challenging to quantify, especially considering the intricate events that happen simultaneously in different locations and time. Micro- and more recently nano-computed tomography (micro/nanoCT) has been used for the past 15 years to characterize large 3D fields of tortuous geometries at high spatial resolution. We and others have advanced micro/nanoCT imaging strategies for quantifying tissue- and organ-level fate changes throughout morphogenesis. Exogenous soft tissue contrast media enables visualization of vascular lumens and tissues via extravasation. Furthermore, the emergence of antigen-specific tissue contrast enables direct quantitative visualization of protein and mRNA expression. Micro-CT X-ray doses appear to be non-embryotoxic, enabling longitudinal imaging studies in live embryos. In this chapter we present established soft tissue contrast protocols for obtaining high-quality micro/nanoCT images and the image processing techniques useful for quantifying anatomical and physiological information from the data sets.

  14. Quantitative experimental monitoring of molecular diffusion in clay with positron emission tomography

    NASA Astrophysics Data System (ADS)

    Kulenkampff, Johannes; Zakhnini, Abdelhamid; Gründig, Marion; Lippmann-Pipke, Johanna

    2016-08-01

    Clay plays a prominent role as barrier material in the geosphere. The small particle sizes cause extremely small pore sizes and induce low permeability and high sorption capacity. Transport of dissolved species by molecular diffusion, driven only by a concentration gradient, is less sensitive to the pore size. Heterogeneous structures on the centimetre scale could cause heterogeneous effects, like preferential transport zones, which are difficult to assess. Laboratory measurements with diffusion cells yield limited information on heterogeneity, and pore space imaging methods have to consider scale effects. We established positron emission tomography (PET), applying a high-resolution PET scanner as a spatially resolved quantitative method for direct laboratory observation of the molecular diffusion process of a PET tracer on the prominent scale of 1-100 mm. Although PET is rather insensitive to bulk effects, quantification required significant improvements of the image reconstruction procedure with respect to Compton scatter and attenuation. The experiments were conducted with 22Na and 124I over periods of 100 and 25 days, respectively. From the images we derived trustable anisotropic diffusion coefficients and, in addition, we identified indications of preferential transport zones. We thus demonstrated the unique potential of the PET imaging modality for geoscientific process monitoring under conditions where other methods fail, taking advantage of the extremely high detection sensitivity that is typical of radiotracer applications.

  15. The Effect of Quantitative Computed Tomography Acquisition Protocols on Bone Mineral Density Estimation.

    PubMed

    Giambini, Hugo; Dragomir-Daescu, Dan; Huddleston, Paul M; Camp, Jon J; An, Kai-Nan; Nassr, Ahmad

    2015-11-01

    Osteoporosis is characterized by bony material loss and decreased bone strength leading to a significant increase in fracture risk. Patient-specific quantitative computed tomography (QCT) finite element (FE) models may be used to predict fracture under physiological loading. Material properties for the FE models used to predict fracture are obtained by converting grayscale values from the CT into volumetric bone mineral density (vBMD) using calibration phantoms. If there are any variations arising from the CT acquisition protocol, vBMD estimation and material property assignment could be affected, thus, affecting fracture risk prediction. We hypothesized that material property assignments may be dependent on scanning and postprocessing settings including voltage, current, and reconstruction kernel, thus potentially having an effect in fracture risk prediction. A rabbit femur and a standard calibration phantom were imaged by QCT using different protocols. Cortical and cancellous regions were segmented, their average Hounsfield unit (HU) values obtained and converted to vBMD. Estimated vBMD for the cortical and cancellous regions were affected by voltage and kernel but not by current. Our study demonstrated that there exists a significant variation in the estimated vBMD values obtained with different scanning acquisitions. In addition, the large noise differences observed utilizing different scanning parameters could have an important negative effect on small subregions containing fewer voxels. PMID:26355694

  16. Imaging and quantifying Brownian motion of micro- and nanoparticles using phase-resolved Doppler variance optical coherence tomography.

    PubMed

    Kim, Chang Soo; Qi, Wenjuan; Zhang, Jun; Kwon, Young Jik; Chen, Zhongping

    2013-03-01

    Different types and sizes of micro- and nanoparticles have been synthesized and developed for numerous applications. It is crucial to characterize the particle sizes. Traditional dynamic light scattering, a predominant method used to characterize particle size, is unable to provide depth resolved information or imaging functions. Doppler variance optical coherence tomography (OCT) measures the spectral bandwidth of the Doppler frequency shift due to the Brownian motion of the particles utilizing the phase-resolved approach and can provide quantitative information about particle size. Spectral bandwidths of Doppler frequency shifts for various sized particles were quantified and were demonstrated to be inversely proportional to the diameter of the particles. The study demonstrates the phase-resolved Doppler variance spectral domain OCT technique has the potential to be used to investigate the properties of particles in highly scattering media. PMID:23515863

  17. Dynamic phase imaging of host cells attacked by Vibrio vulnificus using quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Lee, Seungrag; Yang, Wenzhong; Lee, Ji Yong; Cha, Mi Hye; Kim, Young Ran; Kim, Dug Young

    2010-02-01

    We present the real time quantitative analysis of Vibrio vulnificus-infected host cells using high stability quantitative phase microscopy (HSQPM). It provides the ability to retrieve the phase or optical path length distribution over the cell from a single interferogram image, which has been measured with nanometer path length sensitivity for long periods of time. We have applied HSQPM to study dynamic cell morphologic changes and to quantify noninvasively cell volumes of rat basophilic leukemia RBL-2H3 cells infected with pathogenic bacteria V. vulnificus strains, wild type (MO6-24/O) and RTX toxin mutant (CMM770). During the process of V. vulnificus wild type infection to RBL-2H3 cells, the dynamic changes of quantitative phase images, cell volumes and areas were observed in real time using HSQPM. In contrast, the dramatic changes were not detected in RBL-2H3 cells infected with RTX toxin mutant. The results showed the good correlation between HSQPM analysis and biochemical assays such as lactate dehydrogenase (LDH) assay and β-hexosaminidase release assay. We suggest that HSQPM is useful real time quantitative method to study the dynamic process of host cells infected with pathogen in a noninvasive manner.

  18. Phase Tomography Reconstructed by 3D TIE in Hard X-ray Microscope

    SciTech Connect

    Yin, G.-C.; Chen, F.-R.; Pyun, Ahram; Je, Jung Ho; Hwu, Yeukuang; Liang, Keng S.

    2007-01-19

    X-ray phase tomography and phase imaging are promising ways of investigation on low Z material. A polymer blend of PE/PS sample was used to test the 3D phase retrieval method in the parallel beam illuminated microscope. Because the polymer sample is thick, the phase retardation is quite mixed and the image can not be distinguished when the 2D transport intensity equation (TIE) is applied. In this study, we have provided a different approach for solving the phase in three dimensions for thick sample. Our method involves integration of 3D TIE/Fourier slice theorem for solving thick phase sample. In our experiment, eight sets of de-focal series image data sets were recorded covering the angular range of 0 to 180 degree. Only three set of image cubes were used in 3D TIE equation for solving the phase tomography. The phase contrast of the polymer blend in 3D is obviously enhanced, and the two different groups of polymer blend can be distinguished in the phase tomography.

  19. Quantitative computed tomography measurements of emphysema for diagnosing asthma-chronic obstructive pulmonary disease overlap syndrome

    PubMed Central

    Xie, Mengshuang; Wang, Wei; Dou, Shuang; Cui, Liwei; Xiao, Wei

    2016-01-01

    Background The diagnostic criteria of asthma–COPD overlap syndrome (ACOS) are controversial. Emphysema is characteristic of COPD and usually does not exist in typical asthma patients. Emphysema in patients with asthma suggests the coexistence of COPD. Quantitative computed tomography (CT) allows repeated evaluation of emphysema noninvasively. We investigated the value of quantitative CT measurements of emphysema in the diagnosis of ACOS. Methods This study included 404 participants; 151 asthma patients, 125 COPD patients, and 128 normal control subjects. All the participants underwent pulmonary function tests and a high-resolution CT scan. Emphysema measurements were taken with an Airway Inspector software. The asthma patients were divided into high and low emphysema index (EI) groups based on the percentage of low attenuation areas less than −950 Hounsfield units. The characteristics of asthma patients with high EI were compared with those having low EI or COPD. Results The normal value of percentage of low attenuation areas less than −950 Hounsfield units in Chinese aged >40 years was 2.79%±2.37%. COPD patients indicated more severe emphysema and more upper-zone-predominant distribution of emphysema than asthma patients or controls. Thirty-two (21.2%) of the 151 asthma patients had high EI. Compared with asthma patients with low EI, those with high EI were significantly older, more likely to be male, had more pack-years of smoking, had more upper-zone-predominant distribution of emphysema, and had greater airflow limitation. There were no significant differences in sex ratios, pack-years of smoking, airflow limitation, or emphysema distribution between asthma patients with high EI and COPD patients. A greater number of acute exacerbations were seen in asthma patients with high EI compared with those with low EI or COPD. Conclusion Asthma patients with high EI fulfill the features of ACOS, as described in the Global Initiative for Asthma and Global

  20. Quantitative reflection phase mesoscopy by remote coherence tuning of phase-shift interference patterns

    PubMed Central

    Arbel, Elad; Bilenca, Alberto

    2015-01-01

    Conventional low-magnification phase-contrast microscopy is an invaluable, yet a qualitative, imaging tool for the interrogation of transparent objects over a mesoscopic millimeter-scale field-of-view in physical and biological settings. Here, we demonstrate that introducing a compact, unbalanced phase-shifting Michelson interferometer into a standard reflected brightfield microscope equipped with low-power infinity-corrected objectives and white light illumination forms a phase mesoscope that retrieves remotely and quantitatively the reflection phase distribution of thin, transparent, and weakly scattering samples with high temporal (1.38 nm) and spatial (0.87 nm) axial-displacement sensitivity and micrometer lateral resolution (2.3 μm) across a mesoscopic field-of-view (2.25 × 1.19 mm2). Using the system, we evaluate the etch-depth uniformity of a large-area nanometer-thick glass grating and show quantitative mesoscopic maps of the optical thickness of human cancer cells without any area scanning. Furthermore, we provide proof-of-principle of the utility of the system for the quantitative monitoring of fluid dynamics within a wide region. PMID:26216719

  1. Enhanced joint spectral and time domain optical coherence tomography for quantitative flow velocity measurement

    NASA Astrophysics Data System (ADS)

    Walther, Julia; Koch, Edmund

    2011-06-01

    Recently, a new method called joint spectral and time domain optical coherence tomography (STdOCT) for flow velocity measurement in spectral domain OCT (SD OCT) was presented. This method analyzes the detected timeresolved interference fringe spectra by using a two-dimensional fast Fourier transformation (2D FFT) to determine directly the Doppler frequency shift instead of calculating the phase difference at each depth position of adjacent A-scans. There, it was found that STdOCT is more robust for measurements with low signal to noise ratio than the classic phase-resolved Doppler OCT (DOCT) making it attractive first for imaging fast flow velocities at which a strong Doppler angle dependent signal damping occurs due to interference fringe washout and second for investigating large blood vessels with a big diameter and a highly damped signal of blood with increasing depth due to strong scattering and absorption in the near-infrared wavelength range. In the present study, we would like to introduce an enhanced algorithm for STdOCT permitting a more precise flow velocity measurement in comparison to the conventional STdOCT. The new method determines the amplitude of the broadened Doppler frequency shift by calculating the center of gravity via the complex analytical signal as a result of the second FFT instead of detecting the maximum intensity signal. Furthermore, the comparison with phase-resolved DOCT was done experimentally by using a flow phantom consisting of a 1% Intralipid emulsion and a 320 μm glass capillary. As a result, the enhanced STdOCT and DOCT processed data are completely equivalent.

  2. Integration of Quantitative Positron Emission Tomography Absolute Myocardial Blood Flow Measurements in the Clinical Management of Coronary Artery Disease.

    PubMed

    Gewirtz, Henry; Dilsizian, Vasken

    2016-05-31

    In the >40 years since planar myocardial imaging with(43)K-potassium was introduced into clinical research and management of patients with coronary artery disease (CAD), diagnosis and treatment have undergone profound scientific and technological changes. One such innovation is the current state-of-the-art hardware and software for positron emission tomography myocardial perfusion imaging, which has advanced it from a strictly research-oriented modality to a clinically valuable tool. This review traces the evolving role of quantitative positron emission tomography measurements of myocardial blood flow in the evaluation and management of patients with CAD. It presents methodology, currently or soon to be available, that offers a paradigm shift in CAD management. Heretofore, radionuclide myocardial perfusion imaging has been primarily qualitative or at best semiquantitative in nature, assessing regional perfusion in relative terms. Thus, unlike so many facets of modern cardiovascular practice and CAD management, which depend, for example, on absolute values of key parameters such as arterial and left ventricular pressures, serum lipoprotein, and other biomarker levels, the absolute levels of rest and maximal myocardial blood flow have yet to be incorporated into routine clinical practice even in most positron emission tomography centers where the potential to do so exists. Accordingly, this review focuses on potential value added for improving clinical CAD practice by measuring the absolute level of rest and maximal myocardial blood flow. Physiological principles and imaging fundamentals necessary to understand how positron emission tomography makes robust, quantitative measurements of myocardial blood flow possible are highlighted.

  3. Emission Computed Tomography: A New Technique for the Quantitative Physiologic Study of Brain and Heart in Vivo

    DOE R&D Accomplishments Database

    Phelps, M. E.; Hoffman, E. J.; Huang, S. C.; Schelbert, H. R.; Kuhl, D. E.

    1978-01-01

    Emission computed tomography can provide a quantitative in vivo measurement of regional tissue radionuclide tracer concentrations. This facility when combined with physiologic models and radioactively labeled physiologic tracers that behave in a predictable manner allow measurement of a wide variety of physiologic variables. This integrated technique has been referred to as Physiologic Tomography (PT). PT requires labeled compounds which trace physiologic processes in a known and predictable manner, and physiologic models which are appropriately formulated and validated to derive physiologic variables from ECT data. In order to effectively achieve this goal, PT requires an ECT system that is capable of performing truly quantitative or analytical measurements of tissue tracer concentrations and which has been well characterized in terms of spatial resolution, sensitivity and signal to noise ratios in the tomographic image. This paper illustrates the capabilities of emission computed tomography and provides examples of physiologic tomography for the regional measurement of cerebral and myocardial metabolic rate for glucose, regional measurement of cerebral blood volume, gated cardiac blood pools and capillary perfusion in brain and heart. Studies on patients with stroke and myocardial ischemia are also presented.

  4. Integration of Quantitative Positron Emission Tomography Absolute Myocardial Blood Flow Measurements in the Clinical Management of Coronary Artery Disease.

    PubMed

    Gewirtz, Henry; Dilsizian, Vasken

    2016-05-31

    In the >40 years since planar myocardial imaging with(43)K-potassium was introduced into clinical research and management of patients with coronary artery disease (CAD), diagnosis and treatment have undergone profound scientific and technological changes. One such innovation is the current state-of-the-art hardware and software for positron emission tomography myocardial perfusion imaging, which has advanced it from a strictly research-oriented modality to a clinically valuable tool. This review traces the evolving role of quantitative positron emission tomography measurements of myocardial blood flow in the evaluation and management of patients with CAD. It presents methodology, currently or soon to be available, that offers a paradigm shift in CAD management. Heretofore, radionuclide myocardial perfusion imaging has been primarily qualitative or at best semiquantitative in nature, assessing regional perfusion in relative terms. Thus, unlike so many facets of modern cardiovascular practice and CAD management, which depend, for example, on absolute values of key parameters such as arterial and left ventricular pressures, serum lipoprotein, and other biomarker levels, the absolute levels of rest and maximal myocardial blood flow have yet to be incorporated into routine clinical practice even in most positron emission tomography centers where the potential to do so exists. Accordingly, this review focuses on potential value added for improving clinical CAD practice by measuring the absolute level of rest and maximal myocardial blood flow. Physiological principles and imaging fundamentals necessary to understand how positron emission tomography makes robust, quantitative measurements of myocardial blood flow possible are highlighted. PMID:27245647

  5. Visualisation by high resolution synchrotron X-ray phase contrast micro-tomography of gas films on submerged superhydrophobic leaves.

    PubMed

    Lauridsen, Torsten; Glavina, Kyriaki; Colmer, Timothy David; Winkel, Anders; Irvine, Sarah; Lefmann, Kim; Feidenhans'l, Robert; Pedersen, Ole

    2014-10-01

    Floods can completely submerge terrestrial plants but some wetland species can sustain O2 and CO2 exchange with the environment via gas films forming on superhydrophobic leaf surfaces. We used high resolution synchrotron X-ray phase contrast micro-tomography in a novel approach to visualise gas films on submerged leaves of common cordgrass (Spartina anglica). 3D tomograms enabled a hitherto unmatched level of detail regarding the micro-topography of leaf gas films. Gas films formed only on the superhydrophobic adaxial leaf side (water droplet contact angle, Φ=162°) but not on the abaxial side (Φ=135°). The adaxial side of the leaves of common cordgrass is plicate with a longitudinal system of parallel grooves and ridges and the vast majority of the gas film volume was found in large ∼180μm deep elongated triangular volumes in the grooves and these volumes were connected to each neighbouring groove via a fine network of gas tubules (∼1.7μm diameter) across the ridges. In addition to the gas film retained on the leaf exterior, the X-ray phase contrast micro-tomography also successfully distinguished gas spaces internally in the leaf tissues, and the tissue porosity (gas volume per unit tissue volume) ranged from 6.3% to 20.3% in tip and base leaf segments, respectively. We conclude that X-ray phase contrast micro-tomography is a powerful tool to obtain quantitative data of exterior gas features on biological samples because of the significant difference in electron density between air, biological tissues and water. PMID:25175398

  6. Quantification of Lower Leg Arterial Calcifications by High-Resolution Peripheral Quantitative Computed Tomography

    PubMed Central

    Patsch, Janina M.; Zulliger, Martin A.; Vilayphou, Nicolas; Samelson, Elizabeth J.; Cejka, Daniel; Diarra, Danielle; Berzaczy, Gundula; Burghardt, Andrew J.; Link, Thomas M.; Weber, Michael; Loewe, Christian

    2014-01-01

    Vascular calcifications and bone health seem to be etiologically linked via common risk factors such as aging and subclinical chronic inflammation. Epidemiologic studies have shown significant associations between low bone mineral density (BMD), fragility fractures and calcifications of the coronary arteries and the abdominal aorta. In the last decade, high-resolution peripheral quantitative computed tomography (HR-pQCT) has emerged as in-vivo research tool for the assessment of peripheral bone geometry, density, and microarchitecture. Although vascular calcifications are frequently observed as incidental findings in HR-pQCT scans, they have not yet been incorporated into quantitative HR-pQCT analyses. We developed a semi-automated algorithm to quantify lower leg arterial calcifications (LLAC), captured by HR-pQCT. The objective of our study was to determine validity and reliability of the LLAC measure. HR-pQCT scans were downscaled to a voxel size of 250 µm. After subtraction of bone volumes from the scans, LLAC were detected and contoured by a semi-automated, dual-threshold seed-point segmentation. LLAC mass (in mg hydroxyapatite; HA) was calculated as the product of voxel-based calcification volume (mm3) and mean calcification density (mgHA/cm3)/1000. To determine validity, we compared LLAC to coronary artery calcifications (CAC), as quantified by multi-detector computed tomography (MDCT) and Agatston scoring in forty-six patients on chronic hemodialysis. Moreover, we investigated associations of LLAC with age, time on dialysis, type-2 diabetes mellitus, history of stroke, and myocardial infarction. In a second step, we determined intra- and inter-reader reliability of the LLAC measure. In the validity study, LLAC were present (>0 mgHA) in 76% of patients, 78% of patients had CAC (>0 mgHA). Median LLAC was 6.65 (0.08 – 24.40) mgHA and median CAC as expressed by Agatston score was 266.3 (15.88 – 1877.28). We found a significant positive correlation between

  7. PITRE: software for phase-sensitive X-ray image processing and tomography reconstruction.

    PubMed

    Chen, Rong Chang; Dreossi, Diego; Mancini, Lucia; Menk, Ralf; Rigon, Luigi; Xiao, Ti Qiao; Longo, Renata

    2012-09-01

    Synchrotron-radiation computed tomography has been applied in many research fields. Here, PITRE (Phase-sensitive X-ray Image processing and Tomography REconstruction) and PITRE_BM (PITRE Batch Manager) are presented. PITRE supports phase retrieval for propagation-based phase-contrast imaging/tomography (PPCI/PPCT), extracts apparent absorption, refractive and scattering information of diffraction enhanced imaging (DEI), and allows parallel-beam tomography reconstruction for conventional absorption CT data and for PPCT phase retrieved and DEI-CT extracted information. PITRE_BM is a batch processing manager for PITRE: it executes a series of tasks, created via PITRE, without manual intervention. Both PITRE and PITRE_BM are coded in Interactive Data Language (IDL), and have a user-friendly graphical user interface. They are freeware and can run on Microsoft Windows systems via IDL Virtual Machine, which can be downloaded for free and does not require a license. The data-processing principle and some examples of application will be presented.

  8. Bone structure and volumetric density in young adults born prematurely: a peripheral quantitative computed tomography study.

    PubMed

    Backström, M C; Kuusela, A-L; Koivisto, A-M; Sievänen, H

    2005-04-01

    Prematurity is known to be associated with reduced bone mineral density (BMD) in childhood, but whether this condition has long-term detrimental consequences on adult bone structure is not known. In this study, we measured with peripheral quantitative computed tomography (pQCT) the total bone cross-sectional area, cortical area and wall thickness, cortical and trabecular density, and a density-weighed polar section modulus as a bone strength index (BSI) at distal and shaft sites of right radius and tibia in a group of 40 prematurely born, otherwise normally developed and healthy young adults (17 women and 23 men, aged 18 to 27 years) and compared their data to corresponding data obtained from a group of 42 control subjects born term (20 women and 22 men, aged 18 to 28 years). Body height and weight were similar in both groups, but the preterm group had significantly lower BSI values at distal sites of tibia (approximately -16%) and radius (approximately -13%) and at tibial shaft (approximately -11%) as compared to control group. In the weight-bearing tibia, BMC was lower and the lower BSI values were mainly due to smaller total bone cross-sectional area. For unknown reason, this prematurity-associated detrimental effect seemed to concern more men than women. In contrast, prematurity was not associated with volumetric trabecular and cortical densities at any measured bone site while the typical sex differences in bone density were observed. We conclude that prematurity is associated with somewhat smaller cross-sectional bone dimensions in terms of body size in young adulthood. Due to the cross-sectional design, this study could not reveal specific reasons but they may pertain to nutrition during the neonatal period and living habits in general.

  9. Characterizing trabecular bone structure for assessing vertebral fracture risk on volumetric quantitative computed tomography

    NASA Astrophysics Data System (ADS)

    Nagarajan, Mahesh B.; Checefsky, Walter A.; Abidin, Anas Z.; Tsai, Halley; Wang, Xixi; Hobbs, Susan K.; Bauer, Jan S.; Baum, Thomas; Wismüller, Axel

    2015-03-01

    While the proximal femur is preferred for measuring bone mineral density (BMD) in fracture risk estimation, the introduction of volumetric quantitative computed tomography has revealed stronger associations between BMD and spinal fracture status. In this study, we propose to capture properties of trabecular bone structure in spinal vertebrae with advanced second-order statistical features for purposes of fracture risk assessment. For this purpose, axial multi-detector CT (MDCT) images were acquired from 28 spinal vertebrae specimens using a whole-body 256-row CT scanner with a dedicated calibration phantom. A semi-automated method was used to annotate the trabecular compartment in the central vertebral slice with a circular region of interest (ROI) to exclude cortical bone; pixels within were converted to values indicative of BMD. Six second-order statistical features derived from gray-level co-occurrence matrices (GLCM) and the mean BMD within the ROI were then extracted and used in conjunction with a generalized radial basis functions (GRBF) neural network to predict the failure load of the specimens; true failure load was measured through biomechanical testing. Prediction performance was evaluated with a root-mean-square error (RMSE) metric. The best prediction performance was observed with GLCM feature `correlation' (RMSE = 1.02 ± 0.18), which significantly outperformed all other GLCM features (p < 0.01). GLCM feature correlation also significantly outperformed MDCTmeasured mean BMD (RMSE = 1.11 ± 0.17) (p< 10-4). These results suggest that biomechanical strength prediction in spinal vertebrae can be significantly improved through characterization of trabecular bone structure with GLCM-derived texture features.

  10. Peripheral Quantitative Computed Tomography Predicts Humeral Diaphysis Torsional Mechanical Properties With Good Short-Term Precision.

    PubMed

    Weatherholt, Alyssa M; Avin, Keith G; Hurd, Andrea L; Cox, Jacob L; Marberry, Scott T; Santoni, Brandon G; Warden, Stuart J

    2015-01-01

    Peripheral quantitative computed tomography (pQCT) is a popular tool for noninvasively estimating bone mechanical properties. Previous studies have demonstrated that pQCT provides precise estimates that are good predictors of actual bone mechanical properties at popular distal imaging sites (tibia and radius). The predictive ability and precision of pQCT at more proximal sites remain unknown. The aim of the present study was to explore the predictive ability and short-term precision of pQCT estimates of mechanical properties of the midshaft humerus, a site gaining popularity for exploring the skeletal benefits of exercise. Predictive ability was determined ex vivo by assessing the ability of pQCT-derived estimates of torsional mechanical properties in cadaver humeri (density-weighted polar moment of inertia [I(P)] and polar strength-strain index [SSI(P)]) to predict actual torsional properties. Short-term precision was assessed in vivo by performing 6 repeat pQCT scans at the level of the midshaft humerus in 30 young, healthy individuals (degrees of freedom = 150), with repeat scans performed by the same and different testers and on the same and different days to explore the influences of different testers and time between repeat scans on precision errors. IP and SSI(P) both independently predicted at least 90% of the variance in ex vivo midshaft humerus mechanical properties in cadaveric bones. Overall values for relative precision error (root mean squared coefficients of variation) for in vivo measures of IP and SSI(P) at the midshaft humerus were <1.5% and were not influenced by pQCT assessments being performed by different testers or on different days. These data indicate that pQCT provides very good prediction of midshaft humerus mechanical properties with good short-term precision, with measures being robust against the influences of different testers and time between repeat scans. PMID:25454307

  11. Quantitative monitoring of laser-treated engineered skin using optical coherence tomography

    PubMed Central

    Ahn, Yujin; Lee, Chan-Young; Baek, Songyee; Kim, Taeho; Kim, Pilun; Lee, Sunghoon; Min, Daejin; Lee, Haekwang; Kim, Jeehyun; Jung, Woonggyu

    2016-01-01

    Nowadays, laser therapy is a common method for treating various dermatological troubles such as acne and wrinkles because of its efficient and immediate skin enhancement. Although laser treatment has become a routine procedure in medical and cosmetic fields, the prevention of side-effects, such as hyperpigmentation, redness and burning, still remains a critical issue that needs to be addressed. In order to reduce the side-effects while attaining efficient therapeutic outcomes, it is essential to understand the light-skin interaction through evaluation of physiological changes before and after laser therapy. In this study, we introduce a quantitative tissue monitoring method based on optical coherence tomography (OCT) for the evaluation of tissue regeneration after laser irradiation. To create a skin injury model, we applied a fractional CO2 laser on a customized engineered skin model, which is analogous to human skin in terms of its basic biological function and morphology. The irradiated region in the skin was then imaged by a high-speed OCT system, and its morphologic changes were analyzed by automatic segmentation software. Volumetric OCT images in the laser treated area clearly visualized the wound healing progress at different time points and provided comprehensive information which cannot be acquired through conventional monitoring methods. The results showed that the laser wound in engineered skins was mostly recovered from within 1~2 days with a fast recovery time in the vertical direction. However, the entire recovery period varied widely depending on laser doses and skin type. Our results also indicated that OCT-guided laser therapy would be a very promising protocol for optimizing laser treatment for skin therapy. PMID:27231605

  12. Quantitative carbon ion beam radiography and tomography with a flat-panel detector.

    PubMed

    Telsemeyer, Julia; Jäkel, Oliver; Martišíková, Mária

    2012-12-01

    High dose gradients are inherent to ion beam therapy. This results in high sensitivity to discrepancies between planned and delivered dose distributions. Therefore an accurate knowledge of the ion stopping power of the traversed tissue is critical. One proposed method to ensure high quality dose deposition is to measure the stopping power by ion radiography. Although the idea of imaging with highly energetic ions is more than forty years old, there is a lack of simple detectors suitable for this purpose. In this study the performance of an amorphous silicon flat-panel detector, originally designed for photon imaging, was investigated for quantitative carbon ion radiography and tomography. The flat-panel detector was exploited to measure the water equivalent thickness (WET) and water equivalent path length (WEPL) of a phantom at the Heidelberg Ion-Beam Therapy Center (HIT). To do so, the ambiguous correlation of detector signal to particle energy was overcome by active or passive variation of carbon ion beam energy and measurement of the signal-to-beam energy correlation. The active method enables one to determine the WET of the imaged object with an uncertainty of 0.5 mm WET. For tomographic WEPL measurements the passive method was exploited resulting in an accuracy of 0.01 WEPL. The developed imaging technique presents a method to measure the two-dimensional maps of WET and WEPL of phantoms with a simple and commercially available detector. High spatial resolution of 0.8 × 0.8 mm(2) is given by the detector design. In the future this powerful tool will be used to evaluate the performance of the treatment planning algorithm by studying WET uncertainties.

  13. Distinct Quantitative Computed Tomography Emphysema Patterns Are Associated with Physiology and Function in Smokers

    PubMed Central

    San José Estépar, Raúl; Mendoza, Carlos S.; Hersh, Craig P.; Laird, Nan; Crapo, James D.; Lynch, David A.; Silverman, Edwin K.; Washko, George R.

    2013-01-01

    Rationale: Emphysema occurs in distinct pathologic patterns, but little is known about the epidemiologic associations of these patterns. Standard quantitative measures of emphysema from computed tomography (CT) do not distinguish between distinct patterns of parenchymal destruction. Objectives: To study the epidemiologic associations of distinct emphysema patterns with measures of lung-related physiology, function, and health care use in smokers. Methods: Using a local histogram-based assessment of lung density, we quantified distinct patterns of low attenuation in 9,313 smokers in the COPDGene Study. To determine if such patterns provide novel insights into chronic obstructive pulmonary disease epidemiology, we tested for their association with measures of physiology, function, and health care use. Measurements and Main Results: Compared with percentage of low-attenuation area less than −950 Hounsfield units (%LAA-950), local histogram-based measures of distinct CT low-attenuation patterns are more predictive of measures of lung function, dyspnea, quality of life, and health care use. These patterns are strongly associated with a wide array of measures of respiratory physiology and function, and most of these associations remain highly significant (P < 0.005) after adjusting for %LAA-950. In smokers without evidence of chronic obstructive pulmonary disease, the mild centrilobular disease pattern is associated with lower FEV1 and worse functional status (P < 0.005). Conclusions: Measures of distinct CT emphysema patterns provide novel information about the relationship between emphysema and key measures of physiology, physical function, and health care use. Measures of mild emphysema in smokers with preserved lung function can be extracted from CT scans and are significantly associated with functional measures. PMID:23980521

  14. High Resolution Peripheral Quantitative Computed Tomography for Assessment of Bone Quality

    NASA Astrophysics Data System (ADS)

    Kazakia, Galateia

    2014-03-01

    The study of bone quality is motivated by the high morbidity, mortality, and societal cost of skeletal fractures. Over 10 million people are diagnosed with osteoporosis in the US alone, suffering 1.5 million osteoporotic fractures and costing the health care system over 17 billion annually. Accurate assessment of fracture risk is necessary to ensure that pharmacological and other interventions are appropriately administered. Currently, areal bone mineral density (aBMD) based on 2D dual-energy X-ray absorptiometry (DXA) is used to determine osteoporotic status and predict fracture risk. Though aBMD is a significant predictor of fracture risk, it does not completely explain bone strength or fracture incidence. The major limitation of aBMD is the lack of 3D information, which is necessary to distinguish between cortical and trabecular bone and to quantify bone geometry and microarchitecture. High resolution peripheral quantitative computed tomography (HR-pQCT) enables in vivo assessment of volumetric BMD within specific bone compartments as well as quantification of geometric and microarchitectural measures of bone quality. HR-pQCT studies have documented that trabecular bone microstructure alterations are associated with fracture risk independent of aBMD.... Cortical bone microstructure - specifically porosity - is a major determinant of strength, stiffness, and fracture toughness of cortical tissue and may further explain the aBMD-independent effect of age on bone fragility and fracture risk. The application of finite element analysis (FEA) to HR-pQCT data permits estimation of patient-specific bone strength, shown to be associated with fracture incidence independent of aBMD. This talk will describe the HR-pQCT scanner, established metrics of bone quality derived from HR-pQCT data, and novel analyses of bone quality currently in development. Cross-sectional and longitudinal HR-pQCT studies investigating the impact of aging, disease, injury, gender, race, and

  15. [High resolution peripheral quantitative computed tomography for the assessment of morphological and mechanical bone parameters].

    PubMed

    Fuller, Henrique; Fuller, Ricardo; Pereira, Rosa Maria R

    2015-01-01

    High resolution peripheral quantitative computed tomography (HR-pQCT) is a new technology commercially available for less than 10 years that allows performing in vivo assessment of bone parameters. HR-pQCT assesses the trabecular thickness, trabecular separation, trabecular number and connectivity density and, in addition, cortical bone density and thickness and total bone volume and density in high-definition mode, which additionally allows obtaining digital constructs of bone microarchitecture. The application of mathematics to captured data, a method called finite element analysis (FEA), allows the estimation of the physical properties of the tissue, simulating supported loads in a non-invasive way. Thus, HR-pQCT simultaneously acquires data previously provided separately by dual energy x-ray absorptiometry (DXA), magnetic resonance imaging and histomorphometry, aggregating biomechanical estimates previously only possible in extracted tissues. This method has a satisfactory reproducibility, with coefficients of variation rarely exceeding 3%. Regarding accuracy, the method shows a fair to good agreement (r(2) = 0.37-0.97). The main clinical application of this method is in the quantification and monitoring of metabolic bone disorders, more fully evaluating bone strength and fracture risk. In rheumatoid arthritis patients, this allows gauging the number and size of erosions and cysts, in addition to joint space. In osteoarthritis, it is possible to characterize the bone marrow edema-like areas that show a correlation with cartilage breakdown. Given its high cost, HR-pQCT is still a research tool, but the high resolution and efficiency of this method reveal advantages over the methods currently used for bone assessment, with a potential to become an important tool in clinical practice.

  16. Quantitative material analysis by dual-energy computed tomography for industrial NDT applications

    NASA Astrophysics Data System (ADS)

    Nachtrab, F.; Weis, S.; Keßling, P.; Sukowski, F.; Haßler, U.; Fuchs, T.; Uhlmann, N.; Hanke, R.

    2011-05-01

    Dual-energy computed tomography (DECT) is an established method in the field of medical CT to obtain quantitative information on a material of interest instead of mean attenuation coefficients only. In the field of industrial X-ray imaging dual-energy techniques have been used to solve special problems on a case-by-case basis rather than as a standard tool. Our goal is to develop an easy-to-use dual-energy solution that can be handled by the average industrial operator without the need for a specialist. We are aiming at providing dual-energy CT as a measurement tool for those cases where qualitative images are not enough and one needs additional quantitative information (e.g. mass density ρ and atomic number Z) about the sample at hand. Our solution is based on an algorithm proposed by Heismann et al. (2003) [1] for application in medical CT . As input data this algorithm needs two CT data sets, one with low (LE) and one with high effective energy (HE). A first order linearization is applied to the raw data, and two volumes are reconstructed thereafter. The dual-energy analysis is done voxel by voxel, using a pre-calculated function F(Z) that implies the parameters of the low and high energy measurement (such as tube voltage, filtration and detector sensitivity). As a result, two volume data sets are obtained, one providing information about the mass density ρ in each voxel, the other providing the effective atomic number Z of the material therein. One main difference between medical and industrial CT is that the range of materials that can be contained in a sample is much wider and can cover the whole range of elements, from hydrogen to uranium. Heismann's algorithm is limited to the range of elements Z=1-30, because for Z>30 the function F(Z) as given by Heismann is not a bijective function anymore. While this still seems very suitable for medical application, it is not enough to cover the complete range of industrial applications. We therefore investigated the

  17. Quantitative optical coherence tomography angiography of choroidal neovascularization in age-related macular degeneration

    PubMed Central

    Jia, Yali; Bailey, Steven T.; Wilson, David J.; Tan, Ou; Klein, Michael L.; Flaxel, Christina J.; Potsaid, Benjamin; Liu, Jonathan J.; Lu, Chen D.; Kraus, Martin F.; Fujimoto, James G.; Huang, David

    2014-01-01

    Purpose To detect and quantify choroidal neovascularization (CNV) in age-related macular degeneration (AMD) patients using optical coherence tomography (OCT) angiography. Design Observational, cross-sectional study. Participants Five normal subjects and five neovascular AMD patients were included. Methods Five eyes with neovascular AMD and five normal age-matched controls were scanned by a high-speed (100,000 A-scans/sec) 1050 nm wavelength swept-source OCT. The macular angiography scan covered a 3×3 mm area and comprised 200×200×8 A-scans acquired in 3.5 sec. Flow was detected using the split-spectrum amplitude-decorrelation angiography (SSADA) algorithm. Motion artifacts were removed by three dimensional (3D) orthogonal registration and merging of 4 scans. The 3D angiography was segmented into 3 layers: inner retina (to show retinal vasculature), outer retina (to identify CNV), and choroid. En face maximum projection was used to obtain 2D angiograms from the 3 layers. CNV area and flow index were computed from the en face OCT angiogram of the outer retinal layer. Flow (decorrelation) and structural data were combined in composite color angiograms for both en face and cross-sectional views. Main Outcome Measurements CNV angiogram, CNV area, and CNV flow index. Results En face OCT angiograms of CNVs showed sizes and locations that were confirmed by fluorescein angiography. OCT angiography provided more distinct vascular network patterns that were less obscured by subretinal hemorrhage. The en face angiograms also showed areas of reduced choroidal flow adjacent to the CNV in all cases and significantly reduced retinal flow in one case. Cross-sectional angiograms were used to visualize CNV location relative to the retinal pigment epithelium and Bruch’s layer and classify type I and type II CNV. A feeder vessel could be identified in one case. Higher flow indexes were associated with larger CNV and type II CNV. Conclusions OCT angiography provides depth

  18. Quantitative assessment of scatter correction techniques incorporated in next generation dual-source computed tomography

    NASA Astrophysics Data System (ADS)

    Mobberley, Sean David

    Accurate, cross-scanner assessment of in-vivo air density used to quantitatively assess amount and distribution of emphysema in COPD subjects has remained elusive. Hounsfield units (HU) within tracheal air can be considerably more positive than -1000 HU. With the advent of new dual-source scanners which employ dedicated scatter correction techniques, it is of interest to evaluate how the quantitative measures of lung density compare between dual-source and single-source scan modes. This study has sought to characterize in-vivo and phantom-based air metrics using dual-energy computed tomography technology where the nature of the technology has required adjustments to scatter correction. Anesthetized ovine (N=6), swine (N=13: more human-like rib cage shape), lung phantom and a thoracic phantom were studied using a dual-source MDCT scanner (Siemens Definition Flash. Multiple dual-source dual-energy (DSDE) and single-source (SS) scans taken at different energy levels and scan settings were acquired for direct quantitative comparison. Density histograms were evaluated for the lung, tracheal, water and blood segments. Image data were obtained at 80, 100, 120, and 140 kVp in the SS mode (B35f kernel) and at 80, 100, 140, and 140-Sn (tin filtered) kVp in the DSDE mode (B35f and D30f kernels), in addition to variations in dose, rotation time, and pitch. To minimize the effect of cross-scatter, the phantom scans in the DSDE mode was obtained by reducing the tube current of one of the tubes to its minimum (near zero) value. When using image data obtained in the DSDE mode, the median HU values in the tracheal regions of all animals and the phantom were consistently closer to -1000 HU regardless of reconstruction kernel (chapters 3 and 4). Similarly, HU values of water and blood were consistently closer to their nominal values of 0 HU and 55 HU respectively. When using image data obtained in the SS mode the air CT numbers demonstrated a consistent positive shift of up to 35 HU

  19. Phase aberration correction by multi-stencils fast marching method using sound speed image in ultrasound computed tomography

    NASA Astrophysics Data System (ADS)

    Qu, Xiaolei; Azuma, Takashi; Lin, Hongxiang; Imoto, Haruka; Tamano, Satoshi; Takagi, Shu; Umemura, Shin-Ichiro; Sakuma, Ichiro; Matsumoto, Yoichiro

    2016-04-01

    Reflection image from ultrasound computed tomography (USCT) system can be obtained by synthetic aperture technique, however its quality is decreased by phase aberration caused by inhomogeneous media. Therefore, phase aberration correction is important to improve image quality. In this study, multi-stencils fast marching method (MSFMM) is employed for phase correction. The MSFMM is an accurate and fast solution of Eikonal equation which considers the refraction. The proposed method includes two steps. First, the MSFMM is used to compute sound propagation time from each element to each image gird point using sound speed image of USCT. Second, synthetic aperture technique is employed to obtain reflection image using the computed propagation time. To evaluate the proposed method, both numerical simulation and phantom experiment were conducted. With regard to numerical simulation, both quantitative and qualitative comparisons between reflection images with and without phase aberration correction were given. In the quantitative comparison, the diameters of point spread function (PSF) in reflection images of a two layer structure were presented. In the qualitative comparison, reflection images of simple circle and complex breast modes with phase aberration correction show higher quality than that without the correction. In respect to phantom experiment, a piece of breast phantom with artificial glandular structure inside was scanned by a USCT prototype, and the artificial glandular structure is able to be visible more clearly in the reflection image with phase aberration correction than in that without the correction. In this study, a phase aberration correction method by the MSFMM are proposed for reflection image of the USCT.

  20. Quality of the reconstruction in x-ray phase contrast tomography

    NASA Astrophysics Data System (ADS)

    Arhatari, B. D.; Peele, A. G.; Nugent, K. A.; De Carlo, F.

    2006-06-01

    We develop an analytical model for three dimensional phase contrast tomography for a pure phase object. The model incorporates an extended source, which is suitable for a laboratory based microfocus x-ray source. From the modeled intensities for the tomographic data set we obtain a model reconstruction and define a reconstruction quality factor that allows us to optimize the tomographic reconstruction for given feature sizes in an object.

  1. A compressed sensing based reconstruction algorithm for synchrotron source propagation-based X-ray phase contrast computed tomography

    NASA Astrophysics Data System (ADS)

    Melli, Seyed Ali; Wahid, Khan A.; Babyn, Paul; Montgomery, James; Snead, Elisabeth; El-Gayed, Ali; Pettitt, Murray; Wolkowski, Bailey; Wesolowski, Michal

    2016-01-01

    Synchrotron source propagation-based X-ray phase contrast computed tomography is increasingly used in pre-clinical imaging. However, it typically requires a large number of projections, and subsequently a large radiation dose, to produce high quality images. To improve the applicability of this imaging technique, reconstruction algorithms that can reduce the radiation dose and acquisition time without degrading image quality are needed. The proposed research focused on using a novel combination of Douglas-Rachford splitting and randomized Kaczmarz algorithms to solve large-scale total variation based optimization in a compressed sensing framework to reconstruct 2D images from a reduced number of projections. Visual assessment and quantitative performance evaluations of a synthetic abdomen phantom and real reconstructed image of an ex-vivo slice of canine prostate tissue demonstrate that the proposed algorithm is competitive in reconstruction process compared with other well-known algorithms. An additional potential benefit of reducing the number of projections would be reduction of time for motion artifact to occur if the sample moves during image acquisition. Use of this reconstruction algorithm to reduce the required number of projections in synchrotron source propagation-based X-ray phase contrast computed tomography is an effective form of dose reduction that may pave the way for imaging of in-vivo samples.

  2. A multi-phase level set framework for source reconstruction in bioluminescence tomography

    SciTech Connect

    Huang Heyu; Qu Xiaochao; Liang Jimin; He Xiaowei; Chen Xueli; Yang Da'an; Tian Jie

    2010-07-01

    We propose a novel multi-phase level set algorithm for solving the inverse problem of bioluminescence tomography. The distribution of unknown interior source is considered as piecewise constant and represented by using multiple level set functions. The localization of interior bioluminescence source is implemented by tracing the evolution of level set function. An alternate search scheme is incorporated to ensure the global optimal of reconstruction. Both numerical and physical experiments are performed to evaluate the developed level set reconstruction method. Reconstruction results show that the proposed method can stably resolve the interior source of bioluminescence tomography.

  3. Gas-Phase Database for Quantitative Infrared Spectroscopy

    SciTech Connect

    Sharpe, Steven W.; Johnson, Timothy J.; Sams, Robert L.; Chu, Pamela M.; Rhoderick, G C.; Johnson, P A.

    2004-12-10

    The National Institute of Standards and Technology (NIST) and the Pacific Northwest National Laboratory (PNNL) are each creating quantitative databases containing the vapor-phase infrared spectra of pure chemicals. The digital databases have been created with both laboratory and remote-sensing applications in mind. A spectral resolution of {approx} 0.1 cm{sup -1} was selected to avoid degrading sharp spectral features, while also realizing that atmospheric broadening typically limits line widths to 0.1 cm{sup -1}. Calculated positional (wave number, cm{sup -1}) uncertainty is {le} 0.005 cm{sup -1}, while the 1{sigma} statistical uncertainty in absorbance values is <2% for most compounds. The latter was achieved by measuring multiple (typically {ge} 9) path length-concentration burdens and fitting a weighted Beer's law plot to each wave number channel. The two databases include different classes of compounds and were compared using 12 samples. Though these 12 samples span a range of polarities, absorption strengths, and vapor pressures, the data agree to within experimental uncertainties with only one exception.

  4. Real time blood testing using quantitative phase imaging.

    PubMed

    Pham, Hoa V; Bhaduri, Basanta; Tangella, Krishnarao; Best-Popescu, Catherine; Popescu, Gabriel

    2013-01-01

    We demonstrate a real-time blood testing system that can provide remote diagnosis with minimal human intervention in economically challenged areas. Our instrument combines novel advances in label-free optical imaging with parallel computing. Specifically, we use quantitative phase imaging for extracting red blood cell morphology with nanoscale sensitivity and NVIDIA's CUDA programming language to perform real time cellular-level analysis. While the blood smear is translated through focus, our system is able to segment and analyze all the cells in the one megapixel field of view, at a rate of 40 frames/s. The variety of diagnostic parameters measured from each cell (e.g., surface area, sphericity, and minimum cylindrical diameter) are currently not available with current state of the art clinical instruments. In addition, we show that our instrument correctly recovers the red blood cell volume distribution, as evidenced by the excellent agreement with the cell counter results obtained on normal patients and those with microcytic and macrocytic anemia. The final data outputted by our instrument represent arrays of numbers associated with these morphological parameters and not images. Thus, the memory necessary to store these data is of the order of kilobytes, which allows for their remote transmission via, for example, the cellular network. We envision that such a system will dramatically increase access for blood testing and furthermore, may pave the way to digital hematology. PMID:23405194

  5. Silver nanoparticle-induced degranulation observed with quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Yang, Wenzhong; Lee, Seungrag; Lee, Jiyong; Bae, Yoonsung; Kim, Dugyoung

    2010-07-01

    Monitoring a degranulation process in a live mast cell is a quite important issue in immunology and pharmacology. Because the size of a granule is normally much smaller than the resolution limit of an optical microscope system, there is no direct real-time live cell imaging technique for observing degranulation processes except for fluorescence imaging techniques. In this research, we propose optical quantitative phase microscopy (QPM) as a new observation tool to study degranulation processes in a live mast cell without any fluorescence labeling. We measure the cell volumes and the cross sectional profiles (x-z plane) of an RBL-2H3 cell and a HeLa cell, before and after they are exposed to calcium ionophore A23187 and silver nanoparticles (AgNPs). We verify that the volume and the cross sectional line profile of the RBL-2H3 cell were changed significantly when it was exposed to A23187. When 50 μg/mL of AgNP is used instead of A23187, the measurements of cell volume and cross sectional profiles indicate that RBL-2H3 cells also follow degranulation processes. Degranulation processes for these cells are verified by monitoring the increase of intracellular calcium ([Ca2+]i) and histamine with fluorescent methods.

  6. How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

    PubMed Central

    Jørgensen, J. S.; Sidky, E. Y.

    2015-01-01

    We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization. PMID:25939620

  7. Polarization-phase tomography of biological fluids polycrystalline structure

    NASA Astrophysics Data System (ADS)

    Dubolazov, A. V.; Vanchuliak, O. Ya.; Garazdiuk, M.; Sidor, M. I.; Motrich, A. V.; Kostiuk, S. V.

    2013-12-01

    Our research is aimed at designing an experimental method of Fourier's laser polarization phasometry of the layers of human effusion for an express diagnostics during surgery and a differentiation of the degree of severity (acute - gangrenous) appendectomy by means of statistical, correlation and fractal analysis of the coherent scattered field. A model of generalized optical anisotropy of polycrystal networks of albumin and globulin of the effusion of appendicitis has been suggested and the method of Fourier's phasometry of linear (a phase shift between the orthogonal components of the laser wave amplitude) and circular (the angle of rotation of the polarization plane) birefringence with a spatial-frequency selection of the coordinate distributions for the differentiation of acute and gangrenous conditions have been analytically substantiated. Comparative studies of the efficacy of the methods of direct mapping of phase distributions and Fourier's phasometry of a laser radiation field transformed by the dendritic and spherolitic networks of albumin and globulin of the layers of effusion of appendicitis on the basis of complex statistical, correlation and fractal analysis of the structure of phase maps.

  8. Three-dimensional motion correction using speckle and phase for in vivo computed optical interferometric tomography

    PubMed Central

    Shemonski, Nathan D.; Ahn, Shawn S.; Liu, Yuan-Zhi; South, Fredrick A.; Carney, P. Scott; Boppart, Stephen A.

    2014-01-01

    Over the years, many computed optical interferometric techniques have been developed to perform high-resolution volumetric tomography. By utilizing the phase and amplitude information provided with interferometric detection, post-acquisition corrections for defocus and optical aberrations can be performed. The introduction of the phase, though, can dramatically increase the sensitivity to motion (most prominently along the optical axis). In this paper, we present two algorithms which, together, can correct for motion in all three dimensions with enough accuracy for defocus and aberration correction in computed optical interferometric tomography. The first algorithm utilizes phase differences within the acquired data to correct for motion along the optical axis. The second algorithm utilizes the addition of a speckle tracking system using temporally- and spatially-coherent illumination to measure motion orthogonal to the optical axis. The use of coherent illumination allows for high-contrast speckle patterns even when imaging apparently uniform samples or when highly aberrated beams cannot be avoided. PMID:25574426

  9. X-ray imaging: a generalized approach using phase-space tomography

    NASA Astrophysics Data System (ADS)

    Tran, Chanh Q.; Peele, Andrew G.; Roberts, Ann; Nugent, Keith A.; Paterson, David; McNulty, Ian

    2005-08-01

    We discuss the role of coherence in x-ray imaging and consider how phase-space tomography can be used to extract information about partial coherence. We describe the application of phase-space tomography to x-ray imaging and recover the spatial coherence properties of a one-dimensional soft (1.5 keV) x-ray beam from a synchrotron undulator source. We present phase-space information from a Young's experiment and observe negative regions in the quasi-probability distribution. We show that, given knowledge of the coherence of the beam, we can use partially coherent diffraction data to recover fully coherent information, and we present some simple experimental demonstrations of this capability.

  10. Optical digital coherent detection technology enabled flexible and ultra-fast quantitative phase imaging.

    PubMed

    Feng, Yuan-Hua; Lu, Xing; Song, Lu; Guo, Xiaojie; Wang, Yawei; Zhu, Linyan; Sui, Qi; Li, Jianping; Shi, Kebin; Li, Zhaohui

    2016-07-25

    Quantitative phase imaging has been an important labeling-free microscopy modality for many biomedical and material science applications. In which, ultra-fast quantitative phase imaging is indispensable for dynamic or transient characteristics analysis. Conventional wide field optical interferometry is a common scheme for quantitative phase imaging, while its data acquisition rate is usually hindered by the frame rate of arrayed detector. By utilizing novel balanced-photo-detector based digital optics coherent detection techniques, we report on a method of constructing ultra-fast quantitative phase microscopy at the line-scan rate of 100 MHz with ~2 μm spatial resolution. PMID:27464166

  11. Imaging of Metastatic Lymph Nodes by X-ray Phase-Contrast Micro-Tomography

    PubMed Central

    Jensen, Torben Haugaard; Bech, Martin; Binderup, Tina; Böttiger, Arvid; David, Christian; Weitkamp, Timm; Zanette, Irene; Reznikova, Elena; Mohr, Jürgen; Rank, Fritz; Feidenhans’l, Robert; Kjær, Andreas; Højgaard, Liselotte; Pfeiffer, Franz

    2013-01-01

    Invasive cancer causes a change in density in the affected tissue, which can be visualized by x-ray phase-contrast tomography. However, the diagnostic value of this method has so far not been investigated in detail. Therefore, the purpose of this study was, in a blinded manner, to investigate whether malignancy could be revealed by non-invasive x-ray phase-contrast tomography in lymph nodes from breast cancer patients. Seventeen formalin-fixed paraffin-embedded lymph nodes from 10 female patients (age range 37–83 years) diagnosed with invasive ductal carcinomas were analyzed by X-ray phase-contrast tomography. Ten lymph nodes had metastatic deposits and 7 were benign. The phase-contrast images were analyzed according to standards for conventional CT images looking for characteristics usually only visible by pathological examinations. Histopathology was used as reference. The result of this study was that the diagnostic sensitivity of the image analysis for detecting malignancy was 100% and the specificity was 87%. The positive predictive value was 91% for detecting malignancy and the negative predictive value was 100%. We conclude that x-ray phase-contrast imaging can accurately detect density variations to obtain information regarding lymph node involvement previously inaccessible with standard absorption x-ray imaging. PMID:23349784

  12. Quantitative 3D petrography using X-ray tomography 2: Combining information at various resolutions

    SciTech Connect

    Pamukcu, Ayla S.; Gualda, Guilherme A.R.

    2010-12-02

    X-ray tomography is a nondestructive technique that can be used to study rocks and other materials in three dimensions over a wide range of sizes. Samples that range from decimeters to micrometers in size can be analyzed, and micrometer- to centimeter-sized crystals, vesicles, and other particles can be identified and quantified. In many applications, quantification of a large spectrum of sizes is important, but this cannot be easily accomplished using a single tomogram due to a common trade-off between sample size and image resolution. This problem can be circumvented by combining tomograms acquired for a single sample at a variety of resolutions. We have successfully applied this method to obtain crystal size distributions (CSDs) for magnetite, pyroxene + biotite, and quartz + feldspar in Bishop Tuff pumice. Five cylinders of systematically varying size (1-10 mm diameter and height) were analyzed from each of five pumice clasts. Cylinder size is inversely proportional to image resolution, such that resolution ranges from 2.5 to 17 {micro}m/voxel with increasing sample size. This allows quantification of crystals 10-1000 {micro}m in size. We obtained CSDs for each phase in each sample by combining information from all resolutions, each size bin containing data from the resolution that best characterizes crystals of that size. CSDs for magnetite and pyroxene + biotite in late-erupted Bishop pumice obtained using this method are fractal, but do not seem to result from crystal fragmentation. CSDs for quartz + feldspar reveal a population of abundant crystals <35 {micro}m in size, and a population of crystals >50 {micro}m in size, which will be the focus of a separate publication.

  13. Quantitative material decomposition using spectral computed tomography with an energy-resolved photon-counting detector.

    PubMed

    Lee, Seungwan; Choi, Yu-Na; Kim, Hee-Joung

    2014-09-21

    Dual-energy computed tomography (CT) techniques have been used to decompose materials and characterize tissues according to their physical and chemical compositions. However, these techniques are hampered by the limitations of conventional x-ray detectors operated in charge integrating mode. Energy-resolved photon-counting detectors provide spectral information from polychromatic x-rays using multiple energy thresholds. These detectors allow simultaneous acquisition of data in different energy ranges without spectral overlap, resulting in more efficient material decomposition and quantification for dual-energy CT. In this study, a pre-reconstruction dual-energy CT technique based on volume conservation was proposed for three-material decomposition. The technique was combined with iterative reconstruction algorithms by using a ray-driven projector in order to improve the quality of decomposition images and reduce radiation dose. A spectral CT system equipped with a CZT-based photon-counting detector was used to implement the proposed dual-energy CT technique. We obtained dual-energy images of calibration and three-material phantoms consisting of low atomic number materials from the optimal energy bins determined by Monte Carlo simulations. The material decomposition process was accomplished by both the proposed and post-reconstruction dual-energy CT techniques. Linear regression and normalized root-mean-square error (NRMSE) analyses were performed to evaluate the quantitative accuracy of decomposition images. The calibration accuracy of the proposed dual-energy CT technique was higher than that of the post-reconstruction dual-energy CT technique, with fitted slopes of 0.97-1.01 and NRMSEs of 0.20-4.50% for all basis materials. In the three-material phantom study, the proposed dual-energy CT technique decreased the NRMSEs of measured volume fractions by factors of 0.17-0.28 compared to the post-reconstruction dual-energy CT technique. It was concluded that the

  14. COMPARISON OF QUANTITATIVE COMPUTED TOMOGRAPHY-BASED MEASURES IN PREDICTING VERTEBRAL COMPRESSIVE STRENGTH

    PubMed Central

    Buckley, Jenni M.; Loo, Kenneth; Motherway, Julie

    2007-01-01

    Patient-specific measures derived from quantitative computed tomography (QCT) scans are currently being developed as a clinical tool for vertebral strength prediction. QCT-based measurement techniques vary greatly in structural complexity and generally fall into one of three categories: 1) bone mineral density (BMD), 2) “mechanics of solids” (MOS) models, such as minimum axial rigidity (the product of axial stiffness and vertebral height), or 3) three dimensional finite element (FE) models. There is no clear consensus as to the relative performance of these measures due to differences in experimental protocols, sample sizes and demographics, and outcome metrics. The goal of this study was to directly compare the performance of QCT-based assessment techniques of varying degrees of structural sophistication in predicting experimental vertebral compressive strength. Eighty-one human thoracic vertebrae (T6 – T10) from 44 donors cadavers (F = 32, M = 12; 85 + 8 y.o., max = 97 y.o., min = 54 y.o.) were QCT scanned and destructively tested in uniaxial compression. The QCT scans were processed to generate FE models and various BMD and MOS measures, including trabecular bone mineral density (tBMD), integral bone mineral density (iBMD), and axial rigidity. Bone mineral density was weakly to moderately predictive of compressive strength (R2 = 0.16 and 0.62 for tBMD and iBMD, respectively). Ex vivo vertebral strength was strongly correlated with both axial rigidity (R2 = 0.81) and FE strength measurements (R2 = 0.80), and the predictive capabilities of these two metrics were statistically equivalent (p > 0.05 for differences between FE and axial rigidity). The results of this study indicate that non-invasive predictive measures of vertebral strength should include some level of structural sophistication, specifically, gross geometric and material property distribution information. However, for uniaxial compression of isolated vertebrae, which is the current biomechanical

  15. Task-oriented quantitative image reconstruction in emission tomography for single- and multi-subject studies

    NASA Astrophysics Data System (ADS)

    Verhaeghe, Jeroen; Gravel, Paul; Reader, Andrew J.

    2010-12-01

    Task-based selection of image reconstruction methodology in emission tomography is a critically important step when designing a PET study. This paper concerns optimizing, given the measured data of the study only, reconstruction performance for a range of quantification tasks: finding the mean radioactivity concentration for different regions of interests (ROIs), different ROI sizes and different group sizes (i.e. the number of subjects in the PET study). At present, the variability of quantification performance of different reconstruction methods, according to both the ROI and group sizes, is largely ignored. In this paper, it is shown that both the ROI and group size have a tremendous impact on the error of the estimator for the task of ROI quantification. A study-specific, task-oriented and space-variant selection rule is proposed that selects a close to optimal estimate drawn from a series of estimates obtained by filtered backprojection (FBP) and different OSEM (ordered subset expectation maximization) iterations. The optimality criterion is to minimize an estimated mean square error (MSE), where the MSE is estimated from the data in the study using the bootstrap resampling technique. The proposed approach is appropriate for both pixel-level estimates and ROI estimates in single- and multi-subject studies. An extensive multi-trial simulation study using a 2D numerical phantom and relevant count levels shows that the proposed selection rule can produce quantitative estimates that are close to the estimates that minimize the true MSE (where the true MSE can only be obtained from many independent Monte-Carlo realizations with knowledge of the ground truth). This indicates that with the proposed selection rule one can obtain a close to optimal estimate while avoiding the critical step of selecting user-defined reconstruction settings (such as an OSEM iteration number or the choice between FBP and OSEM). In this initial 2D study, only FBP and OSEM reconstruction

  16. Does peripheral quantitative computed tomography ignore tissue density of cancellous bone?

    PubMed

    Banse, X; Devogelaer, J P

    2002-01-01

    The purpose of this work was to determine the capacity of peripheral quantitative computed tomography (pQCT) to accurately measure the true physical properties of vertebral cancellous bone samples and to predict their stiffness. pQCT bone mineral density (BMD) was first measured in ideal conditions. Ten cubic specimens of vertebral cancellous bone (10 x 10 x 10 mm) were washed with a water jet, defatted, and scanned in saline after elimination of air bubbles; thirteen slices were obtained. Seventy-one unprepared cylindrical samples were scanned in more realistic conditions, which allow further biomechanical testing. After extraction from the vertebral body, the samples were pushed into a plastic tube (no effort was made to remove the marrow or air bubbles), and only four slices were obtained to reduce the duration of scan. For the 81 samples, the true bone volume fraction (BV/TV, %), true apparent density (rho(app), g/cm(3)), and tissue density (rho(tiss), g/cm(3)) (an indicator of the degree of mineralization of the matrix) were then measured using Archimedes principle. rho(app) was closely correlated to BV/TV (r(2) = 0.97). rho(tiss) (1.58 +/- 0.08 g/cm(2)) was almost constant but had some influence on rho(app) (r(2) = 0.03, p < 0.001). The pQCT BMD predicted accurately rho(app) (r(2) = 0.96) and BV/TV (r(2) = 0.93) for the cylinders. For the cubes, in ideal conditions, the same correlations were even better (r(2) > 0.99, both). Analysis of covariance indicated no difference (p > 0.05) in the regressions due to preparation of the samples. The stiffness was better predicted by the true rho(app) (r(2) = 0.87) than by BV/TV (r(2) = 0.83), indicating that stiffness was influenced by small differences in the tissue density. Consequently, the correlation between pQCT BMD and stiffness was excellent (r(2) = 0.84). The fact that pQCT did not ignore this tissue density information compensated for the inaccuracies linked to realistic scanning conditions of the cylinder

  17. Assessment of the healing process in distal radius fractures by high resolution peripheral quantitative computed tomography.

    PubMed

    de Jong, Joost J A; Willems, Paul C; Arts, Jacobus J; Bours, Sandrine G P; Brink, Peter R G; van Geel, Tineke A C M; Poeze, Martijn; Geusens, Piet P; van Rietbergen, Bert; van den Bergh, Joop P W

    2014-07-01

    In clinical practice, fracture healing is evaluated by clinical judgment in combination with conventional radiography. Due to limited resolution, radiographs don't provide detailed information regarding the bone micro-architecture and bone strength. Recently, assessment of in vivo bone density, architectural and mechanical properties at the microscale became possible using high resolution peripheral quantitative computed tomography (HR-pQCT) in combination with micro finite element analysis (μFEA). So far, such techniques have been used mainly to study intact bone. The aim of this study was to explore whether these techniques can also be used to assess changes in bone density, micro-architecture and bone stiffness during fracture healing. Therefore, the fracture region in eighteen women, aged 50 years or older with a stable distal radius fracture, was scanned using HR-pQCT at 1-2 (baseline), 3-4, 6-8 and 12weeks post-fracture. At 1-2 and 12 weeks post-fracture the distal radius at the contra-lateral side was also scanned as control. Standard bone density, micro-architectural and geometric parameters were calculated and bone stiffness in compression, torsion and bending was assessed using μFEA. A linear mixed effect model with time post-fracture as fixed effect was used to detect significant (p-value ≤0.05) changes from baseline. Wrist pain and function were scored using the patient-rated wrist evaluation (PRWE) questionnaire. Correlations between the bone parameters and the PRWE score were calculated by Spearman's correlation coefficient. At the fracture site, total and trabecular bone density increased by 11% and 20%, respectively, at 6-8 weeks, whereas cortical density was decreased by 4%. Trabecular thickness increased by 23-31% at 6-8 and 12 weeks and the intertrabecular area became blurred, indicating intertrabecular bone formation. Compared to baseline, calculated bone stiffness in compression, torsion and bending was increased by 31% after 12 weeks. A

  18. Silver nanoparticle-induced degranulation observed with quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Yang, Wenzhong; Lee, Seungrag; Lee, Jiyong; Bae, Yoonsung; Kim, Dugyoung

    2010-02-01

    The use of AgNP is becoming more and more widespread in biomedical field. But compared with the promising bactericidal function, other physiological effects of AgNP on cells are relatively scant. In this research, we propose quantitative phase microscopy (QPM) as a new method to study the degranulation, and AgNP-induced RBL-2H3 cell degranulation is studied as well. Firstly, HeLa cells as the cell control and PBS as the solvent control, we measured the cell volume and cross section profile (x-z plane) with QPM. The results showed that the volume and cross section profile changed only the RBL-2H3 cells exposed to calcium ionophore A23187, which demonstrates the validity of QPM in degranulation research. Secondly, 50μg/mL of AgNP was used instead of A23187, and the measurement of cell volume and cross section profile was carried out again. RBL-2H3 cell volume increased immediately after AgNP was added, and cross section profile showed that the cell surface became granulated, but HeLa cell was lack of that effect. Phase images obviously indicated the RBL-2H3 cell deformation. Thirdly, stained with Fluo-3/AM, intracellular calcium Ca2+]i of single RBL-2H3 cell treated with AgNP was observed with fluorescent microscopy; incubated with AgNP for 20min, the supernatant of RBL-2H3 cells was collected and reacted with o-phthalaldehyde (OPA), then the fluorescent intensity of histamine-OPA complex was assayed with spectrofluorometer. The results of Ca2+]i and histamine increase showed that degranulation of AgNP-induced RBL-2H3 cell occurred. So, the cell volume was used as a parameter of degranulation in our study and AgNP-induced RBL-2H3 cells degranulation was confirmed by the cell volume increment, cross section profile change, and [Ca2+]i and histamine in supernatant increase.

  19. Experimental Realisation of High-sensitivity Laboratory X-ray Grating-based Phase-contrast Computed Tomography

    PubMed Central

    Birnbacher, Lorenz; Willner, Marian; Velroyen, Astrid; Marschner, Mathias; Hipp, Alexander; Meiser, Jan; Koch, Frieder; Schröter, Tobias; Kunka, Danays; Mohr, Jürgen; Pfeiffer, Franz; Herzen, Julia

    2016-01-01

    The possibility to perform high-sensitivity X-ray phase-contrast imaging with laboratory grating-based phase-contrast computed tomography (gbPC-CT) setups is of great interest for a broad range of high-resolution biomedical applications. However, achieving high sensitivity with laboratory gbPC-CT setups still poses a challenge because several factors such as the reduced flux, the polychromaticity of the spectrum, and the limited coherence of the X-ray source reduce the performance of laboratory gbPC-CT in comparison to gbPC-CT at synchrotron facilities. In this work, we present our laboratory X-ray Talbot-Lau interferometry setup operating at 40 kVp and describe how we achieve the high sensitivity yet unrivalled by any other laboratory X-ray phase-contrast technique. We provide the angular sensitivity expressed via the minimum resolvable refraction angle both in theory and experiment, and compare our data with other differential phase-contrast setups. Furthermore, we show that the good stability of our high-sensitivity setup allows for tomographic scans, by which even the electron density can be retrieved quantitatively as has been demonstrated in several preclinical studies. PMID:27040492

  20. Direct visualization of dispersed lipid bicontinuous cubic phases by cryo-electron tomography.

    PubMed

    Demurtas, Davide; Guichard, Paul; Martiel, Isabelle; Mezzenga, Raffaele; Hébert, Cécile; Sagalowicz, Laurent

    2015-01-01

    Bulk and dispersed cubic liquid crystalline phases (cubosomes), present in the body and in living cell membranes, are believed to play an essential role in biological phenomena. Moreover, their biocompatibility is attractive for nutrient or drug delivery system applications. Here the three-dimensional organization of dispersed cubic lipid self-assembled phases is fully revealed by cryo-electron tomography and compared with simulated structures. It is demonstrated that the interior is constituted of a perfect bicontinuous cubic phase, while the outside shows interlamellar attachments, which represent a transition state between the liquid crystalline interior phase and the outside vesicular structure. Therefore, compositional gradients within cubosomes are inferred, with a lipid bilayer separating at least one water channel set from the external aqueous phase. This is crucial to understand and enhance controlled release of target molecules and calls for a revision of postulated transport mechanisms from cubosomes to the aqueous phase. PMID:26573367

  1. Direct visualization of dispersed lipid bicontinuous cubic phases by cryo-electron tomography

    NASA Astrophysics Data System (ADS)

    Demurtas, Davide; Guichard, Paul; Martiel, Isabelle; Mezzenga, Raffaele; Hébert, Cécile; Sagalowicz, Laurent

    2015-11-01

    Bulk and dispersed cubic liquid crystalline phases (cubosomes), present in the body and in living cell membranes, are believed to play an essential role in biological phenomena. Moreover, their biocompatibility is attractive for nutrient or drug delivery system applications. Here the three-dimensional organization of dispersed cubic lipid self-assembled phases is fully revealed by cryo-electron tomography and compared with simulated structures. It is demonstrated that the interior is constituted of a perfect bicontinuous cubic phase, while the outside shows interlamellar attachments, which represent a transition state between the liquid crystalline interior phase and the outside vesicular structure. Therefore, compositional gradients within cubosomes are inferred, with a lipid bilayer separating at least one water channel set from the external aqueous phase. This is crucial to understand and enhance controlled release of target molecules and calls for a revision of postulated transport mechanisms from cubosomes to the aqueous phase.

  2. The existence of amorphous phase in Portland cements: Physical factors affecting Rietveld quantitative phase analysis

    SciTech Connect

    Snellings, Ruben Bazzoni, Amélie Scrivener, Karen

    2014-05-01

    Rietveld quantitative phase analysis has become a widespread tool for the characterization of Portland cement, both for research and production control purposes. One of the major remaining points of debate is whether Portland cements contain amorphous content or not. This paper presents detailed analyses of the amorphous phase contents in a set of commercial Portland cements, clinker, synthetic alite and limestone by Rietveld refinement of X-ray powder diffraction measurements using both external and internal standard methods. A systematic study showed that the sample preparation and comminution procedure is closely linked to the calculated amorphous contents. Particle size reduction by wet-grinding lowered the calculated amorphous contents to insignificant quantities for all materials studied. No amorphous content was identified in the final analysis of the Portland cements under investigation.

  3. Quantitative Phase Determination by Using a Michelson Interferometer

    ERIC Educational Resources Information Center

    Pomarico, Juan A.; Molina, Pablo F.; D'Angelo, Cristian

    2007-01-01

    The Michelson interferometer is one of the best established tools for quantitative interferometric measurements. It has been, and is still successfully used, not only for scientific purposes, but it is also introduced in undergraduate courses for qualitative demonstrations as well as for quantitative determination of several properties such as…

  4. 28 MHz swept source at 1.0 μm for ultrafast quantitative phase imaging

    PubMed Central

    Wei, Xiaoming; Lau, Andy K. S.; Xu, Yiqing; Tsia, Kevin K.; Wong, Kenneth K. Y.

    2015-01-01

    Emerging high-throughput optical imaging modalities, in particular those providing phase information, necessitate a demanding speed regime (e.g. megahertz sweep rate) for those conventional swept sources; while an effective solution is yet to be demonstrated. We demonstrate a stable breathing laser as inertia-free swept source (BLISS) operating at a wavelength sweep rate of 28 MHz, particularly for the ultrafast interferometric imaging modality at 1.0 μm. Leveraging a tunable dispersion compensation element inside the laser cavity, the wavelength sweep range of BLISS can be tuned from ~10 nm to ~63 nm. It exhibits a good intensity stability, which is quantified by the ratio of standard deviation to the mean of the pulse intensity, i.e. 1.6%. Its excellent wavelength repeatability, <0.05% per sweep, enables the single-shot imaging at an ultrafast line-scan rate without averaging. To showcase its potential applications, it is applied to the ultrafast (28-MHz line-scan rate) interferometric time-stretch (iTS) microscope to provide quantitative morphological information on a biological specimen at a lateral resolution of 1.2 μm. This fiber-based inertia-free swept source is demonstrated to be robust and broadband, and can be applied to other established imaging modalities, such as optical coherence tomography (OCT), of which an axial resolution better than 12 μm can be achieved. PMID:26504636

  5. 28 MHz swept source at 1.0 μm for ultrafast quantitative phase imaging.

    PubMed

    Wei, Xiaoming; Lau, Andy K S; Xu, Yiqing; Tsia, Kevin K; Wong, Kenneth K Y

    2015-10-01

    Emerging high-throughput optical imaging modalities, in particular those providing phase information, necessitate a demanding speed regime (e.g. megahertz sweep rate) for those conventional swept sources; while an effective solution is yet to be demonstrated. We demonstrate a stable breathing laser as inertia-free swept source (BLISS) operating at a wavelength sweep rate of 28 MHz, particularly for the ultrafast interferometric imaging modality at 1.0 μm. Leveraging a tunable dispersion compensation element inside the laser cavity, the wavelength sweep range of BLISS can be tuned from ~10 nm to ~63 nm. It exhibits a good intensity stability, which is quantified by the ratio of standard deviation to the mean of the pulse intensity, i.e. 1.6%. Its excellent wavelength repeatability, <0.05% per sweep, enables the single-shot imaging at an ultrafast line-scan rate without averaging. To showcase its potential applications, it is applied to the ultrafast (28-MHz line-scan rate) interferometric time-stretch (iTS) microscope to provide quantitative morphological information on a biological specimen at a lateral resolution of 1.2 μm. This fiber-based inertia-free swept source is demonstrated to be robust and broadband, and can be applied to other established imaging modalities, such as optical coherence tomography (OCT), of which an axial resolution better than 12 μm can be achieved. PMID:26504636

  6. Phase-sensitive multiple reference optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Dsouza, Roshan I.; Subhash, Hrebesh; Neuhaus, Kai; Hogan, Josh; Wilson, Carol; Leahy, Martin

    2016-03-01

    Multiple reference OCT (MR-OCT) is a recently developed novel time-domain OCT platform based on a miniature reference arm optical delay, which utilizes a single miniature actuator and a partial mirror to generate recirculating optical delay for extended axial-scan range. MR-OCT technology promises to fit into a robust and cost-effective design, compatible with integration into consumer-level devices for addressing wide applications in mobile healthcare and biometry applications. Using conventional intensity based OCT processing techniques, the high-resolution structural imaging capability of MR-OCT has been recently demonstrated for various applications including in vivo human samples. In this study, we demonstrate the feasibility of implementing phase based processing with MR-OCT for various functional applications such as Doppler imaging and sensing of blood vessels, and for tissue vibrography applications. The MR-OCT system operates at 1310nm with a spatial resolution of ~26 µm and an axial scan rate of 600Hz. Initial studies show a displacement-sensitivity of ~20 nm to ~120 nm for the first 1 to 9 orders of reflections, respectively with a mirror as test-sample. The corresponding minimum resolvable velocity for these orders are ~2.3 µm/sec and ~15 µm/sec respectively. Data from a chick chorioallantoic membrane (CAM) model will be shown to demonstrate the feasibility of MR-OCT for imaging in-vivo blood flow.

  7. Propagation-based phase-contrast tomography for high-resolution lung imaging with laboratory sources

    NASA Astrophysics Data System (ADS)

    Krenkel, Martin; Töpperwien, Mareike; Dullin, Christian; Alves, Frauke; Salditt, Tim

    2016-03-01

    We have performed high-resolution phase-contrast tomography on whole mice with a laboratory setup. Enabled by a high-brilliance liquid-metal-jet source, we show the feasibility of propagation-based phase contrast in local tomography even in the presence of strongly absorbing surrounding tissue as it is the case in small animal imaging of the lung. We demonstrate the technique by reconstructions of the mouse lung for two different fields of view, covering the whole organ, and a zoom to the local finer structure of terminal airways and alveoli. With a resolution of a few micrometers and the wide availability of the technique, studies of larger biological samples at the cellular level become possible.

  8. High speed optical tomography system for quantitative measurement and visualization of dynamic features in a round jet

    NASA Astrophysics Data System (ADS)

    McMackin, L.; Hugo, R. J.; Bishop, K. P.; Chen, E. Y.; Pierson, R. E.; Truman, C. R.

    An optical tomography system that is capable of operating at frame rates of up to 5 kHz has been used to obtain spatially resolved cross-sectional temperature images of a heated round jet. These tomographic images show dynamic details in the evolving vortical flow structures found in the near field of the jet that are consistent with previous studies of low speed jet flow. Reconstructions produced by the system are quantitative temperature distributions of a planar cross section of the jet measuring temperature differences with a spatial resolution of 1.4 mm.

  9. Myelinated mouse nerves studied by X-ray phase contrast zoom tomography.

    PubMed

    Bartels, M; Krenkel, M; Cloetens, P; Möbius, W; Salditt, T

    2015-12-01

    We have used X-ray phase contrast tomography to resolve the structure of uncut, entire myelinated optic, saphenous and sciatic mouse nerves. Intrinsic electron density contrast suffices to identify axonal structures. Specific myelin labeling by an osmium tetroxide stain enables distinction between axon and surrounding myelin sheath. Utilization of spherical wave illumination enables zooming capabilities which enable imaging of entire sciatic internodes as well as identification of sub-structures such as nodes of Ranvier and Schmidt-Lanterman incisures. PMID:26546551

  10. Myelinated mouse nerves studied by X-ray phase contrast zoom tomography.

    PubMed

    Bartels, M; Krenkel, M; Cloetens, P; Möbius, W; Salditt, T

    2015-12-01

    We have used X-ray phase contrast tomography to resolve the structure of uncut, entire myelinated optic, saphenous and sciatic mouse nerves. Intrinsic electron density contrast suffices to identify axonal structures. Specific myelin labeling by an osmium tetroxide stain enables distinction between axon and surrounding myelin sheath. Utilization of spherical wave illumination enables zooming capabilities which enable imaging of entire sciatic internodes as well as identification of sub-structures such as nodes of Ranvier and Schmidt-Lanterman incisures.

  11. Quantum Process Tomography of a Room Temperature Optically-Controlled Phase Shift

    NASA Astrophysics Data System (ADS)

    Kupchak, Connor; Rind, Samuel; Figueroa, Eden; Stony Brook University Team

    2015-05-01

    We have developed a room temperature setup capable of optically controlled phase shifts on a weak probe field. Our system is realized in a vapor of 87Rb atoms under the conditions of electromagnetically induced transparency utilizing a N-type energy level scheme coupled by three optical fields. By varying the power of the signal field, we can control the size of an optical phase shift experienced by weak coherent state pulses of < n > ~ 1 , propagating through the vapor. We quantify the optical phase shift by measuring the process output via balanced homodyne tomography which provides us with the complete quadrature and phase information of the output states. Furthermore, we measure the output for a set of states over a subspace of the coherent state basis and gain the information to completely reconstruct our phase shift procedure by coherent state quantum process tomography. The reconstruction yields a rank-4 process superoperator which grants the ability to predict how our phase shift process will behave on an arbitrary quantum optical state in the mode of the reconstruction. Our results demonstrate progress towards room temperature systems for possible quantum gates; a key component of a future quantum processor designed to operate at room temperature. US-Navy Office of Naval Research N00141410801, National Science Foundation PHY-1404398, Natural Sciences and Engineering Research Council of Canada.

  12. Characterization of cardiac quiescence from retrospective cardiac computed tomography using a correlation-based phase-to-phase deviation measure

    SciTech Connect

    Wick, Carson A.; McClellan, James H.; Arepalli, Chesnal D.; Auffermann, William F.; Henry, Travis S.; Khosa, Faisal; Coy, Adam M.; Tridandapani, Srini

    2015-02-15

    Purpose: Accurate knowledge of cardiac quiescence is crucial to the performance of many cardiac imaging modalities, including computed tomography coronary angiography (CTCA). To accurately quantify quiescence, a method for detecting the quiescent periods of the heart from retrospective cardiac computed tomography (CT) using a correlation-based, phase-to-phase deviation measure was developed. Methods: Retrospective cardiac CT data were obtained from 20 patients (11 male, 9 female, 33–74 yr) and the left main, left anterior descending, left circumflex, right coronary artery (RCA), and interventricular septum (IVS) were segmented for each phase using a semiautomated technique. Cardiac motion of individual coronary vessels as well as the IVS was calculated using phase-to-phase deviation. As an easily identifiable feature, the IVS was analyzed to assess how well it predicts vessel quiescence. Finally, the diagnostic quality of the reconstructed volumes from the quiescent phases determined using the deviation measure from the vessels in aggregate and the IVS was compared to that from quiescent phases calculated by the CT scanner. Three board-certified radiologists, fellowship-trained in cardiothoracic imaging, graded the diagnostic quality of the reconstructions using a Likert response format: 1 = excellent, 2 = good, 3 = adequate, 4 = nondiagnostic. Results: Systolic and diastolic quiescent periods were identified for each subject from the vessel motion calculated using the phase-to-phase deviation measure. The motion of the IVS was found to be similar to the aggregate vessel (AGG) motion. The diagnostic quality of the coronary vessels for the quiescent phases calculated from the aggregate vessel (P{sub AGG}) and IVS (P{sub IV} {sub S}) deviation signal using the proposed methods was comparable to the quiescent phases calculated by the CT scanner (P{sub CT}). The one exception was the RCA, which improved for P{sub AGG} for 18 of the 20 subjects when compared to P

  13. Bending magnet source: A radiation source for X-ray phase contrast tomography

    NASA Astrophysics Data System (ADS)

    Dhal, B. B.; Peele, A. G.; McMahon, P. J.; De Carlo, F.; Nugent, K. A.

    2006-11-01

    The rapid development of electronic data processing and phase retrieval technique for image reconstruction leads to new opportunities in X-ray phase tomography. A range of radiographic and tomographic demonstrations have now been made, typically utilizing the coherent flux from an insertion device at a synchrotron or a micro-focus laboratory source. In this paper we demonstrate that useful results may be obtained using a bending magnet source at a synchrotron. In particular we show that the same beamline can be used to make and characterize a sample made by X-ray lithographic methods.

  14. Phase-resolved optical coherence tomography and optical Doppler tomography for imaging blood flow in human skin with fast scanning speed and high velocity sensitivity

    SciTech Connect

    Zhao, Yonghua; Chen, Zhongping; Saxer, Christopher; Xiang, Shaohua; Boer, Johannes F. de; Nelson, J. Stuart

    2000-01-15

    We have developed a novel phase-resolved optical coherence tomography (OCT) and optical Doppler tomography (ODT) system that uses phase information derived from a Hilbert transformation to image blood flow in human skin with fast scanning speed and high velocity sensitivity. Using the phase change between sequential scans to construct flow-velocity imaging, this technique decouples spatial resolution and velocity sensitivity in flow images and increases imaging speed by more than 2 orders of magnitude without compromising spatial resolution or velocity sensitivity. The minimum flow velocity that can be detected with an axial-line scanning speed of 400 Hz and an average phase change over eight sequential scans is as low as 10 {mu}m/s , while a spatial resolution of 10 {mu}m is maintained. Using this technique, we present what are to our knowledge the first phase-resolved OCT/ODT images of blood flow in human skin. (c) 2000 Optical Society of America.

  15. Dual-wavelength in-line phase-shifting interferometry based on two dc-term-suppressed intensities with a special phase shift for quantitative phase extraction.

    PubMed

    Xu, Xiaoqing; Wang, Yawei; Xu, Yuanyuan; Jin, Weifeng

    2016-06-01

    To efficiently promote the phase retrieval in quantitative phase imaging, a new approach of quantitative phase extraction is proposed based on two intensities with dual wavelength after filtering the corresponding dc terms for each wavelength, in which a special phase shift is used. In this approach, only the combination of the phase-shifting technique and subtraction procedures is needed, and no additional algorithms are required. The thickness of the phase object can be achieved from the phase image, which is related to the synthetic beat wavelength. The feasibility of this method is verified by the simulated experiments of the optically transparent objects. PMID:27244381

  16. Breast tumor segmentation in high resolution x-ray phase contrast analyzer based computed tomography

    SciTech Connect

    Brun, E.; Grandl, S.; Sztrókay-Gaul, A.; Gasilov, S.; Barbone, G.; Mittone, A.; Coan, P.; Bravin, A.

    2014-11-01

    Purpose: Phase contrast computed tomography has emerged as an imaging method, which is able to outperform present day clinical mammography in breast tumor visualization while maintaining an equivalent average dose. To this day, no segmentation technique takes into account the specificity of the phase contrast signal. In this study, the authors propose a new mathematical framework for human-guided breast tumor segmentation. This method has been applied to high-resolution images of excised human organs, each of several gigabytes. Methods: The authors present a segmentation procedure based on the viscous watershed transform and demonstrate the efficacy of this method on analyzer based phase contrast images. The segmentation of tumors inside two full human breasts is then shown as an example of this procedure’s possible applications. Results: A correct and precise identification of the tumor boundaries was obtained and confirmed by manual contouring performed independently by four experienced radiologists. Conclusions: The authors demonstrate that applying the watershed viscous transform allows them to perform the segmentation of tumors in high-resolution x-ray analyzer based phase contrast breast computed tomography images. Combining the additional information provided by the segmentation procedure with the already high definition of morphological details and tissue boundaries offered by phase contrast imaging techniques, will represent a valuable multistep procedure to be used in future medical diagnostic applications.

  17. A method to calibrate phase fluctuation in polarization-sensitive swept-source optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Lu, Zenghai; Kasaragod, Deepa K.; Matcher, Stephen J.

    2011-06-01

    A phase fluctuation calibration method is presented for polarization-sensitive swept-source optical coherence tomography (PS-SS-OCT) using continuous polarization modulation. The method consists of the generation of a continuous triggered tone-burst waveform rather than an asynchronous waveform by use of a function generator and the removal of the global phases of the measured Jones matrices by use of matrix normalization. This could remove the use of auxiliary optical components for the phase fluctuation compensation in the system, which reduces the system complexity. Phase fluctuation calibration is necessary to obtain the reference Jones matrix by averaging the measured Jones matrices at sample surfaces. Measurements on an equine tendon sample were made by the PS-SS-OCT system to validate the proposed method.

  18. Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs

    NASA Astrophysics Data System (ADS)

    Krenkel, Martin; Markus, Andrea; Bartels, Matthias; Dullin, Christian; Alves, Frauke; Salditt, Tim

    2015-05-01

    We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium.

  19. Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs

    PubMed Central

    Krenkel, Martin; Markus, Andrea; Bartels, Matthias; Dullin, Christian; Alves, Frauke; Salditt, Tim

    2015-01-01

    We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium. PMID:25966338

  20. Electrical impedance tomography spectroscopy method for characterising particles in solid-liquid phase

    SciTech Connect

    Zhao, Yanlin; Wang, Mi; Yao, Jun

    2014-04-11

    Electrical impedance tomography (EIT) is one of the process tomography techniques to provide an on-line non-invasive imaging for multiphase flow measurement. With EIT measurements, the images of impedance real part, impedance imaginary part, phase angle, and magnitude can be obtained. However, most of the applications of EIT in the process industries rely on the conductivity difference between two phases in fluids to obtain the concentration profiles. It is not common to use the imaginary part or phase angle due to the dominant change in conductivity or complication in the use of other impedance information. In a solid-liquid two phases system involving nano- or submicro-particles, characterisation of particles (e.g. particle size and concentration) have to rely on the measurement of impedance phase angle or imaginary part. Particles in a solution usually have an electrical double layer associated with their surfaces and can form an induced electrical dipole moment due to the polarization of the electrical double layer under the influence of an alternating electric field. Similar to EIT, electrical impedance spectroscopy (EIS) measurement can record the electrical impedance data, including impedance real part, imaginary part and phase angle (θ), which are caused by the polarization of the electrical double layer. These impedance data are related to the particle characteristics e.g. particle size, particle and ionic concentrations in the aqueous medium, therefore EIS method provides a capability for characterising the particles in suspensions. Electrical impedance tomography based on EIS measurement or namely, electrical impedance tomography spectroscopy (EITS) could image the spatial distribution of particle characteristics. In this paper, a new method, including test set-up and data analysis, for characterisation of particles in suspensions are developed through the experimental approach. The experimental results on tomographic imaging of colloidal particles

  1. Electrical impedance tomography spectroscopy method for characterising particles in solid-liquid phase

    NASA Astrophysics Data System (ADS)

    Zhao, Yanlin; Wang, Mi; Yao, Jun

    2014-04-01

    Electrical impedance tomography (EIT) is one of the process tomography techniques to provide an on-line non-invasive imaging for multiphase flow measurement. With EIT measurements, the images of impedance real part, impedance imaginary part, phase angle, and magnitude can be obtained. However, most of the applications of EIT in the process industries rely on the conductivity difference between two phases in fluids to obtain the concentration profiles. It is not common to use the imaginary part or phase angle due to the dominant change in conductivity or complication in the use of other impedance information. In a solid-liquid two phases system involving nano- or submicro-particles, characterisation of particles (e.g. particle size and concentration) have to rely on the measurement of impedance phase angle or imaginary part. Particles in a solution usually have an electrical double layer associated with their surfaces and can form an induced electrical dipole moment due to the polarization of the electrical double layer under the influence of an alternating electric field. Similar to EIT, electrical impedance spectroscopy (EIS) measurement can record the electrical impedance data, including impedance real part, imaginary part and phase angle (θ), which are caused by the polarization of the electrical double layer. These impedance data are related to the particle characteristics e.g. particle size, particle and ionic concentrations in the aqueous medium, therefore EIS method provides a capability for characterising the particles in suspensions. Electrical impedance tomography based on EIS measurement or namely, electrical impedance tomography spectroscopy (EITS) could image the spatial distribution of particle characteristics. In this paper, a new method, including test set-up and data analysis, for characterisation of particles in suspensions are developed through the experimental approach. The experimental results on tomographic imaging of colloidal particles

  2. Quantitative phase imaging of human red blood cells using phase-shifting white light interference microscopy with colour fringe analysis

    NASA Astrophysics Data System (ADS)

    Singh Mehta, Dalip; Srivastava, Vishal

    2012-11-01

    We report quantitative phase imaging of human red blood cells (RBCs) using phase-shifting interference microscopy. Five phase-shifted white light interferograms are recorded using colour charge coupled device camera. White light interferograms were decomposed into red, green, and blue colour components. The phase-shifted interferograms of each colour were then processed by phase-shifting analysis and phase maps for red, green, and blue colours were reconstructed. Wavelength dependent refractive index profiles of RBCs were computed from the single set of white light interferogram. The present technique has great potential for non-invasive determination of refractive index variation and morphological features of cells and tissues.

  3. Surface wave phase-velocity tomography based on multichannel cross-correlation

    NASA Astrophysics Data System (ADS)

    Jin, Ge; Gaherty, James B.

    2015-06-01

    We have developed a new method to retrieve seismic surface wave phase velocity using dense seismic arrays. The method measures phase variations between nearby stations based on waveform cross-correlation. The coherence in waveforms between adjacent stations results in highly precise relative phase estimates. Frequency-dependent phase variations are then inverted for spatial variations in apparent phase velocity via the Eikonal equation. Frequency-dependent surface wave amplitudes measured on individual stations are used to correct the apparent phase velocity to account for multipathing via the Helmholtz equation. By using coherence and other data selection criteria, we construct an automated system that retrieves structural phase-velocity maps directly from raw seismic waveforms for individual earthquakes without human intervention. The system is applied to broad-band seismic data from over 800 events recorded on EarthScope's USArray from 2006 to 2014, systematically building up Rayleigh-wave phase-velocity maps between the periods of 20 and 100 s for the entire continental United States. At the highest frequencies, the resulting maps are highly correlated with phase-velocity maps derived from ambient noise tomography. At all frequencies, we observe a significant contrast in Rayleigh-wave phase velocity between the tectonically active western US and the stable eastern US, with the phase velocity variations in the western US being 1-2 times greater. The Love wave phase-velocity maps are also calculated. We find that overtone contamination may produce systemic bias for the Love-wave phase-velocity measurements.

  4. Eddy current pulsed phase thermography for subsurface defect quantitatively evaluation

    NASA Astrophysics Data System (ADS)

    He, Yunze; Pan, Mengchun; Tian, GuiYun; Chen, Dixiang; Tang, Ying; Zhang, Hong

    2013-09-01

    This Letter verified eddy current pulse phase thermography through numerical and experimental studies. During the numerical studies, two characteristic features, blind frequency and min phase, were extracted from differential phase spectra, and their monotonic relationships with defects' depth under different heating time were compared. According to the numerical studies, 100 ms was employed as heating time during the improved experimental studies. The experimental results agreed with the numerical results. Based on their linear relationship with defects' depths, both features can be used to measure the defect's depth.

  5. Quantitative phase-field model of alloy solidification.

    PubMed

    Echebarria, Blas; Folch, Roger; Karma, Alain; Plapp, Mathis

    2004-12-01

    We present a detailed derivation and thin interface analysis of a phase-field model that can accurately simulate microstructural pattern formation for low-speed directional solidification of a dilute binary alloy. This advance with respect to previous phase-field models is achieved by the addition of a phenomenological "antitrapping" solute current in the mass conservation relation [Phys. Rev. Lett. 87, 115701 (2001)

  6. Adaptive anisotropic diffusion for noise reduction of phase images in Fourier domain Doppler optical coherence tomography.

    PubMed

    Xia, Shaoyan; Huang, Yong; Peng, Shizhao; Wu, Yanfeng; Tan, Xiaodi

    2016-08-01

    Phase image in Fourier domain Doppler optical coherence tomography offers additional flow information of investigated samples, which provides valuable evidence towards accurate medical diagnosis. High quality phase images are thus desirable. We propose a noise reduction method for phase images by combining a synthetic noise estimation criteria based on local noise estimator (LNE) and distance median value (DMV) with anisotropic diffusion model. By identifying noise and signal pixels accurately and diffusing them with different coefficients respectively and adaptive iteration steps, we demonstrated the effectiveness of our proposed method in both phantom and mouse artery images. Comparison with other methods such as filtering method (mean, median filtering), wavelet method, probabilistic method and partial differential equation based methods in terms of peak signal-to-noise ratio (PSNR), equivalent number of looks (ENL) and contrast-to-noise ratio (CNR) showed the advantages of our method in reserving image energy and removing noise. PMID:27570687

  7. Polarization-sensitive optical coherence tomography using continuous polarization modulation with arbitrary phase modulation amplitude

    NASA Astrophysics Data System (ADS)

    Lu, Zenghai; Kasaragod, Deepa K.; Matcher, Stephen J.

    2012-03-01

    We demonstrate theoretically and experimentally that the phase retardance and relative optic-axis orientation of a sample can be calculated without prior knowledge of the actual value of the phase modulation amplitude when using a polarization-sensitive optical coherence tomography system based on continuous polarization modulation (CPM-PS-OCT). We also demonstrate that the sample Jones matrix can be calculated at any values of the phase modulation amplitude in a reasonable range depending on the system effective signal-to-noise ratio. This has fundamental importance for the development of clinical systems by simplifying the polarization modulator drive instrumentation and eliminating its calibration procedure. This was validated on measurements of a three-quarter waveplate and an equine tendon sample by a fiber-based swept-source CPM-PS-OCT system.

  8. Adaptive anisotropic diffusion for noise reduction of phase images in Fourier domain Doppler optical coherence tomography

    PubMed Central

    Xia, Shaoyan; Huang, Yong; Peng, Shizhao; Wu, Yanfeng; Tan, Xiaodi

    2016-01-01

    Phase image in Fourier domain Doppler optical coherence tomography offers additional flow information of investigated samples, which provides valuable evidence towards accurate medical diagnosis. High quality phase images are thus desirable. We propose a noise reduction method for phase images by combining a synthetic noise estimation criteria based on local noise estimator (LNE) and distance median value (DMV) with anisotropic diffusion model. By identifying noise and signal pixels accurately and diffusing them with different coefficients respectively and adaptive iteration steps, we demonstrated the effectiveness of our proposed method in both phantom and mouse artery images. Comparison with other methods such as filtering method (mean, median filtering), wavelet method, probabilistic method and partial differential equation based methods in terms of peak signal-to-noise ratio (PSNR), equivalent number of looks (ENL) and contrast-to-noise ratio (CNR) showed the advantages of our method in reserving image energy and removing noise. PMID:27570687

  9. Nonstationary phase boundary estimation in electrical impedance tomography using unscented Kalman filter

    SciTech Connect

    Ijaz, Umer Zeeshan; Khambampati, Anil Kumar; Lee, Jeong Seong; Kim, Sin; Kim, Kyung Youn

    2008-07-20

    In this paper, an effective nonstationary phase boundary estimation scheme in electrical impedance tomography is presented based on the unscented Kalman filter. The inverse problem is treated as a stochastic nonlinear state estimation problem with the nonstationary phase boundary (state) being estimated online with the aid of unscented Kalman filter. This research targets the industrial applications, such as imaging of stirrer vessel for detection of air distribution or detecting large air bubbles in pipelines. Within the domains, there exist 'voids' having zero conductivity. The design variables for phase boundary estimation are truncated Fourier coefficients. Computer simulations and experimental results are provided to evaluate the performance of unscented Kalman filter in comparison with extended Kalman filter to show a better performance of the unscented Kalman filter approach.

  10. Quantitative phase imaging by wide field lensless digital holographic microscope

    NASA Astrophysics Data System (ADS)

    Adinda-Ougba, A.; Koukourakis, N.; Essaidi, A.; Ger­hardt, N. C.; Hofmann, M. R.

    2015-05-01

    Wide field, lensless microscopes have been developed for telemedicine and for resource limited setting [1]. They are based on in-line digital holography which is capable to provide amplitude and phase information resulting from numerical reconstruction. The phase information enables achieving axial resolution in the nanometer range. Hence, such microscopes provide a powerful tool to determine three-dimensional topologies of microstructures. In this contribution, a compact, low-cost, wide field, lensless microscope is presented, which is capable of providing topological profiles of microstructures in transparent material. Our setup consist only of two main components: a CMOSsensor chip and a laser diode without any need of a pinhole. We use this very simple setup to record holograms of microobjects. A wide field of view of ~24 mm², and a lateral resolution of ~2 μm are achieved. Moreover, amplitude and phase information are obtained from the numerical reconstruction of the holograms using a phase retrieval algorithm together with the angular spectrum propagation method. Topographic information of highly transparent micro-objects is obtained from the phase data. We evaluate our system by recording holograms of lines with different depths written by a focused laser beam. A reliable characterization of laser written microstructures is crucial for their functionality. Our results show that this system is valuable for determination of topological profiles of microstructures in transparent material.

  11. Online quantitative phase imaging of vascular endothelial cells under fluid shear stress utilizing digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Odenthal-Schnittler, Maria; Schnittler, Hans Joachim; Kemper, Björn

    2016-03-01

    We have explored the utilization of quantitative phase imaging with digital holographic microscopy (DHM) as a novel tool for quantifying the dynamics of morphologic parameters (morphodynamics) of confluent endothelial cell layers under fluid shear stress conditions. Human umbilical vein endothelial cells (HUVECs) were exposed to fluid shear stress in a transparent cone/plate flow device (BioTech-Flow-System) and imaged with a modular setup for quantitative DHM phase imaging for up to 48 h. The resulting series of quantitative phase image sequences were analyzed for the average surface roughness of the cell layers and cell alignment. Our results demonstrate that quantitative phase imaging is a powerful and reliable tool to quantify the dynamics of morphological adaptation of endothelial cells to fluid shear stress.

  12. Simplified approach for quantitative digital holographic phase contrast imaging of living cells

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Vollmer, Angelika; Rommel, Christina E.; Schnekenburger, Jürgen; Bally, Gert Von

    2011-02-01

    Many interferometry-based quantitative phase contrast imaging techniques require a separately generated coherent reference wave. This results in a low phase stability and the demand for a precise adjustment of the intensity ratio between object and reference wave. To overcome these problems, the performance of a Michelson interferometer approach for digital holographic microscopy was analyzed that avoids a separately generated reference wave by superposition of different image areas. It is shown that this simplified arrangement yields improved phase stability. Furthermore, results from time-lapse investigations on living pancreas tumor cells demonstrate the capability of the method for reliable quantitative phase contrast imaging.

  13. Feasibility of spectral-domain phase-sensitive optical coherence tomography for middle ear vibrometry.

    PubMed

    Subhash, Hrebesh M; Nguyen-Huynh, Anh; Wang, Ruikang K; Jacques, Steven L; Choudhury, Niloy; Nuttall, Alfred L

    2012-06-01

    We describe a novel application of spectral-domain phase-sensitive optical coherence tomography (SD PS-OCT) to detect the tiny motions of the middle ear structures, such as the tympanic membrane and ossicular chain, and their morphological features for differential diagnosis of CHL. This technique has the potential to provide meaningful vibration of ossicles with a vibration sensitivity of ≈ 0.5 nm at 1 kHz of acoustic stimulation. To the best of our knowledge, this is the first demonstration of depth-resolved vibration imaging of ossicles with a PS-OCT system at a nanometer scale.

  14. Phase contrast tomography of the mouse cochlea at microfocus x-ray sources

    NASA Astrophysics Data System (ADS)

    Bartels, Matthias; Hernandez, Victor H.; Krenkel, Martin; Moser, Tobias; Salditt, Tim

    2013-08-01

    We present phase contrast x-ray tomography of functional soft tissue within the bony cochlear capsule of mice, carried out at laboratory microfocus sources with well-matched source, detector, geometry, and reconstruction algorithms at spatial resolutions down to 2 μm. Contrast, data quality and resolution enable the visualization of thin membranes and nerve fibers as well as automated segmentation of surrounding bone. By complementing synchrotron radiation imaging techniques, a broad range of biomedical applications becomes possible as demonstrated for optogenetic cochlear implant research.

  15. Phase contrast tomography of the mouse cochlea at microfocus x-ray sources

    SciTech Connect

    Bartels, Matthias; Krenkel, Martin; Hernandez, Victor H.; Moser, Tobias; Salditt, Tim

    2013-08-19

    We present phase contrast x-ray tomography of functional soft tissue within the bony cochlear capsule of mice, carried out at laboratory microfocus sources with well-matched source, detector, geometry, and reconstruction algorithms at spatial resolutions down to 2 μm. Contrast, data quality and resolution enable the visualization of thin membranes and nerve fibers as well as automated segmentation of surrounding bone. By complementing synchrotron radiation imaging techniques, a broad range of biomedical applications becomes possible as demonstrated for optogenetic cochlear implant research.

  16. Enlightening intracellular complexity of living cells with quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Martinez Torres, C.; Laperrousaz, B.; Berguiga, L.; Boyer Provera, E.; Elezgaray, J.; Nicolini, F. E.; Maguer-Satta, V.; Arneodo, A.; Argoul, F.

    2016-03-01

    The internal distribution of refractive indices (RIs) of a living cell is much more complex than usually admitted in multi-shell models. The reconstruction of RI maps from single phase images has rarely been achieved for several reasons: (i) we still have very little knowledge of the impact of internal macromolecular complexes on the local RI and (ii) phase changes produced by light propagation through the sample are mixed with diffraction effects by internal cell bodies. We propose the implementation a 2D wavelet-based contour chain detection method to distinguish internal boundaries thanks to their greatest optical path difference gradients. These contour chains correspond to the highest image phase contrast and follow the local RI inhomogeneities linked to the intracellular structural intricacy. Their statistics and spatial distribution are morphological indicators for distinguishing cells of different origins and to follow their transformation in pathologic situations. We use this method to compare non adherent blood cells from primary and laboratory culture origins, in healthy and pathological situations (chronic myelogenous leukaemia). In a second part of this presentation, we concentrate on the temporal dynamics of the phase contour chains and we discuss the spectral decomposition of their dynamics in both health and disease.

  17. X-ray computed tomography observations of phase distribution during methane hydrate formation and dissociation process in a sediment sample

    NASA Astrophysics Data System (ADS)

    Ahn, Taewoong; Lee, Jaehyoung; Lee, Joo Yong; Kim, Se-Joon; Seo, Young-ju

    2016-04-01

    The recovery schemes for natural gas caged in the solid state have not been commercialized. Depressurization has been known as a promising method due to its economic feasibility according to previous lab-scale experiments and simulation studies. However, the results of few field tests showed that the production characteristics of real field differed from that of predicted results. To reliably predict the production performance of real fields, it is necessary to understand quantitative changes of phase distribution and fluid flow in sediments in response to hydrate dissociation by depressurization. In this study, we observed and analyzed the phase distribution and flow behavior during methane hydrate formation and dissociation using X-ray computed tomography which provides high-resolution density distribution. Artificial particles having similar grain size distribution of sandy layers found in real hydrate field were packed into X-ray transparent aluminum vessel. Information on pore distribution within a sediment sample was achieved by comparing CT images between dry condition and fully water-saturated condition. Dynamic changes of phase saturation were observed during gas flooding, through which potential flow pathway was estimated. Hydrate formation and dissociation significantly affected phase distribution and flow pathway. Hydrate distribution was extremely heterogeneous in every tests of hydrate formation repeated with same amount of water. It was inferred that water saturation prior to hydrate formation was not directly correlated to the hydrate distribution. There were definite differences of hydrate dissociation behavior between gas-saturated and water-saturated hydrate-bearing sample. The production of gas and water lasted quite a while even after the production pressure reached the target level of depressurization.

  18. Bone Health Monitoring in Astronauts: Recommended Use of Quantitative Computed Tomography [QCT] for Clinical and Operational Decisions

    NASA Technical Reports Server (NTRS)

    Sibonga, J. D.; Truskowski, P.

    2010-01-01

    This slide presentation reviews the concerns that astronauts in long duration flights might have a greater risk of bone fracture as they age than the general population. A panel of experts was convened to review the information and recommend mechanisms to monitor the health of bones in astronauts. The use of Quantitative Computed Tomography (QCT) scans for risk surveillance to detect the clinical trigger and to inform countermeasure evaluation is reviewed. An added benefit of QCT is that it facilitates an individualized estimation of bone strength by Finite Element Modeling (FEM), that can inform approaches for bone rehabilitation. The use of FEM is reviewed as a process that arrives at a composite number to estimate bone strength, because it integrates multiple factors.

  19. Quantitative chemical-structure evaluation using atom probe tomography: Short-range order analysis of Fe-Al.

    PubMed

    Marceau, R K W; Ceguerra, A V; Breen, A J; Raabe, D; Ringer, S P

    2015-10-01

    Short-range-order (SRO) has been quantitatively evaluated in an Fe-18Al (at%) alloy using atom probe tomography (APT) data and by calculation of the generalised multicomponent short-range order (GM-SRO) parameters, which have been determined by shell-based analysis of the three-dimensional atomic positions. The accuracy of this method with respect to limited detector efficiency and spatial resolution is tested against simulated D03 ordered data. Whilst there is minimal adverse effect from limited atom probe instrument detector efficiency, the combination of this with imperfect spatial resolution has the effect of making the data appear more randomised. The value of lattice rectification of the experimental APT data prior to GM-SRO analysis is demonstrated through improved information sensitivity.

  20. Quantitative phase-field modeling for wetting phenomena.

    PubMed

    Badillo, Arnoldo

    2015-03-01

    A new phase-field model is developed for studying partial wetting. The introduction of a third phase representing a solid wall allows for the derivation of a new surface tension force that accounts for energy changes at the contact line. In contrast to other multi-phase-field formulations, the present model does not need the introduction of surface energies for the fluid-wall interactions. Instead, all wetting properties are included in a unique parameter known as the equilibrium contact angle θeq. The model requires the solution of a single elliptic phase-field equation, which, coupled to conservation laws for mass and linear momentum, admits the existence of steady and unsteady compact solutions (compactons). The representation of the wall by an additional phase field allows for the study of wetting phenomena on flat, rough, or patterned surfaces in a straightforward manner. The model contains only two free parameters, a measure of interface thickness W and β, which is used in the definition of the mixture viscosity μ=μlϕl+μvϕv+βμlϕw. The former controls the convergence towards the sharp interface limit and the latter the energy dissipation at the contact line. Simulations on rough surfaces show that by taking values for β higher than 1, the model can reproduce, on average, the effects of pinning events of the contact line during its dynamic motion. The model is able to capture, in good agreement with experimental observations, many physical phenomena fundamental to wetting science, such as the wetting transition on micro-structured surfaces and droplet dynamics on solid substrates. PMID:25871200

  1. Report of improved performance in Talbot–Lau phase-contrast computed tomography

    SciTech Connect

    Weber, Thomas Pelzer, Georg; Rieger, Jens; Ritter, André; Anton, Gisela

    2015-06-15

    Purpose: Many expectations have been raised since the use of conventional x-ray tubes on grating-based x-ray phase-contrast imaging. Despite a reported increase in contrast-to-noise ratio (CNR) in many publications, there is doubt on whether phase-contrast computed tomography (CT) is advantageous in clinical CT scanners in vivo. The aim of this paper is to contribute to this discussion by analyzing the performance of a phase-contrast CT laboratory setup. Methods: A phase-contrast CT performance analysis was done. Projection images of a phantom were recorded, and image slices were reconstructed using standard filtered back projection methods. The resulting image slices were analyzed by determining the CNRs in the attenuation and phase image. These results were compared to analytically calculated expectations according to the already published phase-contrast CT performance analysis by Raupach and Flohr [Med. Phys. 39, 4761–4774 (2012)]. There, a severe mistake was found leading to wrong predictions of the performance of phase-contrast CT. The error was corrected and with the new formulae, the experimentally obtained results matched the analytical calculations. Results: The squared ratios of the phase-contrast CNR and the attenuation CNR obtained in the authors’ experiment are five- to ten-fold higher than predicted by Raupach and Flohr [Med. Phys. 39, 4761–4774 (2012)]. The effective lateral spatial coherence length deduced outnumbers the already optimistic assumption of Raupach and Flohr [Med. Phys. 39, 4761–4774 (2012)] by a factor of 3. Conclusions: The authors’ results indicate that the assumptions made in former performance analyses are pessimistic. The break-even point, when phase-contrast CT outperforms attenuation CT, is within reach even with realistic, nonperfect gratings. Further improvements to state-of-the-art clinical CT scanners, like increasing the spatial resolution, could change the balance in favor of phase-contrast computed tomography

  2. Heart-beat-phase-coherent Doppler optical coherence tomography for measuring pulsatile ocular blood flow.

    PubMed

    Schmoll, Tilman; Leitgeb, Rainer A

    2013-03-01

    We introduce a Doppler OCT (DOCT) platform that is fully synchronized with the heart-beat via a pulse oximeter. The system allows reconstructing heart-beat-phase-coherent quantitative DOCT volumes. The method is to acquire a series of DOCT volumes and to record the pulse in parallel. The heartbeat data is used for triggering the start of each DOCT volume acquisition. The recorded volume series is registered to the level of capillaries using a cross-volume registration. The information of the pulse phase is used to rearrange the tomograms in time, to obtain a series of phase coherent DOCT volumes over a pulse. We present Doppler angle independent quantitative evaluation of the absolute pulsatile blood flow within individual retinal vessels as well as of the total retinal blood flow over a full heartbeat cycle.

  3. [Quantitative structure characteristics and fractal dimension of Chinese medicine granules measured by synchrotron radiation X-ray computed micro tomography].

    PubMed

    Lu, Xiao-long; Zheng, Qin; Yin, Xian-zhen; Xiao, Guang-qing; Liao, Zu-hua; Yang, Ming; Zhang, Ji-wen

    2015-06-01

    The shape and structure of granules are controlled by the granulation process, which is one of the main factors to determine the nature of the solid dosage forms. In this article, three kinds of granules of a traditional Chinese medicine for improving appetite and promoting digestion, namely, Jianwei Granules, were prepared using granulation technologies as pendular granulation, high speed stirring granulation, and fluidized bed granulation and the powder properties of them were investigated. Meanwhile, synchrotron radiation X-ray computed micro tomography (SR-µCT) was applied to quantitatively determine the irregular internal structures of the granules. The three-dimensional (3D) structure models were obtained by 3D reconstruction, which were more accurately to characterize the three-dimensional structures of the particles through the quantitative data. The models were also used to quantitatively compare the structural differences of granules prepared by different granulation processes with the same formula, so as to characterize how the production process plays a role in the pharmaceutical behaviors of the granules. To focus on the irregularity of the particle structure, the box counting method was used to calculate the fractal dimensions of the granules. The results showed that the fractal dimension is more sensitive to reflect the minor differences in the structure features than the conventional parameters, and capable to specifically distinct granules in structure. It is proved that the fractal dimension could quantitatively characterize the structural information of irregular granules. It is the first time suggested by our research that the fractal dimension difference (Df,c) between two fractal dimension parameters, namely, the volume matrix fractal dimension and the surface matrix fractal dimension, is a new index to characterize granules with irregular structures and evaluate the effects of production processes on the structures of granules as a new

  4. [Quantitative structure characteristics and fractal dimension of Chinese medicine granules measured by synchrotron radiation X-ray computed micro tomography].

    PubMed

    Lu, Xiao-long; Zheng, Qin; Yin, Xian-zhen; Xiao, Guang-qing; Liao, Zu-hua; Yang, Ming; Zhang, Ji-wen

    2015-06-01

    The shape and structure of granules are controlled by the granulation process, which is one of the main factors to determine the nature of the solid dosage forms. In this article, three kinds of granules of a traditional Chinese medicine for improving appetite and promoting digestion, namely, Jianwei Granules, were prepared using granulation technologies as pendular granulation, high speed stirring granulation, and fluidized bed granulation and the powder properties of them were investigated. Meanwhile, synchrotron radiation X-ray computed micro tomography (SR-µCT) was applied to quantitatively determine the irregular internal structures of the granules. The three-dimensional (3D) structure models were obtained by 3D reconstruction, which were more accurately to characterize the three-dimensional structures of the particles through the quantitative data. The models were also used to quantitatively compare the structural differences of granules prepared by different granulation processes with the same formula, so as to characterize how the production process plays a role in the pharmaceutical behaviors of the granules. To focus on the irregularity of the particle structure, the box counting method was used to calculate the fractal dimensions of the granules. The results showed that the fractal dimension is more sensitive to reflect the minor differences in the structure features than the conventional parameters, and capable to specifically distinct granules in structure. It is proved that the fractal dimension could quantitatively characterize the structural information of irregular granules. It is the first time suggested by our research that the fractal dimension difference (Df,c) between two fractal dimension parameters, namely, the volume matrix fractal dimension and the surface matrix fractal dimension, is a new index to characterize granules with irregular structures and evaluate the effects of production processes on the structures of granules as a new

  5. Off-axis digital holographic camera for quantitative phase microscopy.

    PubMed

    Monemhaghdoust, Zahra; Montfort, Frédéric; Emery, Yves; Depeursinge, Christian; Moser, Christophe

    2014-06-01

    We propose and experimentally demonstrate a digital holographic camera which can be attached to the camera port of a conventional microscope for obtaining digital holograms in a self-reference configuration, under short coherence illumination and in a single shot. A thick holographic grating filters the beam containing the sample information in two dimensions through diffraction. The filtered beam creates the reference arm of the interferometer. The spatial filtering method, based on the high angular selectivity of the thick grating, reduces the alignment sensitivity to angular displacements compared with pinhole based Fourier filtering. The addition of a thin holographic grating alters the coherence plane tilt introduced by the thick grating so as to create high-visibility interference over the entire field of view. The acquired full-field off-axis holograms are processed to retrieve the amplitude and phase information of the sample. The system produces phase images of cheek cells qualitatively similar to phase images extracted with a standard commercial DHM.

  6. Prospects and challenges of quantitative phase imaging in tumor cell biology

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Götte, Martin; Greve, Burkhard; Ketelhut, Steffi

    2016-03-01

    Quantitative phase imaging (QPI) techniques provide high resolution label-free quantitative live cell imaging. Here, prospects and challenges of QPI in tumor cell biology are presented, using the example of digital holographic microscopy (DHM). It is shown that the evaluation of quantitative DHM phase images allows the retrieval of different parameter sets for quantification of cellular motion changes in migration and motility assays that are caused by genetic modifications. Furthermore, we demonstrate simultaneously label-free imaging of cell growth and morphology properties.

  7. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues.

    PubMed

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-01-01

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology. PMID:27358000

  8. Quantitative optical coherence tomography imaging of intermediate flow defect phenotypes in ciliary physiology and pathophysiology

    NASA Astrophysics Data System (ADS)

    Huang, Brendan K.; Gamm, Ute A.; Jonas, Stephan; Khokha, Mustafa K.; Choma, Michael A.

    2015-03-01

    Cilia-driven fluid flow is a critical yet poorly understood aspect of pulmonary physiology. Here, we demonstrate that optical coherence tomography-based particle tracking velocimetry can be used to quantify subtle variability in cilia-driven flow performance in Xenopus, an important animal model of ciliary biology. Changes in flow performance were quantified in the setting of normal development, as well as in response to three types of perturbations: mechanical (increased fluid viscosity), pharmacological (disrupted serotonin signaling), and genetic (diminished ciliary motor protein expression). Of note, we demonstrate decreased flow secondary to gene knockdown of kif3a, a protein involved in ciliogenesis, as well as a dose-response decrease in flow secondary to knockdown of dnah9, an important ciliary motor protein.

  9. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues

    NASA Astrophysics Data System (ADS)

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-06-01

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology.

  10. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues

    PubMed Central

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-01-01

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology. PMID:27358000

  11. Eigenspectra optoacoustic tomography achieves quantitative blood oxygenation imaging deep in tissues.

    PubMed

    Tzoumas, Stratis; Nunes, Antonio; Olefir, Ivan; Stangl, Stefan; Symvoulidis, Panagiotis; Glasl, Sarah; Bayer, Christine; Multhoff, Gabriele; Ntziachristos, Vasilis

    2016-06-30

    Light propagating in tissue attains a spectrum that varies with location due to wavelength-dependent fluence attenuation, an effect that causes spectral corruption. Spectral corruption has limited the quantification accuracy of optical and optoacoustic spectroscopic methods, and impeded the goal of imaging blood oxygen saturation (sO2) deep in tissues; a critical goal for the assessment of oxygenation in physiological processes and disease. Here we describe light fluence in the spectral domain and introduce eigenspectra multispectral optoacoustic tomography (eMSOT) to account for wavelength-dependent light attenuation, and estimate blood sO2 within deep tissue. We validate eMSOT in simulations, phantoms and animal measurements and spatially resolve sO2 in muscle and tumours, validating our measurements with histology data. eMSOT shows substantial sO2 accuracy enhancement over previous optoacoustic methods, potentially serving as a valuable tool for imaging tissue pathophysiology.

  12. Improved diagnostic differentiation of renal cystic lesions with phase-contrast computed tomography (PCCT)

    NASA Astrophysics Data System (ADS)

    Noel, Peter B.; Willner, Marian; Fingerle, Alexander; Herzen, Julia; Münzel, Daniela; Hahn, Dieter; Rummeny, Ernst J.; Pfeiffer, Franz

    2012-03-01

    The diagnostic quality of phase-contrast computed tomography (PCCT) is one the unexplored areas in medical imaging; at the same time, it seems to offer the opportunity as a fast and highly sensitive diagnostic tool. Conventional computed tomography (CT) has had an enormous impact on medicine, while it is limited in soft-tissue contrast. One example that portrays this challenge is the differentiation between benign and malignant renal cysts. In this work we report on a feasibility study to determine the usefulness of PCCT in differentiation of renal cysts. A renal phantom was imaged with a grating-based PCCT system consisting of a standard rotating anode x-ray tube (40 kV, 70 mA) and a Pilatus II photoncounting detector (pixel size: 172 μm). The phantom is composed of a renal equivalent soft-tissue and cystic lesions grouped in non-enhancing cyst and hemorrhage series and an iodine enhancing series. The acquired projection images (absorption and phase-contrast) are reconstructed with a standard filtered backprojection algorithm. For evaluation both reconstructions are compared in respect to contrast-to-noise ratio (CNR), signal-to-noise ratio (SNR), and subjective image quality. We found that with PCCT a significantly improved differentiation between hemorrhage renal cysts from contrast enhancing malignant cysts is possible. If comparing PCCT and CT with respect to CNR and SNR, PCCT shows significant improvements. In conclusion, PCCT has the potential to improve the diagnostics and characterization of renal cysts without using any contrast agents. These results in combination with a non-synchrotron setup indicate a future paradigm shift in diagnostic computed tomography.

  13. Improving the quantitative accuracy of optical-emission computed tomography by incorporating an attenuation correction: application to HIF1 imaging

    NASA Astrophysics Data System (ADS)

    Kim, E.; Bowsher, J.; Thomas, A. S.; Sakhalkar, H.; Dewhirst, M.; Oldham, M.

    2008-10-01

    Optical computed tomography (optical-CT) and optical-emission computed tomography (optical-ECT) are new techniques for imaging the 3D structure and function (including gene expression) of whole unsectioned tissue samples. This work presents a method of improving the quantitative accuracy of optical-ECT by correcting for the 'self'-attenuation of photons emitted within the sample. The correction is analogous to a method commonly applied in single-photon-emission computed tomography reconstruction. The performance of the correction method was investigated by application to a transparent cylindrical gelatin phantom, containing a known distribution of attenuation (a central ink-doped gelatine core) and a known distribution of fluorescing fibres. Attenuation corrected and uncorrected optical-ECT images were reconstructed on the phantom to enable an evaluation of the effectiveness of the correction. Significant attenuation artefacts were observed in the uncorrected images where the central fibre appeared ~24% less intense due to greater attenuation from the surrounding ink-doped gelatin. This artefact was almost completely removed in the attenuation-corrected image, where the central fibre was within ~4% of the others. The successful phantom test enabled application of attenuation correction to optical-ECT images of an unsectioned human breast xenograft tumour grown subcutaneously on the hind leg of a nude mouse. This tumour cell line had been genetically labelled (pre-implantation) with fluorescent reporter genes such that all viable tumour cells expressed constitutive red fluorescent protein and hypoxia-inducible factor 1 transcription-produced green fluorescent protein. In addition to the fluorescent reporter labelling of gene expression, the tumour microvasculature was labelled by a light-absorbing vasculature contrast agent delivered in vivo by tail-vein injection. Optical-CT transmission images yielded high-resolution 3D images of the absorbing contrast agent, and

  14. Using quantitative interference phase microscopy for sperm acrosome evaluation (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Balberg, Michal; Kalinowski, Ksawery; Levi, Mattan; Shaked, Natan T.

    2016-03-01

    We demonstrate quantitative assessment of sperm cell morphology, primarily acrosomal volume, using quantitative interference phase microscopy (IPM). Normally, the area of the acrosome is assessed using dyes that stain the acrosomal part of the cell. We have imaged fixed individual sperm cells using IPM. Following, the sample was stained and the same cells were imaged using bright field microscopy (BFM). We identified the acrosome using the stained BFM image, and used it to define a quantitative corresponding area in the IPM image and determine a quantitative threshold for evaluating the volume of the acrosome.

  15. Absolute quantitation of iodine-123 epidepride kinetics using single-photon emission tomography: comparison with carbon-11 epidepride and positron emission tomography.

    PubMed

    Almeida, P; Ribeiro, M J; Bottlaender, M; Loc'h, C; Langer, O; Strul, D; Hugonnard, P; Grangeat, P; Mazière, B; Bendriem, B

    1999-12-01

    Epidepride labelled with iodine-123 is a suitable probe for the in vivo imaging of striatal and extrastriatal dopamine D2 receptors using single-photon emission tomography (SPET). Recently, this molecule has also been labelled with carbon-11. The goal of this work was to develop a method allowing the in vivo quantification of radioactivity uptake in baboon brain using SPET and to validate it using positron emission tomography (PET). SPET studies were performed in Papio anubis baboons using 123I-epidepride. Emission and transmission measurements were acquired on a dual-headed system with variable head angulation and low-energy ultra-high resolution (LEUHR) collimation. The imaging protocol consisted of one transmission measurement (24 min, heads at 90 degrees), obtained with two sliding line sources of gadolinium-153 prior to injection of 0.21-0.46 GBq of 123I-epidepride, and 12 emission measurements starting 5 min post injection. For scatter correction (SC) we used a dual-window method adapted to 123I. Collimator blurring correction (CBC) was done by deconvolution in Fourier space and attenuation correction (AT) was applied on a preliminary (CBC) filtered back-projection reconstruction using 12 iterations of a preconditioned, regularized minimal residual algorithm. For each reconstruction, a calibration factor was derived from a uniform cylinder filled with a 123I solution of a known radioactivity concentration. Calibration and baboon images were systematically built with the same reconstruction parameters. Uncorrected (UNC) and (AT), (SC + AT) and (SC + CBC + AT) corrected images were compared. PET acquisitions using 0.11-0.44 GBq of 11C-epidepride were performed on the same baboons and used as a reference. The radioactive concentrations expressed in percent of the injected dose per 100 ml (% ID/100 ml) obtained after (SC + CBC + AT) in SPET are in good agreement with those obtained with PET and 11C-epidepride. A method for the in vivo absolute quantitation of 123

  16. Quantitative phase retrieval with picosecond X-ray pulses from the ATF Inverse Compton Scattering source

    SciTech Connect

    Endrizzi, M.; Pogorelsky, I.; Gureyev, T.E.; Delogu, P.; Oliva, P.; Golosio, B.; Carpinelli, M.; Yakimenko, Y.; Bottigli, U.

    2011-01-28

    Quantitative phase retrieval is experimentally demonstrated using the Inverse Compton Scattering X-ray source available at the Accelerator Test Facility (ATF) in the Brookhaven National Laboratory. Phase-contrast images are collected using in-line geometry, with a single X-ray pulse of approximate duration of one picosecond. The projected thickness of homogeneous samples of various polymers is recovered quantitatively from the time-averaged intensity of transmitted X-rays. The data are in good agreement with the expectations showing that ATF Inverse Compton Scattering source is suitable for performing phase-sensitive quantitative X-ray imaging on the picosecond scale. The method shows promise for quantitative imaging of fast dynamic phenomena.

  17. Method to calibrate phase fluctuation in polarization-sensitive swept-source optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Lu, Zenghai; Kasaragod, Deepa K.; Matcher, Stephen J.

    2011-07-01

    We present a phase fluctuation calibration method for polarization-sensitive swept-source optical coherence tomography (PS-SS-OCT) using continuous polarization modulation. The method uses a low-voltage broadband polarization modulator driven by a synchronized sinusoidal burst waveform rather than an asynchronous waveform, together with the removal of the global phases of the measured Jones matrices by the use of matrix normalization. This makes it possible to average the measured Jones matrices to remove the artifact due to the speckle noise of the signal in the sample without introducing auxiliary optical components into the sample arm. This method was validated on measurements of an equine tendon sample by the PS-SS-OCT system.

  18. Quantitative interferometric microscopy with improved full-field phase aberration compensation

    NASA Astrophysics Data System (ADS)

    Xue, Liang; Wang, Shouyu; Yan, Keding; Sun, Nan; Li, Zhenhua; Liu, Fei

    2014-11-01

    Single-shot quantitative interferometric microscopy (QIM) needs a high-accuracy and rapid phase retrieval algorithm. Retrieved phase distributions are often influenced by phase aberration background caused by both imaging system and phase retrieval algorithms. Here, we propose an improved phase aberration compensation (PAC) approach in order to eliminate the phase aberrations inherent in the data. With this method, sample-free parts are identified and used to calculate the background phase, reducing phase errors induced in samples and providing high-quality phase images. We now demonstrate that QIM based on this PAC approach realizes high-quality phase imaging from a single interferogram. This is of great potential for a real-time speedy diagnosis.

  19. Multicontrast x-ray computed tomography imaging using Talbot-Lau interferometry without phase stepping

    SciTech Connect

    Bevins, Nicholas; Zambelli, Joseph; Li Ke; Qi Zhihua; Chen Guanghong

    2012-01-15

    Purpose: The purpose of this work is to demonstrate that multicontrast computed tomography (CT) imaging can be performed using a Talbot-Lau interferometer without phase stepping, thus allowing for an acquisition scheme like that used for standard absorption CT. Methods: Rather than using phase stepping to extract refraction, small-angle scattering (SAS), and absorption signals, the two gratings of a Talbot-Lau interferometer were rotated slightly to generate a moire pattern on the detector. A Fourier analysis of the moire pattern was performed to obtain separate projection images of each of the three contrast signals, all from the same single-shot of x-ray exposure. After the signals were extracted from the detector data for all view angles, image reconstruction was performed to obtain absorption, refraction, and SAS CT images. A physical phantom was scanned to validate the proposed data acquisition method. The results were compared with a phantom scan using the standard phase stepping approach. Results: The reconstruction of each contrast mechanism produced the expected results. Signal levels and contrasts match those obtained using the phase stepping technique. Conclusions: Absorption, refraction, and SAS CT imaging can be achieved using the Talbot-Lau interferometer without the additional overhead of long scan time and phase stepping.

  20. Quantitative phase contrast imaging using a Nomarski microscope with variable shear distance

    NASA Astrophysics Data System (ADS)

    Falldorf, Claas; Agour, Mostafa; Kötter, Jonas; Bergmann, Ralf B.

    2016-03-01

    We present a Nomarski microscope with variable shear distance that allows for determining the full complex modulation function including the quantitative phase contrast that a specimen imposes on incident light, rather than only its differential phase contrast. The system preserves all beneficial properties of the Nomarski setup with respect to coherence and stability. Hence, we can measure the quantitative phase contrast under Köhler illumination with full condenser aperture and without vibration isolation. We will explain the system, give an analysis of the coherence requirements and provide an example from the field of MEMS inspection.

  1. Microstructural characterization of an Al-li-mg-cu alloy by correlative electron tomography and atom probe tomography.

    PubMed

    Xiong, Xiangyuan; Weyland, Matthew

    2014-08-01

    Correlative electron tomography and atom probe tomography have been carried out successfully on the same region of a commercial 8090 aluminum alloy (Al-Li-Mg-Cu). The combination of the two techniques allows accurate geometric reconstruction of the atom probe tomography data verified by crystallographic information retrieved from the reconstruction. Quantitative analysis of the precipitate phase compositions and volume fractions of each phase have been obtained from the atom probe tomography and electron tomography at various scales, showing strong agreement between both techniques.

  2. In vivo quantitative imaging of normal and cancerous breast tissue using broadband diffuse optical tomography

    PubMed Central

    Wang, Jia; Jiang, Shudong; Li, Zhongze; diFlorio-Alexander, Roberta M.; Barth, Richard J.; Kaufman, Peter A.; Pogue, Brian W.; Paulsen, Keith D.

    2010-01-01

    Purpose: A NIR tomography system that combines frequency domain (FD) and continuous wave (CW) measurements was used to image normal and malignant breast tissues. Methods: FD acquisitions were confined to wavelengths less than 850 nm because of detector limitations, whereas light from longer wavelengths (up to 948 nm) was measured in CW mode with CCD-coupled spectrometer detection. The two data sets were combined and processed in a single spectrally constrained reconstruction to map concentrations of hemoglobin, water, and lipid, as well as scattering parameters in the breast. Results: Chromophore concentrations were imaged in the breasts of nine asymptomatic volunteers to evaluate their intrasubject and intersubject variability. Normal subject data showed physiologically expected trends. Images from three cancer patients indicate that the added CW data is critical to recovering the expected increases in water and decreases in lipid content within malignancies. Contrasts of 1.5 to twofold in hemoglobin and water values were found in cancers. Conclusions:In vivo breast imaging with instrumentation that combines FD and CW NIR data acquisition in a single spectral reconstruction produces more accurate hemoglobin, water, and lipid results relative to FD data alone. PMID:20831079

  3. Quantitation of experimental canine infarct size using multipinhole single-photon tomography

    SciTech Connect

    Stokely, E.M.; Tipton, D.M.; Buja, L.M.; Lewis, S.E.; DeVous, M.D.; Bonte, F.J.; Parkey, R.W.; Willerson, J.T.

    1981-01-01

    A four-pinhole longitudinal tomographic system, with collimator and software, was developed for a standard-field portable scintillation camera. This system was used with technetium-99m pyrophosphate (Tc-PPi) to quantify the volume of infarcted myocardium in 27 dogs with experimental myocardial infarcts. These were induced by ligation of the left anterior descending (LAD) or the circumflex coronary artery. Tomographic estimations of scintigraphic infarct size agreed well with postmortem findings when the circumflex group (r = 0.87) and LAD group (r = 0.83) were considered separately, but the correlation fell when the groups were pooled (r = 0.73). Whereas multipinhole tomography extends Tc-PPi infarct sizing capability in animals to include posterior and subendocardial infarcts as well as anterior lesions, the tomographic sections contain enough blur artifacts to lower the sizing accuracy of the method. The main advantage of the technique may well be its ability to aid in detection and location of small myocardial infarcts.

  4. Small pulmonary vascular alteration and acute exacerbations of COPD: quantitative computed tomography analysis

    PubMed Central

    Wang, Zhiyue; Chen, Xuesong; Liu, Kouying; Xie, Weiping; Wang, Hong; Wei, Yongyue; Tang, Lijun; Zhu, Yinsu

    2016-01-01

    The morphologic alterations of pulmonary small vessels measured by computed tomography (CT) have been used to evaluate chronic obstructive pulmonary disease (COPD). However, the relationship between small pulmonary vascular alteration and acute exacerbations of COPD (AECOPD) is not well understood. The aim of this study was to evaluate the cross-sectional area (CSA) of small pulmonary vessel alterations measured on CT images and investigate its relationship with the COPD severity staged by the degree of airflow limitation and the occurrence of AECOPD. We retrospectively reviewed CT scans, clinical characteristics, and pulmonary function test results of 153 patients with COPD. All the patients were divided into AECOPD and non-AECOPD group according to the COPD staging and pulmonary function test results. The percentages of the total CSA less than 5 mm2 and equal to 5–10 mm2 over the lung area (%CSA<5 and %CSA5–10, respectively) were measured. The %CSA<5 steadily decreased in relation to the increase of COPD severity. In addition, %CSA<5 of the AECOPD group was significantly lower than that of the non-AECOPD group (0.41±0.13 versus 0.68±0.18, P<0.001), and the optimal cutoff value was 0.56 (sensitivity, 0.863; specificity, 0.731). Therefore, small pulmonary vascular alteration, as measured by %CSA<5, could indicate not only the degree of COPD severity, but also the occurrence of AECOPD. PMID:27578971

  5. A novel 3D absorption correction method for quantitative EDX-STEM tomography.

    PubMed

    Burdet, Pierre; Saghi, Z; Filippin, A N; Borrás, A; Midgley, P A

    2016-01-01

    This paper presents a novel 3D method to correct for absorption in energy dispersive X-ray (EDX) microanalysis of heterogeneous samples of unknown structure and composition. By using STEM-based tomography coupled with EDX, an initial 3D reconstruction is used to extract the location of generated X-rays as well as the X-ray path through the sample to the surface. The absorption correction needed to retrieve the generated X-ray intensity is then calculated voxel-by-voxel estimating the different compositions encountered by the X-ray. The method is applied to a core/shell nanowire containing carbon and oxygen, two elements generating highly absorbed low energy X-rays. Absorption is shown to cause major reconstruction artefacts, in the form of an incomplete recovery of the oxide and an erroneous presence of carbon in the shell. By applying the correction method, these artefacts are greatly reduced. The accuracy of the method is assessed using reference X-ray lines with low absorption.

  6. Quantitative Computer Tomography for Determining Composition of Microgravity and Ground Based Solid Solutions

    NASA Technical Reports Server (NTRS)

    Gillies, D. C.; Engel, H. P.

    1999-01-01

    Advances in x-ray Computer Tomography (CT) have been led by the medical profession, and by evaluation of industrial products, particularly castings. Porosity can readily be determined as a function of the density of a material, and CT is thus an industrially important NDE tool. Providing high purity, 100% dense standards of pure elements and compounds can be fabricated, the composition of solid solution alloys can be determined by measuring the CT number, which is a function of the absorption of the sample. Average densities across slices 1 mm thick can generally be determined to better than 1 percent. With present technology this spatial sensitivity is less than ideal, but important benefits can nevertheless be obtained by using CT, particularly single crystals, prior to making any destructive assault upon the sample. The sample can in fact be examined prior to removal from the mold within which it has been grown and, in the cases of microgravity flight samples, before removal from the cartridge assembly. This greatly assists the researcher in the characterization of the products, particularly as a guide to cutting and sampling. Examples of work with germanium-silicon alloys and mercury cadmium telluride taken with a radioactive cobalt source will be demonstrated.

  7. A novel 3D absorption correction method for quantitative EDX-STEM tomography.

    PubMed

    Burdet, Pierre; Saghi, Z; Filippin, A N; Borrás, A; Midgley, P A

    2016-01-01

    This paper presents a novel 3D method to correct for absorption in energy dispersive X-ray (EDX) microanalysis of heterogeneous samples of unknown structure and composition. By using STEM-based tomography coupled with EDX, an initial 3D reconstruction is used to extract the location of generated X-rays as well as the X-ray path through the sample to the surface. The absorption correction needed to retrieve the generated X-ray intensity is then calculated voxel-by-voxel estimating the different compositions encountered by the X-ray. The method is applied to a core/shell nanowire containing carbon and oxygen, two elements generating highly absorbed low energy X-rays. Absorption is shown to cause major reconstruction artefacts, in the form of an incomplete recovery of the oxide and an erroneous presence of carbon in the shell. By applying the correction method, these artefacts are greatly reduced. The accuracy of the method is assessed using reference X-ray lines with low absorption. PMID:26484792

  8. Quantitative spectroscopic diffuse optical tomography of the breast guided by imperfect a priori structural information

    NASA Astrophysics Data System (ADS)

    Boverman, Gregory; Miller, Eric L.; Li, Ang; Zhang, Quan; Chaves, Tina; Brooks, Dana H.; Boas, David A.

    2005-09-01

    Spectroscopic diffuse optical tomography (DOT) can directly image the concentrations of physiologically significant chromophores in the body. This information may be of importance in characterizing breast tumours and distinguishing them from benign structures. This paper studies the accuracy with which lesions can be characterized given a physiologically realistic situation in which the background architecture of the breast is heterogeneous yet highly structured. Specifically, in simulation studies, we assume that the breast is segmented into distinct glandular and adipose regions. Imaging with a high-resolution imaging modality, such as magnetic resonance imaging, in conjunction with a segmentation by a clinical expert, allows the glandular/adipose boundary to be determined. We then apply a two-step approach in which the background chromophore concentrations of each region are estimated in a nonlinear fashion, and a more localized lesion is subsequently estimated using a linear perturbational approach. In addition, we examine the consequences which errors in the breast segmentation have on estimating both the background and inhomogeneity chromophore concentrations.

  9. Small pulmonary vascular alteration and acute exacerbations of COPD: quantitative computed tomography analysis.

    PubMed

    Wang, Zhiyue; Chen, Xuesong; Liu, Kouying; Xie, Weiping; Wang, Hong; Wei, Yongyue; Tang, Lijun; Zhu, Yinsu

    2016-01-01

    The morphologic alterations of pulmonary small vessels measured by computed tomography (CT) have been used to evaluate chronic obstructive pulmonary disease (COPD). However, the relationship between small pulmonary vascular alteration and acute exacerbations of COPD (AECOPD) is not well understood. The aim of this study was to evaluate the cross-sectional area (CSA) of small pulmonary vessel alterations measured on CT images and investigate its relationship with the COPD severity staged by the degree of airflow limitation and the occurrence of AECOPD. We retrospectively reviewed CT scans, clinical characteristics, and pulmonary function test results of 153 patients with COPD. All the patients were divided into AECOPD and non-AECOPD group according to the COPD staging and pulmonary function test results. The percentages of the total CSA less than 5 mm(2) and equal to 5-10 mm(2) over the lung area (%CSA<5 and %CSA5-10, respectively) were measured. The %CSA<5 steadily decreased in relation to the increase of COPD severity. In addition, %CSA<5 of the AECOPD group was significantly lower than that of the non-AECOPD group (0.41±0.13 versus 0.68±0.18, P<0.001), and the optimal cutoff value was 0.56 (sensitivity, 0.863; specificity, 0.731). Therefore, small pulmonary vascular alteration, as measured by %CSA<5, could indicate not only the degree of COPD severity, but also the occurrence of AECOPD. PMID:27578971

  10. Quantitative measurement of regional lung gas volume by synchrotron radiation computed tomography

    NASA Astrophysics Data System (ADS)

    Monfraix, Sylvie; Bayat, Sam; Porra, Liisa; Berruyer, Gilles; Nemoz, Christian; Thomlinson, William; Suortti, Pekka; Sovijärvi, Anssi R. A.

    2005-01-01

    The aim of this study was to assess the feasibility of a novel respiration-gated spiral synchrotron radiation computed tomography (SRCT) technique for direct quantification of absolute regional lung volumes, using stable xenon (Xe) gas as an inhaled indicator. Spiral SRCT with K-edge subtraction using two monochromatic x-ray beams was used to visualize and directly quantify inhaled Xe concentrations and airspace volumes in three-dimensional (3D) reconstructed lung images. Volume measurements were validated using a hollow Xe-filled phantom. Spiral images spanning 49 mm in lung height were acquired following 60 breaths of an 80% Xe-20% O2 gas mixture, in two anaesthetized and mechanically ventilated rabbits at baseline and after histamine aerosol inhalation. Volumetric images of 20 mm lung sections were obtained at functional residual capacity (FRC) and at end-inspiration. 3D images showed large patchy filling defects in peripheral airways and alveoli following histamine provocation. Local specific lung compliance was calculated based on FRC/end-inspiration images in normal lung. This study demonstrates spiral SRCT as a new technique for direct determination of regional lung volume, offering possibilities for non-invasive investigation of regional lung function and mechanics, with a uniquely high spatial resolution. An example of non-uniform volume distribution in rabbit lung following histamine inhalation is presented.

  11. High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography

    NASA Astrophysics Data System (ADS)

    Hagen, Charlotte K.; Maghsoudlou, Panagiotis; Totonelli, Giorgia; Diemoz, Paul C.; Endrizzi, Marco; Rigon, Luigi; Menk, Ralf-Hendrik; Arfelli, Fulvia; Dreossi, Diego; Brun, Emmanuel; Coan, Paola; Bravin, Alberto; de Coppi, Paolo; Olivo, Alessandro

    2015-12-01

    Acellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds’ internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation, and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory.

  12. High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography

    PubMed Central

    Hagen, Charlotte K.; Maghsoudlou, Panagiotis; Totonelli, Giorgia; Diemoz, Paul C.; Endrizzi, Marco; Rigon, Luigi; Menk, Ralf-Hendrik; Arfelli, Fulvia; Dreossi, Diego; Brun, Emmanuel; Coan, Paola; Bravin, Alberto; De Coppi, Paolo; Olivo, Alessandro

    2015-01-01

    Acellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds’ internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation, and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory. PMID:26657471

  13. High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography.

    PubMed

    Hagen, Charlotte K; Maghsoudlou, Panagiotis; Totonelli, Giorgia; Diemoz, Paul C; Endrizzi, Marco; Rigon, Luigi; Menk, Ralf-Hendrik; Arfelli, Fulvia; Dreossi, Diego; Brun, Emmanuel; Coan, Paola; Bravin, Alberto; De Coppi, Paolo; Olivo, Alessandro

    2015-01-01

    Acellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds' internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation, and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory. PMID:26657471

  14. Phase-sensitive optical coherence tomography-based vibrometry using a highly phase-stable akinetic swept laser source

    NASA Astrophysics Data System (ADS)

    Applegate, Brian E.; Park, Jesung; Carbajal, Esteban; Oghalai, John S.

    2015-12-01

    Phase-sensitive Optical Coherence Tomography (PhOCT) is an emerging tool for in vivo investigation of the vibratory function of the intact middle and inner ear. PhOCT is able to resolve micron scale tissue morphology in three dimensions as well as measure picometer scale motion at each spatial position. Most PhOCT systems to date have relied upon the phase stability offered by spectrometer detection. On the other hand swept laser source based PhOCT offers a number of advantages including balanced detection, long imaging depths, and high imaging speeds. Unfortunately the inherent phase instability of traditional swept laser sources has necessitated complex user developed hardware/software solutions to restore phase sensitivity. Here we present recent results using a prototype swept laser that overcomes these issues. The akinetic swept laser is electronically tuned and precisely controls sweeps without any mechanical movement, which results in high phase stability. We have developed an optical fiber based PhOCT system around the akinetic laser source that had a 1550 nm center wavelength and a sweep rate of 140 kHz. The stability of the system was measured to be 4.4 pm with a calibrated reflector, thus demonstrating near shot noise limited performance. Using this PhOCT system, we have acquired structural and vibratory measurements of the middle ear in a mouse model, post mortem. The quality of the results suggest that the akinetic laser source is a superior laser source for PhOCT with many advantages that greatly reduces the required complexity of the imaging system.

  15. Phase-sensitive optical coherence tomography-based vibrometry using a highly phase-stable akinetic swept laser source

    SciTech Connect

    Applegate, Brian E.; Park, Jesung; Carbajal, Esteban; Oghalai, John S.

    2015-12-31

    Phase-sensitive Optical Coherence Tomography (PhOCT) is an emerging tool for in vivo investigation of the vibratory function of the intact middle and inner ear. PhOCT is able to resolve micron scale tissue morphology in three dimensions as well as measure picometer scale motion at each spatial position. Most PhOCT systems to date have relied upon the phase stability offered by spectrometer detection. On the other hand swept laser source based PhOCT offers a number of advantages including balanced detection, long imaging depths, and high imaging speeds. Unfortunately the inherent phase instability of traditional swept laser sources has necessitated complex user developed hardware/software solutions to restore phase sensitivity. Here we present recent results using a prototype swept laser that overcomes these issues. The akinetic swept laser is electronically tuned and precisely controls sweeps without any mechanical movement, which results in high phase stability. We have developed an optical fiber based PhOCT system around the akinetic laser source that had a 1550 nm center wavelength and a sweep rate of 140 kHz. The stability of the system was measured to be 4.4 pm with a calibrated reflector, thus demonstrating near shot noise limited performance. Using this PhOCT system, we have acquired structural and vibratory measurements of the middle ear in a mouse model, post mortem. The quality of the results suggest that the akinetic laser source is a superior laser source for PhOCT with many advantages that greatly reduces the required complexity of the imaging system.

  16. Diagnostic performance of quantitative coronary computed tomography angiography and quantitative coronary angiography to predict hemodynamic significance of intermediate-grade stenoses.

    PubMed

    Ghekiere, Olivier; Dewilde, Willem; Bellekens, Michel; Hoa, Denis; Couvreur, Thierry; Djekic, Julien; Coolen, Tim; Mancini, Isabelle; Vanhoenacker, Piet K; Dendale, Paul; Nchimi, Alain

    2015-12-01

    Fractional flow reserve (FFR) during invasive coronary angiography has become an established tool for guiding treatment. However, only one-third of intermediate-grade coronary artery stenosis (ICAS) are hemodynamically significant and require coronary revascularization. Additionally, the severity of stenosis visually established by coronary computed tomography angiography (CCTA) does not reliably correlate with the functional severity. Therefore, additional angiographic morphologic descriptors affecting hemodynamic significance are required. To evaluate quantitative stenosis analysis and plaque descriptors by CCTA in predicting the hemodynamic significance of ICAS and to compare it with quantitative catheter coronary angiography (QCA). QCA was performed in 65 patients (mean age 63 ± 9 years; 47 men) with 76 ICAS (40-70%) on CCTA. Plaque descriptors were determined including circumferential extent of calcification, plaque composition, minimal lumen diameter (MLD) and area, diameter stenosis percentage (Ds %), area stenosis percentage and stenosis length on CCTA. MLD and Ds % were also analyzed on QCA. FFR was measured on 52 ICAS lesions on CCTA and QCA. The diagnostic values of the best CCTA and QCA descriptors were calculated for ICAS with FFR ≤ 0.80. Of the 76 ICAS on CCTA, 52 (68%) had a Ds % between 40 and 70% on QCA. Significant intertechnique correlations were found between CCTA and QCA for MLD and Ds % (p < 0.001). In 17 (33%) of the 52 ICAS lesions on QCA, FFR values were ≤ 0.80. Calcification circumference extent (p = 0.50) and plaque composition assessment (p = 0.59) did not correlate with the hemodynamic significance. Best predictors for FFR ≤ 0.80 stenosis were ≤ 1.35 mm MLD (82% sensitivity, 66% specificity), and ≤ 2.3 mm(²) minimal lumen area (88% sensitivity, 60% specificity) on CCTA, and ≤ 1.1 mm MLD (59% sensitivity, 77% specificity) on QCA. Quantitative CCTA and QCA poorly predict hemodynamic significance of ICAS, though CCTA seems to

  17. Analysis of mixed cell cultures with quantitative digital holographic phase microscopy

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Wibbeling, Jana; Ketelhut, Steffi

    2014-05-01

    In order to study, for example, the influence of pharmaceuticals or pathogens on different cell types under identical measurement conditions and to analyze interactions between different cellular specimens a minimally-invasive quantitative observation of mixed cell cultures is of particular interest. Quantitative phase microscopy (QPM) provides high resolution detection of optical path length changes that is suitable for stain-free minimally-invasive live cell analysis. Due to low light intensities for object illumination, QPM minimizes the interaction with the sample and is in particular suitable for long term time-lapse investigations, e.g., for the detection of cell morphology alterations due to drugs and toxins. Furthermore, QPM has been demonstrated to be a versatile tool for the quantification of cellular growth, the extraction morphological parameters and cell motility. We studied the feasibility of QPM for the analysis of mixed cell cultures. It was explored if quantitative phase images provide sufficient information to distinguish between different cell types and to extract cell specific parameters. For the experiments quantitative phase imaging with digital holographic microscopy (DHM) was utilized. Mixed cell cultures with different types of human pancreatic tumor cells were observed with quantitative DHM phase contrast up to 35 h. The obtained series of quantitative phase images were evaluated by adapted algorithms for image segmentation. From the segmented images the cellular dry mass and the mean cell thickness were calculated and used in the further analysis as parameters to quantify the reliability the measurement principle. The obtained results demonstrate that it is possible to characterize the growth of cell types with different morphologies in a mixed cell culture separately by consideration of specimen size and cell thickness in the evaluation of quantitative DHM phase images.

  18. Noise properties of grating-based x-ray phase contrast computed tomography

    SciTech Connect

    Koehler, Thomas; Juergen Engel, Klaus; Roessl, Ewald

    2011-05-15

    Purpose: To investigate the properties of tomographic grating-based phase contrast imaging with respect to its noise power spectrum and the energy dependence of the achievable contrast to noise ratio. Methods: Tomographic simulations of an object with 11 cm diameter constituted of materials of biological interest were conducted at different energies ranging from 25 to 85 keV by using a wave propagation approach. Using a Monte Carlo simulation of the x-ray attenuation within the object, it is verified that the simulated measurement deposits the same dose within the object at each energy. Results: The noise in reconstructed phase contrast computed tomography images shows a maximum at low spatial frequencies. The contrast to noise ratio reaches a maximum around 45 keV for the simulated object. The general dependence of the contrast to noise on the energy appears to be independent of the material. Compared with reconstructed absorption contrast images, the reconstructed phase contrast images show sometimes better, sometimes worse, and sometimes similar contrast to noise, depending on the material and the energy. Conclusions: Phase contrast images provide additional information to the conventional absorption contrast images and might thus be useful for medical applications. However, the observed noise power spectrum in reconstructed phase contrast images implies that the usual trade-off between noise and resolution is less efficient for phase contrast imaging compared with absorption contrast imaging. Therefore, high-resolution imaging is a strength of phase contrast imaging, but low-resolution imaging is not. This might hamper the clinical application of the method, in cases where a low spatial resolution is sufficient for diagnosis.

  19. High-speed spectral calibration by complex FIR filter in phase-sensitive optical coherence tomography.

    PubMed

    Kim, Sangmin; Raphael, Patrick D; Oghalai, John S; Applegate, Brian E

    2016-04-01

    Swept-laser sources offer a number of advantages for Phase-sensitive Optical Coherence Tomography (PhOCT). However, inter- and intra-sweep variability leads to calibration errors that adversely affect phase sensitivity. While there are several approaches to overcoming this problem, our preferred method is to simply calibrate every sweep of the laser. This approach offers high accuracy and phase stability at the expense of a substantial processing burden. In this approach, the Hilbert phase of the interferogram from a reference interferometer provides the instantaneous wavenumber of the laser, but is computationally expensive. Fortunately, the Hilbert transform may be approximated by a Finite Impulse-Response (FIR) filter. Here we explore the use of several FIR filter based Hilbert transforms for calibration, explicitly considering the impact of filter choice on phase sensitivity and OCT image quality. Our results indicate that the complex FIR filter approach is the most robust and accurate among those considered. It provides similar image quality and slightly better phase sensitivity than the traditional FFT-IFFT based Hilbert transform while consuming fewer resources in an FPGA implementation. We also explored utilizing the Hilbert magnitude of the reference interferogram to calculate an ideal window function for spectral amplitude calibration. The ideal window function is designed to carefully control sidelobes on the axial point spread function. We found that after a simple chromatic correction, calculating the window function using the complex FIR filter and the reference interferometer gave similar results to window functions calculated using a mirror sample and the FFT-IFFT Hilbert transform. Hence, the complex FIR filter can enable accurate and high-speed calibration of the magnitude and phase of spectral interferograms. PMID:27446666

  20. High-speed spectral calibration by complex FIR filter in phase-sensitive optical coherence tomography

    PubMed Central

    Kim, Sangmin; Raphael, Patrick D.; Oghalai, John S.; Applegate, Brian E.

    2016-01-01

    Swept-laser sources offer a number of advantages for Phase-sensitive Optical Coherence Tomography (PhOCT). However, inter- and intra-sweep variability leads to calibration errors that adversely affect phase sensitivity. While there are several approaches to overcoming this problem, our preferred method is to simply calibrate every sweep of the laser. This approach offers high accuracy and phase stability at the expense of a substantial processing burden. In this approach, the Hilbert phase of the interferogram from a reference interferometer provides the instantaneous wavenumber of the laser, but is computationally expensive. Fortunately, the Hilbert transform may be approximated by a Finite Impulse-Response (FIR) filter. Here we explore the use of several FIR filter based Hilbert transforms for calibration, explicitly considering the impact of filter choice on phase sensitivity and OCT image quality. Our results indicate that the complex FIR filter approach is the most robust and accurate among those considered. It provides similar image quality and slightly better phase sensitivity than the traditional FFT-IFFT based Hilbert transform while consuming fewer resources in an FPGA implementation. We also explored utilizing the Hilbert magnitude of the reference interferogram to calculate an ideal window function for spectral amplitude calibration. The ideal window function is designed to carefully control sidelobes on the axial point spread function. We found that after a simple chromatic correction, calculating the window function using the complex FIR filter and the reference interferometer gave similar results to window functions calculated using a mirror sample and the FFT-IFFT Hilbert transform. Hence, the complex FIR filter can enable accurate and high-speed calibration of the magnitude and phase of spectral interferograms. PMID:27446666

  1. Reverse projection retrieval in edge illumination x-ray phase contrast computed tomography

    NASA Astrophysics Data System (ADS)

    Hagen, Charlotte K.; Endrizzi, Marco; Diemoz, Paul C.; Olivo, Alessandro

    2016-06-01

    Edge illumination (EI) x-ray phase contrast computed tomography (CT) can provide three-dimensional distributions of the real and imaginary parts of the complex refractive index (n=1-δ +\\text{i}β ) of the sample. Phase retrieval, i.e. the separation of attenuation and refraction data from projections that contain a combination of both, is a key step in the image reconstruction process. In EI-based x-ray phase contrast CT, this is conventionally performed on the basis of two projections acquired in opposite illumination configurations (i.e. with different positions of the pre-sample mask) at each CT angle. Displacing the pre-sample mask at each projection makes the scan susceptible to motor-induced misalignment and prevents a continuous sample rotation. We present an alternative method for the retrieval of attenuation and refraction data that does not require repositioning the pre-sample mask. The method is based on the reverse projection relation published by Zhu et al (2010 Proc. Natl Acad. Sci. USA 107 13576–81) for grating interferometry-based x-ray phase contrast CT. We use this relation to derive a simplified acquisition strategy that allows acquiring data with a continuous sample rotation, which can reduce scan time when combined with a fast read-out detector. Besides discussing the theory and the necessary alignment of the experimental setup, we present tomograms obtained with reverse projection retrieval and demonstrate their agreement with those obtained with the conventional EI retrieval.

  2. Reverse projection retrieval in edge illumination x-ray phase contrast computed tomography

    NASA Astrophysics Data System (ADS)

    Hagen, Charlotte K.; Endrizzi, Marco; Diemoz, Paul C.; Olivo, Alessandro

    2016-06-01

    Edge illumination (EI) x-ray phase contrast computed tomography (CT) can provide three-dimensional distributions of the real and imaginary parts of the complex refractive index (n=1-δ +\\text{i}β ) of the sample. Phase retrieval, i.e. the separation of attenuation and refraction data from projections that contain a combination of both, is a key step in the image reconstruction process. In EI-based x-ray phase contrast CT, this is conventionally performed on the basis of two projections acquired in opposite illumination configurations (i.e. with different positions of the pre-sample mask) at each CT angle. Displacing the pre-sample mask at each projection makes the scan susceptible to motor-induced misalignment and prevents a continuous sample rotation. We present an alternative method for the retrieval of attenuation and refraction data that does not require repositioning the pre-sample mask. The method is based on the reverse projection relation published by Zhu et al (2010 Proc. Natl Acad. Sci. USA 107 13576-81) for grating interferometry-based x-ray phase contrast CT. We use this relation to derive a simplified acquisition strategy that allows acquiring data with a continuous sample rotation, which can reduce scan time when combined with a fast read-out detector. Besides discussing the theory and the necessary alignment of the experimental setup, we present tomograms obtained with reverse projection retrieval and demonstrate their agreement with those obtained with the conventional EI retrieval.

  3. Quantitative Fourier Domain Optical Coherence Tomography Imaging of the Ocular Anterior Segment

    NASA Astrophysics Data System (ADS)

    McNabb, Ryan Palmer

    Clinical imaging within ophthalmology has had transformative effects on ocular health over the last century. Imaging has guided clinicians in their pharmaceutical and surgical treatments of macular degeneration, glaucoma, cataracts and numerous other pathologies. Many of the imaging techniques currently used are photography based and are limited to imaging the surface of ocular structures. This limitation forces clinicians to make assumptions about the underlying tissue which may reduce the efficacy of their diagnoses. Optical coherence tomography (OCT) is a non-invasive, non-ionizing imaging modality that has been widely adopted within the field of ophthalmology in the last 15 years. As an optical imaging technique, OCT utilizes low-coherence interferometry to produce micron-scale three-dimensional datasets of a tissue's structure. Much of the human body consists of tissues that significantly scatter and attenuate optical signals limiting the imaging depth of OCT in those tissues to only 1-2mm. However, the ocular anterior segment is unique among human tissue in that it is primarily transparent or translucent. This allows for relatively deep imaging of tissue structure with OCT and is no longer limited by the optical scattering properties of the tissue. This goal of this work is to develop methods utilizing OCT that offer the potential to reduce the assumptions made by clinicians in their evaluations of their patients' ocular anterior segments. We achieved this by first developing a method to reduce the effects of patient motion during OCT volume acquisitions allowing for accurate, three dimensional measurements of corneal shape. Having accurate corneal shape measurements then allowed us to determine corneal spherical and astigmatic refractive contribution in a given individual. This was then validated in a clinical study that showed OCT better measured refractive change due to surgery than other clinical devices. Additionally, a method was developed to combine

  4. Quantitative reconstruction of PIXE-tomography data for thin samples using GUPIX X-ray emission yields

    NASA Astrophysics Data System (ADS)

    Michelet, C.; Barberet, Ph.; Devès, G.; Bouguelmouna, B.; Bourret, S.; Delville, M.-H.; Le Trequesser, Q.; Gordillo, N.; Beasley, D. G.; Marques, A. C.; Farau, R.; Toko, B. R.; Campbell, J.; Maxwell, J.; Moretto, Ph.; Seznec, H.

    2015-04-01

    We present here a new development of the TomoRebuild software package, to perform quantitative Particle Induced X-ray Emission Tomography (PIXET) reconstruction. X-ray yields are obtained from the GUPIX code. The GUPIX data base is available for protons up to 5 MeV and also in the 20-100 MeV energy range, deuterons up to 6 MeV, 3He and alphas up to 12 MeV. In this version, X-ray yields are calculated for thin samples, i.e. without simulating X-ray attenuation. PIXET data reconstruction is kept as long as possible independent from Scanning Transmission Ion Microscopy Tomography (STIMT). In this way, the local mass distribution (in g/cm3) of each X-ray emitting element is reconstructed in all voxels of the analyzed volume, only from PIXET data, without the need of associated STIMT data. Only the very last step of data analysis requires STIMT data, in order to normalize PIXET data to obtain concentration distributions, in terms of normalized mass fractions (in μg/g). For this, a noise correction procedure has been designed in ImageJ. Moreover sinogram or image misalignment can be corrected, as well as the difference in beam size between the two experiments. The main features of the TomoRebuild code, user friendly design and modular C++ implementation, were kept. The software package is portable and can run on Windows and Linux operating systems. An optional user-friendly graphic interface was designed in Java, as a plugin for the ImageJ graphic software package. Reconstruction examples are presented from biological specimens of Caenorhabditis elegans - a small nematode constituting a reference model for biology studies. The reconstruction results are compared between the different codes TomoRebuild, DISRA and JPIXET, and different reconstruction methods: Filtered BackProjection (FBP) and Maximum Likelihood Expectation Maximization (MLEM).

  5. Enhanced x-ray imaging for a thin film cochlear implant with metal artefacts using phase retrieval tomography

    NASA Astrophysics Data System (ADS)

    Arhatari, B. D.; Harris, A. R.; Paolini, A. G.; Peele, A. G.

    2012-06-01

    Phase retrieval tomography has been successfully used to enhance imaging in systems that exhibit poor absorption contrast. However, when highly absorbing regions are present in a sample, so-called metal artefacts can appear in the tomographic reconstruction. We demonstrate that straightforward approaches for metal artefact reconstruction, developed in absorption contrast tomography, can be applied when using phase retrieval. Using a prototype thin film cochlear implant that has high and low absorption components made from iridium (or platinum) and plastic, respectively, we show that segmentation of the various components is possible and hence measurement of the electrode geometry and relative location to other regions of interest can be achieved.

  6. Rayleigh wave phase velocity maps from the ambient noise tomography in central Mongolia

    NASA Astrophysics Data System (ADS)

    Pan, J.; Wu, Q.; Gao, M.; Li, Y.; Demberel, S. G.; Munkhuu, U.

    2013-12-01

    The study area (103°E-111°E, 44°N-49°N) located in the Mongolian fold belts and situated at the southeast of Baikal rift zone which is known as one of the most active regions on the Earth due to integrated influence of the India-Asia collision and compression and the subduction of the Pacific Plate. Additionally, it also located in the north of South-North earthquake belts of China. So, it is believed to be an ideal site for understanding intraplate dynamics. Seismic ambient noise tomography has been performed all over the world these years, and it has been proved it's a powerful way to image and study the structure of crust and uppermost mantle due to its exclusive capability to extract estimated Green's functions for short period surface waves. Compared with traditional earthquake tomography methods of surface waves, ambient noise tomography hasn't limitations related to the distribution of earthquakes as well as errors in earthquake locations and source mechanisms. A new scientific project was carried out in 2011 by Institute of Geophysics of China Earthquake Administration (IGP-CEA) and Research center of Astronomy and Geophysics of Mongolian Academy of Science (RCAG-MAS). In the seismic sub-project 60 portable seismic stations were deployed in central Mongolia in August 2011. Continuous time-series of vertical component between August 2011 and July 2012 have been collected and cross-correlated to obtain estimated Green's functions (EGF) of Rayleigh wave. Using the frequency and time analysis technique based on continuous wavelet transformation, 1258 of phase velocity dispersion curves of Rayleigh wave were extracted from EGFs. High resolution phase velocity maps at periods of 5, 10, 20 and 30 s were reconstructed with grid size 0.5°x0.5° by utilizing a generalized 2-D-linear inversion method developed by Ditmar & Yanovskaya. The tomography results reveal lateral heterogeneity of shear wave structure in the crust and upper mantle in the study region. For

  7. Low-coherence wavelength shifting interferometry for high-speed quantitative phase imaging.

    PubMed

    Chen, Shichao; Li, Chengshuai; Zhu, Yizheng

    2016-08-01

    We propose low-coherence wavelength shifting interferometry and demonstrate its application to quantitative phase imaging of dynamic specimens. By shifting the source wavelength, multiple interferograms of the sample can be acquired at different spectral bands. A sample phase is thus encoded in the phase step between consecutive acquisitions. For the particular case of four-band imaging, we show that the phase can be extracted with a modified Carré algorithm. We describe signal demodulation in detail and discuss its implication on system implementation. A swept laser-based Mach-Zehnder interferometer is used to demonstrate the technique for real-time imaging of live sperm cells at 62.5 Hz. The dynamic dry mass of the sperm head is measured with a full-scale error of ±2%, validating the technique's capability for high-sensitivity, high-speed quantitative phase imaging. PMID:27472586

  8. Global Rayleigh wave phase-velocity maps from finite-frequency tomography

    NASA Astrophysics Data System (ADS)

    Liu, Kui; Zhou, Ying

    2016-04-01

    We report global phase-velocity maps of fundamental-mode Rayleigh waves at periods between 25 and 100 s based on finite-frequency tomography. Rayleigh wave dispersion measurements are made using a multitaper technique for both minor-arc and major-arc wave trains. The global phase-velocity maps confirm many features associated with surface tectonics including the ocean-continent dichotomy and the signature of lithospheric cooling in oceanic plates. In addition, the high-resolution phase-velocity maps reveal a major change in the distribution of small-scale anomalies in the Pacific at different wave periods. We calculate the global average of Rayleigh wave phase velocity in major tectonic regions and show that large discrepancies exist between our model and global crustal and mantle models: (1) In oceanic regions, short-period (<˜40 s) Rayleigh waves are faster than calculations based on models CRUST2.0 and S40RTS. The discrepancies could be explained by a thinner crust or faster wave speeds in the crust or upper mantle. The implementation of model CRUST1.0 significantly improves the agreement, with phase-velocity discrepancies less than 0.5 per cent on average. (2) In Archean cratons, Rayleigh wave phase velocities in our model are faster than calculations based on model S40RTS at periods longer than ˜40 s; and the global average in orogenic belts is ˜1-2 per cent slower than CRUST1.0 at periods shorter than ˜50 s.

  9. A comparison of methods for in situ discrimination of imaged phase boundaries using electrical capacitance tomography

    NASA Astrophysics Data System (ADS)

    Clark, P. J.; Tsoligkas, A. N.; Simmons, M. J. H.; Robbins, P. T.; Stitt, E. H.

    2016-02-01

    The detection of hard boundaries using tomographic techniques is challenging due to the measurement resolution inherent in the hardware and smoothing effects created during image reconstruction. This paper is concerned with the development of data processing approaches which enable the use of electrical capacitance tomography (ECT) in real-time applications to visualise interfaces in liquid/liquid and solid/liquid systems based upon phase permittivity differences in media with a high di-electric continuum. The methodologies developed were applied to a series of phantoms to investigate their validity as a tool for imaging phase boundaries in two and three phase systems. In an ECT based tomogram, the interface between phases is exhibited as a transition region; by applying a threshold technique based upon known areas of each respective phase within the system, the transient region can be resolved into a sharp interface. The image error of a tomogram, defined as the deviation of all pixels from their theoretical value, has been calculated using a pixel-by-pixel approach; however this requires exact a priori knowledge and is unsuitable for in-line application; the areal method used in this paper requires global phase distribution information thereby allowing for real-time application. A range of threshold values were applied to tomograms of phantoms of varying geometry and the corresponding image error for each threshold value calculated using both the areal and pixel-by-pixel approaches given above. The threshold value yielding lowest image error from this range is further used in the binary images giving improved tomograms with approximately 40% increase in image accuracy when compared with a default threshold value. Close to the sensor wall, the image becomes distorted due to reconstruction errors arising from decreased density in the electrical field lines, resulting in a circular phantom appearing elongated by approximately 10% when positioned near the wall.

  10. Optical Coherence Tomography for Quantitative Assessment of Microstructural and Microvascular Alterations in Late Oral Radiation Toxicity

    NASA Astrophysics Data System (ADS)

    Davoudi, Bahar

    More than half of head-and-neck cancer patients undergo radiotherapy at some point during their treatment. Even though the use of conformed therapeutic beams has increased radiation dose localization to the tumor, resulting in more normal tissue sparing, still, in many head-and-neck cancer patients, the healthy tissue of the oral cavity still receives a sizeable amount of radiation. This causes acute and / or late complications in these patients. The latter occur as late as several months or even years after the completion of treatment and are typically associated with severe symptoms. Currently, the clinical method for diagnosing these complications is visual examination of the oral tissue surface. However, it has been well established that such complications originate in subsurface oral tissue layers including its microvasculature. Therefore, to better understand the mechanism of these complications and to be able to diagnose them earlier, there exists a need for subsurface monitoring of the irradiated oral tissue. Histology has been used as such a tool for research purposes; however, its use in clinical diagnosis is limited due to its invasive and hazardous nature. Therefore, in this thesis, I propose to use optical coherence tomography (OCT) as a subsurface, micron-scale resolution optical imaging tool that can provide images of oral tissue subsurface layers down to a depth of 1-2 mm (structural OCT), as well as images demonstrating vessel morphology (speckle variance OCT) and blood flow information (Doppler OCT). This thesis explains the development of an OCT setup and an oral probe to acquire images in-vivo. Moreover, it introduces a software-based quantification platform for extracting specific biologically-meaningful metrics from the structural and vascular OCT images. It then describes the application of the developed imaging and quantification platform in a feasibility clinical study that was performed on 15 late oral radiation toxicity patients and 5 age

  11. Phase-contrast x-ray imaging and tomography of the nematode Caenorhabditis elegans

    NASA Astrophysics Data System (ADS)

    Olendrowitz, C.; Bartels, M.; Krenkel, M.; Beerlink, A.; Mokso, R.; Sprung, M.; Salditt, T.

    2012-08-01

    We have analyzed the model organism Caenorhabditis elegans with the help of phase-contrast x-ray tomography. This work combines techniques from x-ray imaging studies of single biological cells by in-line holography with three-dimensional reconstruction and furthermore extends these studies to the multicellular level. To preserve the sub-cellular ultrastructure of the nematodes, we used the near-native sample preparation of high-pressure freezing as commonly used in the field of electron microscopy. For the presented samples, a standard, non-magnifying parallel-beam setting, as well as a magnifying, divergent-beam setting using nanofocusing optics is evaluated based on their tomographic reconstruction potential. In this paper, we address difficulties in sample preparation and issues of image processing. By experimental refinement and through optimized reconstruction procedures, we were able to perform x-ray imaging studies on a living specimen.

  12. An algebraic iterative reconstruction technique for differential X-ray phase-contrast computed tomography.

    PubMed

    Fu, Jian; Schleede, Simone; Tan, Renbo; Chen, Liyuan; Bech, Martin; Achterhold, Klaus; Gifford, Martin; Loewen, Rod; Ruth, Ronald; Pfeiffer, Franz

    2013-09-01

    Iterative reconstruction has a wide spectrum of proven advantages in the field of conventional X-ray absorption-based computed tomography (CT). In this paper, we report on an algebraic iterative reconstruction technique for grating-based differential phase-contrast CT (DPC-CT). Due to the differential nature of DPC-CT projections, a differential operator and a smoothing operator are added to the iterative reconstruction, compared to the one commonly used for absorption-based CT data. This work comprises a numerical study of the algorithm and its experimental verification using a dataset measured at a two-grating interferometer setup. Since the algorithm is easy to implement and allows for the extension to various regularization possibilities, we expect a significant impact of the method for improving future medical and industrial DPC-CT applications.

  13. Virtual unrolling and deciphering of Herculaneum papyri by X-ray phase-contrast tomography.

    PubMed

    Bukreeva, I; Mittone, A; Bravin, A; Festa, G; Alessandrelli, M; Coan, P; Formoso, V; Agostino, R G; Giocondo, M; Ciuchi, F; Fratini, M; Massimi, L; Lamarra, A; Andreani, C; Bartolino, R; Gigli, G; Ranocchia, G; Cedola, A

    2016-06-06

    A collection of more than 1800 carbonized papyri, discovered in the Roman 'Villa dei Papiri' at Herculaneum is the unique classical library survived from antiquity. These papyri were charred during 79 A.D. Vesuvius eruption, a circumstance which providentially preserved them until now. This magnificent collection contains an impressive amount of treatises by Greek philosophers and, especially, Philodemus of Gadara, an Epicurean thinker of 1st century BC. We read many portions of text hidden inside carbonized Herculaneum papyri using enhanced X-ray phase-contrast tomography non-destructive technique and a new set of numerical algorithms for 'virtual-unrolling'. Our success lies in revealing the largest portion of Greek text ever detected so far inside unopened scrolls, with unprecedented spatial resolution and contrast, all without damaging these precious historical manuscripts. Parts of text have been decoded and the 'voice' of the Epicurean philosopher Philodemus is brought back again after 2000 years from Herculaneum papyri.

  14. Ultrasonic tomography for in-process measurements of temperature in a multi-phase medium

    DOEpatents

    Beller, L.S.

    1993-01-26

    A method and apparatus are described for the in-process measurement of internal particulate temperature utilizing ultrasonic tomography techniques to determine the speed of sound through a specimen material. Ultrasonic pulses are transmitted through a material, which can be a multi-phase material, over known flight paths and the ultrasonic pulse transit times through all sectors of the specimen are measured to determine the speed of sound. The speed of sound being a function of temperature, it is possible to establish the correlation between speed of sound and temperature, throughout a cross-section of the material, which correlation is programmed into a computer to provide for a continuous in-process measurement of temperature throughout the specimen.

  15. X-ray phase contrast tomography with a bending magnet source

    NASA Astrophysics Data System (ADS)

    Peele, A. G.; De Carlo, F.; McMahon, P. J.; Dhal, B. B.; Nugent, K. A.

    2005-08-01

    X-ray radiography and x-ray tomography are important tools for noninvasive characterization of materials. Historically, the contrast mechanism used with these techniques has been absorption. However, for any given sample there are x-ray energies for which absorption contrast is poor. Alternatively, when good contrast can be obtained, radiation damage from an excessive dose may become an issue. Consequently, phase-contrast methods have in recent years been implemented at both synchrotron and laboratory facilities. A range of radiographic and tomographic demonstrations have now been made, typically utilizing the coherent flux from an insertion device at a synchrotron or a microfocus laboratory source. In this paper we demonstrate that useful results may be obtained using a bending magnet source at a synchrotron. In particular we show that the same beamline can be used to make and characterize a sample made by x-ray lithographic methods.

  16. Maximum a posteriori estimation of crystallographic phases in X-ray diffraction tomography

    PubMed Central

    Gürsoy, Doĝa; Biçer, Tekin; Almer, Jonathan D.; Kettimuthu, Raj; Stock, Stuart R.; De Carlo, Francesco

    2015-01-01

    A maximum a posteriori approach is proposed for X-ray diffraction tomography for reconstructing three-dimensional spatial distribution of crystallographic phases and orientations of polycrystalline materials. The approach maximizes the a posteriori density which includes a Poisson log-likelihood and an a priori term that reinforces expected solution properties such as smoothness or local continuity. The reconstruction method is validated with experimental data acquired from a section of the spinous process of a porcine vertebra collected at the 1-ID-C beamline of the Advanced Photon Source, at Argonne National Laboratory. The reconstruction results show significant improvement in the reduction of aliasing and streaking artefacts, and improved robustness to noise and undersampling compared to conventional analytical inversion approaches. The approach has the potential to reduce data acquisition times, and significantly improve beamtime efficiency. PMID:25939627

  17. Ultrasonic tomography for in-process measurements of temperature in a multi-phase medium

    DOEpatents

    Beller, Laurence S.

    1993-01-01

    A method and apparatus for the in-process measurement of internal particulate temperature utilizing ultrasonic tomography techniques to determine the speed of sound through a specimen material. Ultrasonic pulses are transmitted through a material, which can be a multi-phase material, over known flight paths and the ultrasonic pulse transit times through all sectors of the specimen are measured to determine the speed of sound. The speed of sound being a function of temperature, it is possible to establish the correlation between speed of sound and temperature, throughout a cross-section of the material, which correlation is programmed into a computer to provide for a continuous in-process measurement of temperature throughout the specimen.

  18. Virtual unrolling and deciphering of Herculaneum papyri by X-ray phase-contrast tomography.

    PubMed

    Bukreeva, I; Mittone, A; Bravin, A; Festa, G; Alessandrelli, M; Coan, P; Formoso, V; Agostino, R G; Giocondo, M; Ciuchi, F; Fratini, M; Massimi, L; Lamarra, A; Andreani, C; Bartolino, R; Gigli, G; Ranocchia, G; Cedola, A

    2016-01-01

    A collection of more than 1800 carbonized papyri, discovered in the Roman 'Villa dei Papiri' at Herculaneum is the unique classical library survived from antiquity. These papyri were charred during 79 A.D. Vesuvius eruption, a circumstance which providentially preserved them until now. This magnificent collection contains an impressive amount of treatises by Greek philosophers and, especially, Philodemus of Gadara, an Epicurean thinker of 1st century BC. We read many portions of text hidden inside carbonized Herculaneum papyri using enhanced X-ray phase-contrast tomography non-destructive technique and a new set of numerical algorithms for 'virtual-unrolling'. Our success lies in revealing the largest portion of Greek text ever detected so far inside unopened scrolls, with unprecedented spatial resolution and contrast, all without damaging these precious historical manuscripts. Parts of text have been decoded and the 'voice' of the Epicurean philosopher Philodemus is brought back again after 2000 years from Herculaneum papyri. PMID:27265417

  19. Phase-retrieved optical projection tomography for 3D imaging through scattering layers

    NASA Astrophysics Data System (ADS)

    Ancora, Daniele; Di Battista, Diego; Giasafaki, Georgia; Psycharakis, Stylianos; Liapis, Evangelos; Zacharopoulos, Athanasios; Zacharakis, Giannis

    2016-03-01

    Recently great progress has been made in biological and biomedical imaging by combining non-invasive optical methods, novel adaptive light manipulation and computational techniques for intensity-based phase recovery and three dimensional image reconstruction. In particular and in relation to the work presented here, Optical Projection Tomography (OPT) is a well-established technique for imaging mostly transparent absorbing biological models such as C. Elegans and Danio Rerio. On the contrary, scattering layers like the cocoon surrounding the Drosophila during the pupae stage constitutes a challenge for three dimensional imaging through such a complex structure. However, recent studies enabled image reconstruction through scattering curtains up to few transport mean free paths via phase retrieval iterative algorithms allowing to uncover objects hidden behind complex layers. By combining these two techniques we explore the possibility to perform a three dimensional image reconstruction of fluorescent objects embedded between scattering layers without compromising its structural integrity. Dynamical cross correlation registration was implemented for the registration process due to translational and flipping ambiguity of the phase retrieval problem, in order to provide the correct aligned set of data to perform the back-projection reconstruction. We have thus managed to reconstruct a hidden complex object between static scattering curtains and compared with the effective reconstruction to fully understand the process before the in-vivo biological implementation.

  20. Fourier optics analysis of phase-mask-based path-length-multiplexed optical coherence tomography.

    PubMed

    Yin, Biwei; Dwelle, Jordan; Wang, Bingqing; Wang, Tianyi; Feldman, Marc D; Rylander, Henry G; Milner, Thomas E

    2015-11-01

    Optical coherence tomography (OCT) is an imaging technique that constructs a depth-resolved image by measuring the optical path-length difference between broadband light backscattered from a sample and a reference surface. For many OCT sample arm optical configurations, sample illumination and backscattered light detection share a common path. When a phase mask is placed in the sample path, features in the detected signal are observed, which suggests that an analysis of a generic common path OCT imaging system is warranted. In this study, we present a Fourier optics analysis using a Fresnel diffraction approximation of an OCT system with a path-length-multiplexing element (PME) inserted in the sample arm optics. The analysis may be generalized for most phase-mask-based OCT systems. A radial-angle-diverse PME is analyzed in detail, and the point spread function, coherent transfer function, sensitivity of backscattering angular diversity detection, and signal formation in terms of sample spatial frequency are simulated and discussed. The analysis reveals important imaging features and application limitations of OCT imaging systems with a phase mask in the sample path optics.

  1. A reconstruction method for cone-beam differential x-ray phase-contrast computed tomography.

    PubMed

    Fu, Jian; Velroyen, Astrid; Tan, Renbo; Zhang, Junwei; Chen, Liyuan; Tapfer, Arne; Bech, Martin; Pfeiffer, Franz

    2012-09-10

    Most existing differential phase-contrast computed tomography (DPC-CT) approaches are based on three kinds of scanning geometries, described by parallel-beam, fan-beam and cone-beam. Due to the potential of compact imaging systems with magnified spatial resolution, cone-beam DPC-CT has attracted significant interest. In this paper, we report a reconstruction method based on a back-projection filtration (BPF) algorithm for cone-beam DPC-CT. Due to the differential nature of phase contrast projections, the algorithm restrains from differentiation of the projection data prior to back-projection, unlike BPF algorithms commonly used for absorption-based CT data. This work comprises a numerical study of the algorithm and its experimental verification using a dataset measured with a three-grating interferometer and a micro-focus x-ray tube source. Moreover, the numerical simulation and experimental results demonstrate that the proposed method can deal with several classes of truncated cone-beam datasets. We believe that this feature is of particular interest for future medical cone-beam phase-contrast CT imaging applications.

  2. Quantitative analysis of rectal cancer by spectral domain optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhang, Q. Q.; Wu, X. J.; Tang, T.; Zhu, S. W.; Yao, Q.; Gao, Bruce Z.; Yuan, X. C.

    2012-08-01

    To quantify OCT images of rectal tissue for clinic diagnosis, the scattering coefficient of the tissue is extracted by curve fitting the OCT signals to a confocal single model. A total of 1000 measurements (half and half of normal and malignant tissues) were obtained from 16 recta. The normal rectal tissue has a larger scattering coefficient ranging from 1.09 to 5.41 mm-1 with a mean value of 2.29 mm-1 (std:±0.32), while the malignant group shows lower scattering property and the values ranging from 0.25 to 2.69 mm-1 with a mean value of 1.41 mm-1 (std:±0.18). The peri-cancer of recta has also been investigated to distinguish the difference between normal and malignant rectal tissue. The results demonstrate that the quantitative analysis of the rectal tissue can be used as a promising diagnostic criterion of early rectal cancer, which has great value for clinical medical applications.

  3. Off-axis quantitative phase imaging processing using CUDA: toward real-time applications

    PubMed Central

    Pham, Hoa; Ding, Huafeng; Sobh, Nahil; Do, Minh; Patel, Sanjay; Popescu, Gabriel

    2011-01-01

    We demonstrate real time off-axis Quantitative Phase Imaging (QPI) using a phase reconstruction algorithm based on NVIDIA’s CUDA programming model. The phase unwrapping component is based on Goldstein’s algorithm. By mapping the process of extracting phase information and unwrapping to GPU, we are able to speed up the whole procedure by more than 18.8× with respect to CPU processing and ultimately achieve video rate for mega-pixel images. Our CUDA implementation also supports processing of multiple images simultaneously. This enables our imaging system to support high speed, high throughput, and real-time image acquisition and visualization. PMID:21750757

  4. Quantitative model of the phase behavior of recombinant pH-responsive elastin-like polypeptides.

    PubMed

    Mackay, J Andrew; Callahan, Daniel J; Fitzgerald, Kelly N; Chilkoti, Ashutosh

    2010-11-01

    Quantitative models are required to engineer biomaterials with environmentally responsive properties. With this goal in mind, we developed a model that describes the pH-dependent phase behavior of a class of stimulus responsive elastin-like polypeptides (ELPs) that undergo reversible phase separation in response to their solution environment. Under isothermal conditions, charged ELPs can undergo phase separation when their charge is neutralized. Optimization of this behavior has been challenging because the pH at which they phase separate, pHt, depends on their composition, molecular weight, concentration, and temperature. To address this problem, we developed a quantitative model to describe the phase behavior of charged ELPs that uses the Henderson-Hasselbalch relationship to describe the effect of side-chain ionization on the phase-transition temperature of an ELP. The model was validated with pH-responsive ELPs that contained either acidic (Glu) or basic (His) residues. The phase separation of both ELPs fit this model across a range of pH. These results have important implications for applications of pH-responsive ELPs because they provide a quantitative model for the rational design of pH-responsive polypeptides whose transition can be triggered at a specified pH.

  5. Quantitative shear-wave optical coherence elastography with a programmable phased array ultrasound as the wave source.

    PubMed

    Song, Shaozhen; Le, Nhan Minh; Huang, Zhihong; Shen, Tueng; Wang, Ruikang K

    2015-11-01

    The purpose of this study is to implement a beam-steering ultrasound as the wave source for shear-wave optical coherence elastography (SW-OCE) to achieve an extended range of elastic imaging of the tissue sample. We introduce a linear phased array ultrasound transducer (LPAUT) as the remote and programmable wave source and a phase-sensitive optical coherence tomography (OCT) as the sensitive shear-wave detector. The LPAUT is programmed to launch acoustic radiation force impulses (ARFI) focused at desired locations within the range of OCT imaging, upon which the elasticity map of the entire OCT B-scan cross section is recovered by spatial compounding of the elastic maps derived from each launch of AFRIs. We also propose a directional filter to separate the shear-wave propagation at different directions in order to reduce the effect of tissue heterogeneity on the shear-wave propagation within tissue. The feasibility of this proposed approach is then demonstrated by determining the stiffness of tissue-mimicking phantoms with agarose concentrations of 0.5% and 1% and also by imaging the Young's modulus of retinal and choroidal tissues within a porcine eye ball ex vivo. The approach opens up opportunities to combine medical ultrasound imaging and SW-OCE for high-resolution localized quantitative assessment of tissue biomechanical property.

  6. In situ flash x-ray high-speed computed tomography for the quantitative analysis of highly dynamic processes

    NASA Astrophysics Data System (ADS)

    Moser, Stefan; Nau, Siegfried; Salk, Manfred; Thoma, Klaus

    2014-02-01

    The in situ investigation of dynamic events, ranging from car crash to ballistics, often is key to the understanding of dynamic material behavior. In many cases the important processes and interactions happen on the scale of milli- to microseconds at speeds of 1000 m s-1 or more. Often, 3D information is necessary to fully capture and analyze all relevant effects. High-speed 3D-visualization techniques are thus required for the in situ analysis. 3D-capable optical high-speed methods often are impaired by luminous effects and dust, while flash x-ray based methods usually deliver only 2D data. In this paper, a novel 3D-capable flash x-ray based method, in situ flash x-ray high-speed computed tomography is presented. The method is capable of producing 3D reconstructions of high-speed processes based on an undersampled dataset consisting of only a few (typically 3 to 6) x-ray projections. The major challenges are identified, discussed and the chosen solution outlined. The application is illustrated with an exemplary application of a 1000 m s-1 high-speed impact event on the scale of microseconds. A quantitative analysis of the in situ measurement of the material fragments with a 3D reconstruction with 1 mm voxel size is presented and the results are discussed. The results show that the HSCT method allows gaining valuable visual and quantitative mechanical information for the understanding and interpretation of high-speed events.

  7. Dynamic contrast optical coherence tomography: quantitative measurement of microvascular transit-time distributions in vivo (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Merkle, Conrad W.; Srinivasan, Vivek J.

    2016-03-01

    Transit time is a fundamental microcirculatory parameter that is critical in determining oxygen delivery from capillaries to surrounding tissue. Recently, it was demonstrated theoretically that capillary transit-time heterogeneity potentially leads to non-uniform oxygen extraction in micro-domains. However, in spite of its importance, capillary transit-time distribution has been challenging to quantify comprehensively and efficiently at the microscopic level. Here, we introduce a method, called Dynamic Contrast Optical Coherence Tomography (DyC-OCT), based on dynamic cross-sectional OCT imaging of the kinetics of an intravascular tracer during its passage through the field-of-view. DyC-OCT is used to quantitatively measure the transit-time distribution in microvascular networks in cross-section at the single-capillary level. Transit-time metrics are derived from analysis of the temporal characteristics of the dynamic scattering signal, related to tracer concentration, using indicator-dilution theory. Since DyC-OCT does not require calibration of the optical focus, quantitative accuracy is achieved even deep in highly scattering brain tissue where the focal spot degrades. After direct validation of DyC-OCT against the dilution curves measured using a fluorescent plasma label in the surface pial vessels of a mouse brain, imaged through a thinned-skull, glass coverslip-reinforced cranial window, the laminar transit-time distribution was investigated in microvasculature across the entire depth of the mouse somatosensory cortex. Laminar trends were identified, with the earliest transit times in the middle cortical layers, and the lowest heterogeneity in cortical layer 4. The new DyC-OCT technique affords a novel perspective of microvascular networks, with the unique capability of performing simultaneous measurements of transit-time distributions across cortical laminae.

  8. Monitoring six-phase ohmic heating of contaminated soils using electrical resistance tomography

    SciTech Connect

    Ramirez, A.L.; Daily, W.D.

    1994-09-01

    Electrical resistance tomography (ERT) was used to monitor six-phase ohmic heating used for the insitu remediation of volatile organic compounds from subsurface water and soil at the Savannah River Site, near Aiken, South Carolina. The changes in electrical conductivity caused by six-phase ohmic-heating in a clay layer located in the vadose zone were monitored during a period of approximately 2 months, before, during and after heating. From an array of electrodes located in 4 boreholes, we collected electrical resistivity data between five pairs of adjacent holes pairs. This data was used to calculate tomographs which showed the electrical conductivity changes along five vertical planes. The difference tomographs show the combined effects of moisture redistribution and heating caused by six-phase heating and vapor extraction. The tomographs show that most of the clay layer increased in electrical conductivity during the first 3 weeks of the 4 week long heating phase. At this time, the electrical conductivities near the center of the heating array were twice as large as the pre-heat conductivities. Then the electrical conductivity started to decrease for portions of the clay layer closest to the vapor extraction well. We propose that the conductivity decreases are due to the removal of moisture by the heating and vacuum extraction. Parts of the clay layer near the extraction well reached electrical conductivities as low as 40% of the pre-heating values. We propose that these regions of lower than ambient electrical conductivities are indicators of regions where the vapor removal by vacuum extraction was most effective. At the end of the heating phase, our estimates suggest that the clay saturation may have dropped to as low as 10% based on the observed conductivity changes.

  9. X-ray Talbot-Lau interferometer for high-speed phase imaging and tomography using white synchrotron radiation

    SciTech Connect

    Olbinado, Margie P.; Harasse, Sebastien; Yashiro, Wataru; Momose, Atsushi

    2012-07-31

    The Talbot interferometer using white synchrotron radiation has already been demonstrated for high-speed X-ray phase imaging and tomography as well as four-dimensional phase tomography for an observation of a dynamic specimen. In those previous experiments, the grating lines were oriented horizontally because the synchrotron radiation source size is large in the horizontal direction, and only the vertical spatial coherence satisfies the requirement for the operation of the Talbot interferometer given its distance from the source. For non-rigid samples, the horizontal axis of rotation causes unwanted motion of the sample due to gravity which results to artifact in the tomography reconstruction. For fluid samples, a vertical rotation axis is certainly necessary. While it is possible to orient the sample rotation axis perpendicular to the grating lines of the Talbot interferometer, solving the definite integral of the differential phase images to obtain the phase shift for x-ray phase tomography proves to be cumbersome when the sample extends outside the image and there is no null region for which the integration constant is known. In this work we aimed at increasing the spatial coherence of the x-rays along the horizontal so that the grating lines and the sample rotation axis could be oriented vertically. A Talbot-Lau interferometer was constructed by adding an absorption grating which acted as vertical line sources of horizontally spatially coherent white synchrotron radiation to the Talbot interferometer. An average of 20% moire fringe visibility was obtained. The set-up was demonstrated for highspeed phase tomography of a polymer sample.

  10. A quantitative spatial comparison of high-density diffuse optical tomography and fMRI cortical mapping

    PubMed Central

    Eggebrecht, Adam T.; White, Brian R.; Ferradal, Silvina L.; Chen, Chunxiao; Zhan, Yuxuan; Snyder, Abraham Z.; Dehghani, Hamid; Culver, Joseph P.

    2012-01-01

    Functional neuroimaging commands a dominant role in current neuroscience research. However its use in bedside clinical and certain neuro-scientific studies has been limited because the current tools lack the combination of being non-invasive, non-ionizing and portable while maintaining moderate resolution and localization accuracy. Optical neuroimaging satisfies many of these requirements, but, until recent advances in high-density diffuse optical tomography (HD-DOT), has been hampered by limited resolution. While early results of HD-DOT have been promising, a quantitative voxel-wise comparison and validation of HD-DOT against the gold standard of functional magnetic resonance imaging (fMRI) has been lacking. Herein, we provide such an analysis within the visual cortex using matched visual stimulation protocols in a single group of subjects (n=5) during separate HD-DOT and fMRI scanning sessions. To attain the needed voxel-to-voxel co-registration between HD-DOT and fMRI image spaces, we implemented subject-specific head modeling that incorporated MRI anatomy, detailed segmentation, and alignment of source and detector positions. Comparisons of the visual responses found an average localization error between HD-DOT and fMRI of 4.4 +/− 1 mm, significantly less than the average distance between cortical gyri. This specificity demonstrates that HD-DOT has sufficient image quality to be useful as a surrogate for fMRI. PMID:22330315

  11. Effect of Hydroxychloroquine on the Retinal Layers: A Quantitative Evaluation with Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Gurler, Bulent; Yildirim, Aydin; Goker, Hasan; Pehlevan, Hatice Seval

    2016-01-01

    Purpose. To evaluate the effect of hydroxychloroquine on retinal pigment epithelium- (RPE-) Bruch's membrane complex, photoreceptor outer segment, and macular ganglion cell-inner plexiform layer (GCIPL) thicknesses using spectral-domain optical coherence tomography (SD-OCT). Methods. In this prospective case-control study, 51 eyes of 51 hydroxychloroquine patients and 30 eyes of 30 healthy subjects were included. High-quality images were obtained using a Cirrus HD-OCT with 5-line raster mode; the photoreceptor inner segment (IS) and outer segment (OS), sum of the segments (IS + OS), and RPE-Bruch's membrane complex were analyzed. Results. The thicknesses of the IS + OS and OS layers were significantly lower in the hydroxychloroquine subjects compared to the control subjects (P < 0.05). RPE-Bruch's membrane complex thicknesses were significantly higher in the hydroxychloroquine subjects than for those of the control subjects (P < 0.05). The minimum and temporal-inferior macular GCIPL thicknesses were significantly different between the patients with hydroxychloroquine use and the control subjects (P = 0.04 and P = 0.03, resp.). Conclusions. The foveal photoreceptor OS thinning, loss of GCIPL, and RPE-Bruch's membrane thickening were detected in patients with hydroxychloroquine therapy. This quantitative approach using SD-OCT images may have important implications to use as an early indicator of retinal toxicity without any visible signs of hydroxychloroquine retinopathy.

  12. Effect of Hydroxychloroquine on the Retinal Layers: A Quantitative Evaluation with Spectral-Domain Optical Coherence Tomography

    PubMed Central

    Gurler, Bulent; Yildirim, Aydin; Goker, Hasan; Pehlevan, Hatice Seval

    2016-01-01

    Purpose. To evaluate the effect of hydroxychloroquine on retinal pigment epithelium- (RPE-) Bruch's membrane complex, photoreceptor outer segment, and macular ganglion cell-inner plexiform layer (GCIPL) thicknesses using spectral-domain optical coherence tomography (SD-OCT). Methods. In this prospective case-control study, 51 eyes of 51 hydroxychloroquine patients and 30 eyes of 30 healthy subjects were included. High-quality images were obtained using a Cirrus HD-OCT with 5-line raster mode; the photoreceptor inner segment (IS) and outer segment (OS), sum of the segments (IS + OS), and RPE-Bruch's membrane complex were analyzed. Results. The thicknesses of the IS + OS and OS layers were significantly lower in the hydroxychloroquine subjects compared to the control subjects (P < 0.05). RPE-Bruch's membrane complex thicknesses were significantly higher in the hydroxychloroquine subjects than for those of the control subjects (P < 0.05). The minimum and temporal-inferior macular GCIPL thicknesses were significantly different between the patients with hydroxychloroquine use and the control subjects (P = 0.04 and P = 0.03, resp.). Conclusions. The foveal photoreceptor OS thinning, loss of GCIPL, and RPE-Bruch's membrane thickening were detected in patients with hydroxychloroquine therapy. This quantitative approach using SD-OCT images may have important implications to use as an early indicator of retinal toxicity without any visible signs of hydroxychloroquine retinopathy. PMID:27656292

  13. Analysis of strength and failure pattern of human proximal femur using quantitative computed tomography (QCT)-based finite element method.

    PubMed

    Mirzaei, Majid; Keshavarzian, Maziyar; Naeini, Vahid

    2014-07-01

    This paper presents a novel method for fast and reliable prediction of the failure strength of human proximal femur, using the quantitative computed tomography (QCT)-based linear finite element analysis (FEA). Ten fresh frozen human femora (age: 34±16) were QCT-scanned and the pertinent 3D voxel-based finite element models were constructed. A specially-designed holding frame was used to define and maintain a unique geometrical reference system for both FEA and in-vitro mechanical testing. The analyses and tests were carried out at 8 different loading orientations. A new scheme was developed for assortment of the element risk factor (defined as the ratio of the strain energy density to the yield strain energy for each element) and implemented for the prediction of the failure strength. The predicted and observed failure patterns were in correspondence, and the FEA predictions of the failure loads were in very good agreement with the experimental results (R2=0.86, slope=0.96, p<0.01). The average computational time was 5 min (on a regular desktop personal computer) for an average element number of 197,000. Noting that the run-time for a similar nonlinear model is about 8h, it was concluded that the proposed linear scheme is overwhelmingly efficient in terms of computational costs. Thus, it can efficiently be used to predict the femoral failure strength with the same accuracy of similar nonlinear models. PMID:24735974

  14. Effect of Hydroxychloroquine on the Retinal Layers: A Quantitative Evaluation with Spectral-Domain Optical Coherence Tomography.

    PubMed

    Uslu, Hasim; Gurler, Bulent; Yildirim, Aydin; Tatar, Mehmet Gurkan; Aylin Kantarcı, Feride; Goker, Hasan; Pehlevan, Hatice Seval; Colak, Hatice Nur

    2016-01-01

    Purpose. To evaluate the effect of hydroxychloroquine on retinal pigment epithelium- (RPE-) Bruch's membrane complex, photoreceptor outer segment, and macular ganglion cell-inner plexiform layer (GCIPL) thicknesses using spectral-domain optical coherence tomography (SD-OCT). Methods. In this prospective case-control study, 51 eyes of 51 hydroxychloroquine patients and 30 eyes of 30 healthy subjects were included. High-quality images were obtained using a Cirrus HD-OCT with 5-line raster mode; the photoreceptor inner segment (IS) and outer segment (OS), sum of the segments (IS + OS), and RPE-Bruch's membrane complex were analyzed. Results. The thicknesses of the IS + OS and OS layers were significantly lower in the hydroxychloroquine subjects compared to the control subjects (P < 0.05). RPE-Bruch's membrane complex thicknesses were significantly higher in the hydroxychloroquine subjects than for those of the control subjects (P < 0.05). The minimum and temporal-inferior macular GCIPL thicknesses were significantly different between the patients with hydroxychloroquine use and the control subjects (P = 0.04 and P = 0.03, resp.). Conclusions. The foveal photoreceptor OS thinning, loss of GCIPL, and RPE-Bruch's membrane thickening were detected in patients with hydroxychloroquine therapy. This quantitative approach using SD-OCT images may have important implications to use as an early indicator of retinal toxicity without any visible signs of hydroxychloroquine retinopathy. PMID:27656292

  15. Reducing the influence of spatial resolution to improve quantitative accuracy in emission tomography: A comparison of potential strategies

    NASA Astrophysics Data System (ADS)

    Hutton, B. F.; Olsson, A.; Som, S.; Erlandsson, K.; Braun, M.

    2006-12-01

    The goal of this paper is to compare strategies for reducing partial volume effects by either minimizing the cause (i.e. improving resolution) or correcting the effect. Correction for resolution loss can be achieved either by modelling the resolution for use in iterative reconstruction or by imposing constraints based on knowledge of the underlying anatomy. Approaches to partial volume correction largely rely on knowledge of the underlying anatomy, based on well-registered high-resolution anatomical imaging modalities (CT or MRI). Corrections can be applied by considering the signal loss that results by smoothing the high-resolution modality to the same resolution as obtained in emission tomography. A physical phantom representing the central brain structures was used to evaluate the quantitative accuracy of the various strategies for either improving resolution or correcting for partial volume effects. Inclusion of resolution in the reconstruction model improved the measured contrast for the central brain structures but still underestimated the true object contrast (˜0.70). Use of information on the boundaries of the structures in conjunction with a smoothing prior using maximum entropy reconstruction achieved some degree of contrast enhancement and improved the noise properties of the resulting images. Partial volume correction based on segmentation of registered anatomical images and knowledge of the reconstructed resolution permitted more accurate quantification of the target to background ratio for individual brain structures.

  16. Quantitative tool for rapid disease mapping using optical coherence tomography images of azoxymethane-treated mouse colon

    NASA Astrophysics Data System (ADS)

    Winkler, Amy M.; Rice, Photini F. S.; Drezek, Rebekah A.; Barton, Jennifer K.

    2010-07-01

    Optical coherence tomography (OCT) can provide new insight into disease progression and therapy by enabling nondestructive, serial imaging of in vivo cancer models. In previous studies, we have shown the utility of endoscopic OCT for identifying adenomas in the azoxymethane-treated mouse model of colorectal cancer and tracking disease progression over time. Because of improved imaging speed made possible through Fourier domain imaging, three-dimensional imaging of the entire mouse colon is possible. Increased amounts of data can facilitate more accurate classification of tissue but require more time on the part of the researcher to sift through and identify relevant data. We present quantitative software for automatically identifying potentially diseased areas that can be used to create a two-dimensional ``disease map'' from a three-dimensional Fourier domain OCT data set. In addition to sensing inherent changes in tissue that occur during disease development, the algorithm is sensitive to exogeneous highly scattering gold nanoshells that can be targeted to disease biomarkers. The results of the algorithm were compared to histological diagnosis. The algorithm was then used to assess the ability of gold nanoshells targeted to epidermal growth factor receptor in vivo to enable functional OCT imaging.

  17. Quantitative imaging of cerebral blood flow velocity and intracellular motility using dynamic light scattering–optical coherence tomography

    PubMed Central

    Lee, Jonghwan; Radhakrishnan, Harsha; Wu, Weicheng; Daneshmand, Ali; Climov, Mihail; Ayata, Cenk; Boas, David A

    2013-01-01

    This paper describes a novel optical method for label-free quantitative imaging of cerebral blood flow (CBF) and intracellular motility (IM) in the rodent cerebral cortex. This method is based on a technique that integrates dynamic light scattering (DLS) and optical coherence tomography (OCT), named DLS–OCT. The technique measures both the axial and transverse velocities of CBF, whereas conventional Doppler OCT measures only the axial one. In addition, the technique produces a three-dimensional map of the diffusion coefficient quantifying nontranslational motions. In the DLS–OCT diffusion map, we observed high-diffusion spots, whose locations highly correspond to neuronal cell bodies and whose diffusion coefficient agreed with that of the motion of intracellular organelles reported in vitro in the literature. Therefore, the present method has enabled, for the first time to our knowledge, label-free imaging of the diffusion-like motion of intracellular organelles in vivo. As an example application, we used the method to monitor CBF and IM during a brief ischemic stroke, where we observed an induced persistent reduction in IM despite the recovery of CBF after stroke. This result supports that the IM measured in this study represent the cellular energy metabolism-related active motion of intracellular organelles rather than free diffusion of intracellular macromolecules. PMID:23403378

  18. In Vivo Quantitative Assessment of Myocardial Structure, Function, Perfusion and Viability Using Cardiac Micro-computed Tomography

    PubMed Central

    van Deel, Elza; Ridwan, Yanto; van Vliet, J. Nicole; Belenkov, Sasha; Essers, Jeroen

    2016-01-01

    The use of Micro-Computed Tomography (MicroCT) for in vivo studies of small animals as models of human disease has risen tremendously due to the fact that MicroCT provides quantitative high-resolution three-dimensional (3D) anatomical data non-destructively and longitudinally. Most importantly, with the development of a novel preclinical iodinated contrast agent called eXIA160, functional and metabolic assessment of the heart became possible. However, prior to the advent of commercial MicroCT scanners equipped with X-ray flat-panel detector technology and easy-to-use cardio-respiratory gating, preclinical studies of cardiovascular disease (CVD) in small animals required a MicroCT technologist with advanced skills, and thus were impractical for widespread implementation. The goal of this work is to provide a practical guide to the use of the high-speed Quantum FX MicroCT system for comprehensive determination of myocardial global and regional function along with assessment of myocardial perfusion, metabolism and viability in healthy mice and in a cardiac ischemia mouse model induced by permanent occlusion of the left anterior descending coronary artery (LAD). PMID:26967592

  19. In Vivo Quantitative Assessment of Myocardial Structure, Function, Perfusion and Viability Using Cardiac Micro-computed Tomography.

    PubMed

    van Deel, Elza; Ridwan, Yanto; van Vliet, J Nicole; Belenkov, Sasha; Essers, Jeroen

    2016-01-01

    The use of Micro-Computed Tomography (MicroCT) for in vivo studies of small animals as models of human disease has risen tremendously due to the fact that MicroCT provides quantitative high-resolution three-dimensional (3D) anatomical data non-destructively and longitudinally. Most importantly, with the development of a novel preclinical iodinated contrast agent called eXIA160, functional and metabolic assessment of the heart became possible. However, prior to the advent of commercial MicroCT scanners equipped with X-ray flat-panel detector technology and easy-to-use cardio-respiratory gating, preclinical studies of cardiovascular disease (CVD) in small animals required a MicroCT technologist with advanced skills, and thus were impractical for widespread implementation. The goal of this work is to provide a practical guide to the use of the high-speed Quantum FX MicroCT system for comprehensive determination of myocardial global and regional function along with assessment of myocardial perfusion, metabolism and viability in healthy mice and in a cardiac ischemia mouse model induced by permanent occlusion of the left anterior descending coronary artery (LAD). PMID:26967592

  20. Quantitative tool for rapid disease mapping using optical coherence tomography images of azoxymethane-treated mouse colon

    PubMed Central

    Winkler, Amy M.; Rice, Photini F.S.; Drezek, Rebekah A.; Barton, Jennifer K.

    2010-01-01

    Optical coherence tomography (OCT) can provide new insight into disease progression and therapy by enabling nondestructive, serial imaging of in vivo cancer models. In previous studies, we have shown the utility of endoscopic OCT for identifying adenomas in the azoxymethane-treated mouse model of colorectal cancer and tracking disease progression over time. Because of improved imaging speed made possible through Fourier domain imaging, three-dimensional imaging of the entire mouse colon is possible. Increased amounts of data can facilitate more accurate classification of tissue but require more time on the part of the researcher to sift through and identify relevant data. We present quantitative software for automatically identifying potentially diseased areas that can be used to create a two-dimensional “disease map” from a three-dimensional Fourier domain OCT data set. In addition to sensing inherent changes in tissue that occur during disease development, the algorithm is sensitive to exogeneous highly scattering gold nanoshells that can be targeted to disease biomarkers. The results of the algorithm were compared to histological diagnosis. The algorithm was then used to assess the ability of gold nanoshells targeted to epidermal growth factor receptor in vivo to enable functional OCT imaging. PMID:20799790

  1. Refractive-index profiling of optical fibers with axial symmetry by use of quantitative phase microscopy.

    PubMed

    Roberts, A; Ampem-Lassen, E; Barty, A; Nugent, K A; Baxter, G W; Dragomir, N M; Huntington, S T

    2002-12-01

    The application of quantitative phase microscopy to refractive-index profiling of optical fibers is demonstrated. Phase images of axially symmetric optical fibers immersed in index-matching fluid are obtained, and the inverse Abel transform is used to obtain the radial refractive-index profile. This technique is straightforward, nondestructive, repeatable, and accurate. Excellent agreement, to within approximately 0.0005, between this method and the index profile obtained with a commercial profiler is obtained.

  2. Spatial variability in free phase gas dynamics in a Northern peatland using surface resistivity and GPR tomography

    NASA Astrophysics Data System (ADS)

    Terry, N.; Slater, L. D.; Comas, X.; Parsekian, A.; Schafer, K. V.; Reeve, A. S.

    2011-12-01

    Recent research suggests peatlands play a vital role in greenhouse gas exchange between the atmosphere and the terrestrial environment. However, scientific understanding of the mechanisms governing this exchange remains limited, and quantitative data regarding free phase fluxes between peatlands and the atmosphere, particularly those associated with large-scale ebullition events, is largely unavailable. To study these fluxes, recent geophysical techniques, such as ground penetrating radar (GPR), DC resistivity, and electromagnetic induction, have demonstrated potential to monitor 2D or 3D gas dynamics in peatlands non-invasively and in situ. In this research, we acquired bi-daily resistivity and tomographic GPR data over the course of ten days at a field site in Caribou Bog, Maine. Two boreholes spaced approximately 4 m apart and 6.5 m deep to the underlying mineral soil were utilized for the collection of tomographic and zero offset GPR data. Surrounding this area, eight direct current resistivity lines, with line spacing of approximately 4 m and electrode spacing of 1.25 m, were used to create a comprehensive electrical imaging dataset. In addition, continuous pressure and temperature data were collected at varying depths near the resistivity array, and surface gas flux chamber measurements were obtained using a fast methane analyzer (Li7700) located on site. Inversion of the GPR and resistivity data provides evidence for a correlation between free phase gas production and release, and atmospheric pressure and temperature. In this study, we demonstrate the utility of capturing subsurface gas evolution and ebullition in 2D at multiple spatial scales using different geophysical techniques. On the one hand, GPR tomography provides a tool for monitoring the spatial distribution of free phase gas at high resolution in 2D. In contrast, resistivity is a rapid, more autonomous method that samples at coarser resolution. These results spur construction of a stochastic

  3. Food Consumption and Handling Survey for Quantitative Microbiological Consumer Phase Risk Assessments.

    PubMed

    Chardon, Jurgen; Swart, Arno

    2016-07-01

    In the consumer phase of a typical quantitative microbiological risk assessment (QMRA), mathematical equations identify data gaps. To acquire useful data we designed a food consumption and food handling survey (2,226 respondents) for QMRA applications that is especially aimed at obtaining quantitative data. For a broad spectrum of food products, the survey covered the following topics: processing status at retail, consumer storage, preparation, and consumption. Questions were designed to facilitate distribution fitting. In the statistical analysis, special attention was given to the selection of the most adequate distribution to describe the data. Bootstrap procedures were used to describe uncertainty. The final result was a coherent quantitative consumer phase food survey and parameter estimates for food handling and consumption practices in The Netherlands, including variation over individuals and uncertainty estimates.

  4. Monitoring laser treatment of port wine stains using phase-resolved optical Doppler tomography

    NASA Astrophysics Data System (ADS)

    Zhao, Yonghua; Chen, Zhongping; Saxer, Christopher E.; de Boer, Johannes F.; Majaron, Boris; Verkruysse, Wim; Nelson, J. Stuart

    2000-04-01

    We used a novel phase-resolved optical Doppler tomographic (ODT) technique, with very high flow velocity sensitivity and high spatial resolution, to image blood flow in port wine stain (PWS) birthmarks in human skin. The variance of blood flow velocity is used to locate the PWS vessels in addition to the regular ODT images. Our device combines an ODT system and laser so that PWS blood flow can be monitored in situ before and after treatment. To our knowledge, this is the first clinical application of ODT to provide a fast semi-quantitative evaluation of the efficacy of PWS laser therapy in situ and in real-time.

  5. X-ray phase-contrast tomography for high-spatial-resolution zebrafish muscle imaging

    NASA Astrophysics Data System (ADS)

    Vågberg, William; Larsson, Daniel H.; Li, Mei; Arner, Anders; Hertz, Hans M.

    2015-11-01

    Imaging of muscular structure with cellular or subcellular detail in whole-body animal models is of key importance for understanding muscular disease and assessing interventions. Classical histological methods for high-resolution imaging methods require excision, fixation and staining. Here we show that the three-dimensional muscular structure of unstained whole zebrafish can be imaged with sub-5 μm detail with X-ray phase-contrast tomography. Our method relies on a laboratory propagation-based phase-contrast system tailored for detection of low-contrast 4-6 μm subcellular myofibrils. The method is demonstrated on 20 days post fertilization zebrafish larvae and comparative histology confirms that we resolve individual myofibrils in the whole-body animal. X-ray imaging of healthy zebrafish show the expected structured muscle pattern while specimen with a dystrophin deficiency (sapje) displays an unstructured pattern, typical of Duchenne muscular dystrophy. The method opens up for whole-body imaging with sub-cellular detail also of other types of soft tissue and in different animal models.

  6. Optical coherence tomography phase measurement of transient changes in squid giant axons during activity.

    PubMed

    Akkin, Taner; Landowne, David; Sivaprakasam, Aarthi

    2009-09-01

    Noncontact optical measurements reveal that transient changes in squid giant axons are associated with action potential propagation and altered under different environmental (i.e., temperature) and physiological (i.e., ionic concentrations) conditions. Using a spectral-domain optical coherence tomography system, which produces real-time cross-sectional images of the axon in a nerve chamber, axonal surfaces along a depth profile are monitored. Differential phase analyses show transient changes around the membrane on a millisecond timescale, and the response is coincident with the arrival of the action potential at the optical measurement area. Cooling the axon slows the electrical and optical responses and increases the magnitude of the transient signals. Increasing the NaCl concentration bathing the axon, whose diameter is decreased in the hypertonic solution, results in significantly larger transient signals during action potential propagation. While monophasic and biphasic behaviors are observed, biphasic behavior dominates the results. The initial phase detected was constant for a single location but alternated for different locations; therefore, these transient signals acquired around the membrane appear to have local characteristics.

  7. X-ray phase-contrast tomography for high-spatial-resolution zebrafish muscle imaging

    PubMed Central

    Vågberg, William; Larsson, Daniel H.; Li, Mei; Arner, Anders; Hertz, Hans M.

    2015-01-01

    Imaging of muscular structure with cellular or subcellular detail in whole-body animal models is of key importance for understanding muscular disease and assessing interventions. Classical histological methods for high-resolution imaging methods require excision, fixation and staining. Here we show that the three-dimensional muscular structure of unstained whole zebrafish can be imaged with sub-5 μm detail with X-ray phase-contrast tomography. Our method relies on a laboratory propagation-based phase-contrast system tailored for detection of low-contrast 4–6 μm subcellular myofibrils. The method is demonstrated on 20 days post fertilization zebrafish larvae and comparative histology confirms that we resolve individual myofibrils in the whole-body animal. X-ray imaging of healthy zebrafish show the expected structured muscle pattern while specimen with a dystrophin deficiency (sapje) displays an unstructured pattern, typical of Duchenne muscular dystrophy. The method opens up for whole-body imaging with sub-cellular detail also of other types of soft tissue and in different animal models. PMID:26564785

  8. X-ray phase-contrast tomography for high-spatial-resolution zebrafish muscle imaging.

    PubMed

    Vågberg, William; Larsson, Daniel H; Li, Mei; Arner, Anders; Hertz, Hans M

    2015-01-01

    Imaging of muscular structure with cellular or subcellular detail in whole-body animal models is of key importance for understanding muscular disease and assessing interventions. Classical histological methods for high-resolution imaging methods require excision, fixation and staining. Here we show that the three-dimensional muscular structure of unstained whole zebrafish can be imaged with sub-5 μm detail with X-ray phase-contrast tomography. Our method relies on a laboratory propagation-based phase-contrast system tailored for detection of low-contrast 4-6 μm subcellular myofibrils. The method is demonstrated on 20 days post fertilization zebrafish larvae and comparative histology confirms that we resolve individual myofibrils in the whole-body animal. X-ray imaging of healthy zebrafish show the expected structured muscle pattern while specimen with a dystrophin deficiency (sapje) displays an unstructured pattern, typical of Duchenne muscular dystrophy. The method opens up for whole-body imaging with sub-cellular detail also of other types of soft tissue and in different animal models. PMID:26564785

  9. Quantitative Carré differential interference contrast microscopy to assess phase and amplitude.

    PubMed

    Duncan, Donald D; Fischer, David G; Dayton, Amanda; Prahl, Scott A

    2011-06-01

    We present a method of using an unmodified differential interference contrast microscope to acquire quantitative information on scatter and absorption of thin tissue samples. A simple calibration process is discussed that uses a standard optical wedge. Subsequently, we present a phase-stepping procedure for acquiring phase gradient information exclusive of absorption effects. The procedure results in two-dimensional maps of the local angular (polar and azimuthal) ray deviation. We demonstrate the calibration process, discuss details of the phase-stepping algorithm, and present representative results for a porcine skin sample.

  10. In Vitro Validation of an Artefact Suppression Algorithm in X-Ray Phase-Contrast Computed Tomography

    PubMed Central

    Sunaguchi, Naoki; Yuasa, Tetsuya; Hirano, Shin-ichi; Gupta, Rajiv; Ando, Masami

    2015-01-01

    X-ray phase-contrast tomography can significantly increase the contrast-resolution of conventional attenuation-contrast imaging, especially for soft-tissue structures that have very similar attenuation. Just as in attenuation-based tomography, phase contrast tomography requires a linear dependence of aggregate beam direction on the incremental direction alteration caused by individual voxels along the path of the X-ray beam. Dense objects such as calcifications in biological specimens violate this condition. There are extensive beam deflection artefacts in the vicinity of such structures because they result in large distortion of wave front due to the large difference of refractive index; for such large changes in beam direction, the transmittance of the silicon analyzer crystal saturates and is no longer linearly dependent on the angle of refraction. This paper describes a method by which these effects can be overcome and excellent soft-tissue contrast of phase tomography can be preserved in the vicinity of such artefact-producing structures. PMID:26295713

  11. In Vitro Validation of an Artefact Suppression Algorithm in X-Ray Phase-Contrast Computed Tomography.

    PubMed

    Sunaguchi, Naoki; Yuasa, Tetsuya; Hirano, Shin-Ichi; Gupta, Rajiv; Ando, Masami

    2015-01-01

    X-ray phase-contrast tomography can significantly increase the contrast-resolution of conventional attenuation-contrast imaging, especially for soft-tissue structures that have very similar attenuation. Just as in attenuation-based tomography, phase contrast tomography requires a linear dependence of aggregate beam direction on the incremental direction alteration caused by individual voxels along the path of the X-ray beam. Dense objects such as calcifications in biological specimens violate this condition. There are extensive beam deflection artefacts in the vicinity of such structures because they result in large distortion of wave front due to the large difference of refractive index; for such large changes in beam direction, the transmittance of the silicon analyzer crystal saturates and is no longer linearly dependent on the angle of refraction. This paper describes a method by which these effects can be overcome and excellent soft-tissue contrast of phase tomography can be preserved in the vicinity of such artefact-producing structures. PMID:26295713

  12. Confocal reflectance quantitative phase microscopy system for cell biology studies (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Singh, Vijay Raj; So, Peter T. C.

    2016-03-01

    Quantitative phase microscopy (QPM), used to measure the refractive index, provides the optical path delay measurement at each point of the specimen under study and becomes an active field in biological science. In this work we present development of confocal reflection phase microscopy system to provide depth resolved quantitative phase information for investigation of intracellular structures and other biological specimen. The system hardware development is mainly divided into two major parts. First, creates a pinhole array for parallel confocal imaging of specimen at multiple locations simultaneously. Here a digital micro mirror device (DMD) is used to generate pinhole array by turning on a subset micro-mirrors arranged on a grid. Second is the detection of phase information of confocal imaging foci by using a common path interferometer. With this novel approach, it is possible to measure the nuclei membrane fluctuations and distinguish them from the plasma membrane fluctuations. Further, depth resolved quantitative phase can be correlated to the intracellular contents and 3D map of refractive index measurements.

  13. Quantitative strain analysis in analogue modelling experiments: insights from X-ray computed tomography and tomographic image correlation

    NASA Astrophysics Data System (ADS)

    Adam, J.; Klinkmueller, M.; Schreurs, G.; Wieneke, B.

    2009-04-01

    The combination of scaled analogue modelling experiments, advanced research in analogue material mechanics (Lohrmann et al. 2003, Panien et al. 2006), X-ray computed tomography and new high-resolution deformation monitoring techniques (2D/3D Digital Image Correlation) is a new powerful tool not only to examine the evolution and interaction of faulting in analogue models, but also to evaluate relevant controlling factors such as mechanics, sedimentation, erosion and climate. This is of particular interest for applied problems in the energy sector (e.g., structurally complex reservoirs, LG & CO2 underground storage) because the results are essential for geological and seismic interpretation as well as for more realistically constrained fault/fracture simulations and reservoir characterisation. X-ray computed tomography (CT) analysis has been successfully applied to analogue models since the late 1980s. This technique permits visualisation of the interior of an analogue model without destroying it. Technological improvements have resulted in more powerful X-ray CT scanners that allow periodic acquisition of volumetric data sets thus making it possible to follow the 3-D evolution of the model structures with time (e.g. Schreurs et al., 2002, 2003). Optical strain monitoring (Digital Image Correlation, DIC) in analogue experiments (Adam et al., 2005) represents an important advance in quantitative physical modelling and in helping to understand non-linear rock deformation processes. Optical non-intrusive 2D/3D strain and surface flow analysis by DIC is a new methodology in physical modelling that enables the complete quantification of localised and distributed model deformation. The increase in spatial/temporal strain data resolution of several orders of magnitude makes physical modelling - used for decades to visualize the kinematic processes of geological deformation processes - a unique research tool to determine what fundamental physical processes control tectonic

  14. Surface wave phase velocities from 2-D surface wave tomography studies in the Anatolian plate

    NASA Astrophysics Data System (ADS)

    Arif Kutlu, Yusuf; Erduran, Murat; Çakır, Özcan; Vinnik, Lev; Kosarev, Grigoriy; Oreshin, Sergey

    2014-05-01

    We study the Rayleigh and Love surface wave fundamental mode propagation beneath the Anatolian plate. To examine the inter-station phase velocities a two-station method is used along with the Multiple Filter Technique (MFT) in the Computer Programs in Seismology (Herrmann and Ammon, 2004). The near-station waveform is deconvolved from the far-station waveform removing the propagation effects between the source and the station. This method requires that the near and far stations are aligned with the epicentre on a great circle path. The azimuthal difference of the earthquake to the two-stations and the azimuthal difference between the earthquake and the station are restricted to be smaller than 5o. We selected 3378 teleseismic events (Mw >= 5.7) recorded by 394 broadband local stations with high signal-to-noise ratio within the years 1999-2013. Corrected for the instrument response suitable seismogram pairs are analyzed with the two-station method yielding a collection of phase velocity curves in various period ranges (mainly in the range 25-185 sec). Diffraction from lateral heterogeneities, multipathing, interference of Rayleigh and Love waves can alter the dispersion measurements. In order to obtain quality measurements, we select only smooth portions of the phase velocity curves, remove outliers and average over many measurements. We discard these average phase velocity curves suspected of suffering from phase wrapping errors by comparing them with a reference Earth model (IASP91 by Kennett and Engdahl, 1991). The outlined analysis procedure yields 3035 Rayleigh and 1637 Love individual phase velocity curves. To obtain Rayleigh and Love wave travel times for a given region we performed 2-D tomographic inversion for which the Fast Marching Surface Tomography (FMST) code developed by N. Rawlinson at the Australian National University was utilized. This software package is based on the multistage fast marching method by Rawlinson and Sambridge (2004a, 2004b). The

  15. Color-coded LED microscopy for multi-contrast and quantitative phase-gradient imaging.

    PubMed

    Lee, Donghak; Ryu, Suho; Kim, Uihan; Jung, Daeseong; Joo, Chulmin

    2015-12-01

    We present a multi-contrast microscope based on color-coded illumination and computation. A programmable three-color light-emitting diode (LED) array illuminates a specimen, in which each color corresponds to a different illumination angle. A single color image sensor records light transmitted through the specimen, and images at each color channel are then separated and utilized to obtain bright-field, dark-field, and differential phase contrast (DPC) images simultaneously. Quantitative phase imaging is also achieved based on DPC images acquired with two different LED illumination patterns. The multi-contrast and quantitative phase imaging capabilities of our method are demonstrated by presenting images of various transparent biological samples. PMID:26713205

  16. Phase-sensitive optical coherence tomography characterization of pulse-induced trabecular meshwork displacement in ex vivo nonhuman primate eyes

    NASA Astrophysics Data System (ADS)

    Li, Peng; Reif, Roberto; Zhi, Zhongwei; Martin, Elizabeth; Shen, Tueng T.; Johnstone, Murray; Wang, Ruikang K.

    2012-07-01

    Glaucoma is a blinding disease for which intraocular pressure (IOP) is the only treatable risk factor. The mean IOP is regulated through the aqueous outflow system, which contains the trabecular meshwork (TM). Considerable evidence indicates that trabecular tissue movement regulates the aqueous outflow and becomes abnormal during glaucoma; however, such motion has thus far escaped detection. The purpose of this study is to describe anovel use of a phase-sensitive optical coherence tomography (PhS-OCT) method to assess pulse-dependent TM movement. For this study, we used enucleated monkey eyes, each mounted in an anterior segment holder. A perfusion system was used to control the mean IOP as well as to provide IOP sinusoidal transients (amplitude 3 mmHg, frequency 1 pulse/second) in all experiments. Measurements were carried out at seven graded mean IOPs (5, 8, 10, 20, 30, 40, and 50 mm Hg). We demonstrate that PhS-OCT is sensitive enough to image/visualize TM movement synchronous with the pulse-induced IOP transients, providing quantitative measurements of dynamic parameters such as velocity, displacement, and strain rate that are important for assessing the biomechanical compliance of the TM. We find that the largest TM displacement is in the area closest to Schlemm's canal (SC) endothelium. While maintaining constant ocular pulse amplitude, an increase of mean IOP results in a decrease of TM displacement and mean size of the SC. These results demonstrate that the PhS-OCT is a useful imaging technique capable of assessing functional properties necessary to maintain IOP in a healthy range, offering a new diagnostic alternative for glaucoma.

  17. Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

    DOE PAGESBeta

    Dyck, Ondrej; Hu, Sheng; Das, Sanjib; Keum, Jong; Xiao, Kai; Khomami, Bamin; Duscher, Gerd

    2015-11-24

    Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with themore » plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.« less

  18. Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

    SciTech Connect

    Dyck, Ondrej; Hu, Sheng; Das, Sanjib; Keum, Jong; Xiao, Kai; Khomami, Bamin; Duscher, Gerd

    2015-11-24

    Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with the plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.

  19. Practical procedure for retrieval of quantitative phase map for two-phase interface using the transport of intensity equation.

    PubMed

    Zhang, Xiaobin; Oshima, Yoshifumi

    2015-11-01

    A practical procedure for retrieving quantitative phase distribution at the interface between a thin amorphous germanium (a-Ge) film and vacuum based on the transport of intensity equation is proposed. First, small regions were selected in transmission electron microscopy (TEM) images with three different focus settings in order to avoid phase modulation due to low frequency noise. Second, the selected TEM image and its three reflected images were combined for mirror-symmetry to meet the boundary requirements. However, in this symmetrization, extra phase modulation arose due to the discontinuous nature of Fresnel fringes at the boundaries among the four parts of the combined image. Third, a corrected phase map was obtained by subtracting a linear fit to the extra phase modulation. The phase shift for a thin a-Ge film was determined to be approximately 0.5 rad, indicating that the average inner potential was 18.3 V. The validity of the present phase retrieval is discussed using simple simulations. PMID:26177522

  20. Estimation of whole body fat from appendicular soft tissue from peripheral quantitative computed tomography in adolescent girls

    PubMed Central

    Lee, Vinson R.; Blew, Rob M.; Farr, Josh N.; Tomas, Rita; Lohman, Timothy G.; Going, Scott B.

    2013-01-01

    Objective Assess the utility of peripheral quantitative computed tomography (pQCT) for estimating whole body fat in adolescent girls. Research Methods and Procedures Our sample included 458 girls (aged 10.7 ± 1.1y, mean BMI = 18.5 ± 3.3 kg/m2) who had DXA scans for whole body percent fat (DXA %Fat). Soft tissue analysis of pQCT scans provided thigh and calf subcutaneous percent fat and thigh and calf muscle density (muscle fat content surrogates). Anthropometric variables included weight, height and BMI. Indices of maturity included age and maturity offset. The total sample was split into validation (VS; n = 304) and cross-validation (CS; n = 154) samples. Linear regression was used to develop prediction equations for estimating DXA %Fat from anthropometric variables and pQCT-derived soft tissue components in VS and the best prediction equation was applied to CS. Results Thigh and calf SFA %Fat were positively correlated with DXA %Fat (r = 0.84 to 0.85; p <0.001) and thigh and calf muscle densities were inversely related to DXA %Fat (r = −0.30 to −0.44; p < 0.001). The best equation for estimating %Fat included thigh and calf SFA %Fat and thigh and calf muscle density (adj. R2 = 0.90; SEE = 2.7%). Bland-Altman analysis in CS showed accurate estimates of percent fat (adj. R2 = 0.89; SEE = 2.7%) with no bias. Discussion Peripheral QCT derived indices of adiposity can be used to accurately estimate whole body percent fat in adolescent girls. PMID:25147482

  1. Quantitative computed tomography of lung parenchyma in patients with emphysema: analysis of higher-density lung regions

    NASA Astrophysics Data System (ADS)

    Lederman, Dror; Leader, Joseph K.; Zheng, Bin; Sciurba, Frank C.; Tan, Jun; Gur, David

    2011-03-01

    Quantitative computed tomography (CT) has been widely used to detect and evaluate the presence (or absence) of emphysema applying the density masks at specific thresholds, e.g., -910 or -950 Hounsfield Unit (HU). However, it has also been observed that subjects with similar density-mask based emphysema scores could have varying lung function, possibly indicating differences of disease severity. To assess this possible discrepancy, we investigated whether density distribution of "viable" lung parenchyma regions with pixel values > -910 HU correlates with lung function. A dataset of 38 subjects, who underwent both pulmonary function testing and CT examinations in a COPD SCCOR study, was assembled. After the lung regions depicted on CT images were automatically segmented by a computerized scheme, we systematically divided the lung parenchyma into different density groups (bins) and computed a number of statistical features (i.e., mean, standard deviation (STD), skewness of the pixel value distributions) in these density bins. We then analyzed the correlations between each feature and lung function. The correlation between diffusion lung capacity (DLCO) and STD of pixel values in the bin of -910HU <= PV < -750HU was -0.43, as compared with a correlation of -0.49 obtained between the post-bronchodilator ratio (FEV1/FVC) measured by the forced expiratory volume in 1 second (FEV1) dividing the forced vital capacity (FVC) and the STD of pixel values in the bin of -1024HU <= PV < -910HU. The results showed an association between the distribution of pixel values in "viable" lung parenchyma and lung function, which indicates that similar to the conventional density mask method, the pixel value distribution features in "viable" lung parenchyma areas may also provide clinically useful information to improve assessments of lung disease severity as measured by lung functional tests.

  2. In vivo discrimination of hip fracture with quantitative computed tomography: results from the prospective European Femur Fracture Study (EFFECT).

    PubMed

    Bousson, Valérie Danielle; Adams, Judith; Engelke, Klaus; Aout, Mounir; Cohen-Solal, Martine; Bergot, Catherine; Haguenauer, Didier; Goldberg, Daniele; Champion, Karine; Aksouh, Redha; Vicaut, Eric; Laredo, Jean-Denis

    2011-04-01

    In assessing osteoporotic fractures of the proximal femur, the main objective of this in vivo case-control study was to evaluate the performance of quantitative computed tomography (QCT) and a dedicated 3D image analysis tool [Medical Image Analysis Framework--Femur option (MIAF-Femur)] in differentiating hip fracture and non-hip fracture subjects. One-hundred and seven women were recruited in the study, 47 women (mean age 81.6 years) with low-energy hip fractures and 60 female non-hip fracture control subjects (mean age 73.4 years). Bone mineral density (BMD) and geometric variables of cortical and trabecular bone in the femoral head and neck, trochanteric, and intertrochanteric regions and proximal shaft were assessed using QCT and MIAF-Femur. Areal BMD (aBMD) was assessed using dual-energy X-ray absorptiometry (DXA) in 96 (37 hip fracture and 59 non-hip fracture subjects) of the 107 patients. Logistic regressions were computed to extract the best discriminates of hip fracture, and area under the receiver characteristic operating curve (AUC) was calculated. Three logistic models that discriminated the occurrence of hip fracture with QCT variables were obtained (AUC = 0.84). All three models combined one densitometric variable--a trabecular BMD (measured in the femoral head or in the trochanteric region)--and one geometric variable--a cortical thickness value (measured in the femoral neck or proximal shaft). The best discriminant using DXA variables was obtained with total femur aBMD (AUC = 0.80, p = .003). Results highlight a synergistic contribution of trabecular and cortical components in hip fracture risk and the utility of assessing QCT BMD of the femoral head for improved understanding and possible insights into prevention of hip fractures.

  3. Comparison of frequency domain optical coherence tomography and quantitative coronary angiography for the assessment of coronary lesions

    NASA Astrophysics Data System (ADS)

    Zafar, Haroon; Sharif, Faisal; Leahy, Martin J.

    2014-03-01

    Quantitative coronary angiography (QCA) has been used as a standard technique for the evaluation of coronary artery disease for many years. Intracoronary optical coherence tomography (OCT) offers higher resolution, faster image acquisition speeds and greater sensitivity than the intravascular ultrasound (IVUS). Recently developed frequency domain OCT (FD-OCT) systems overcome many technical limitations of conventional time domain OCT systems (TDOCT). The main objective of this study was to compare the FD-OCT and QCA measurements for the assessment of coronary lesions. A total of 21 stenoses in 18 patients were analysed using QCA and FD-OCT. The average minimum lumen diameter (MLD) and percent lumen area stenosis (%AS) by QCA were 1.52+/-0.44 mm and 68+/-9% respectively. The average MLD and %AS by FD-OCT were 1.32+/-0.38 mm and 63+/-14% respectively. There was a moderate but significant correlation between QCA and FD-OCT measured MLD (r = 0.5, p < 0.01) and %AS (r = 0.56, p < 0.01). Bland-Altman analysis showed that the mean differences between the QCA and FD-OCT measurements were 0.18+/-0.81 (limits of agreement: -0.63 to 0.99) for MLD and 4.4+/-22.8 (limits of agreement: -18.4 to 27.2) for %AS. The root mean square error (RMSE) between the QCA and FD-OCT measured MLD and %AS was +/-0.44 mm and +/-12.1% respectively.

  4. Predicting ex vivo failure loads in human metatarsals using bone strength indices derived from volumetric quantitative computed tomography.

    PubMed

    Gutekunst, David J; Patel, Tarpit K; Smith, Kirk E; Commean, Paul K; Silva, Matthew J; Sinacore, David R

    2013-02-22

    We investigated the capacity of bone quantity and bone geometric strength indices to predict ultimate force in the human second metatarsal (Met2) and third metatarsal (Met3). Intact lower extremity cadaver samples were measured using clinical, volumetric quantitative computed tomography (vQCT) with positioning and parameters applicable to in vivo scanning. During processing, raw voxel data (0.4mm isotropic voxels) were converted from Hounsfield units to apparent bone mineral density (BMD) using hydroxyapatite calibration phantoms to allow direct volumetric assessment of whole-bone and subregional metatarsal BMD. Voxel data were realigned to produce cross-sectional slices perpendicular to the longitudinal axes of the metatarsals. Average mid-diaphyseal BMD, bone thickness, and buckling ratio were measured using an optimized threshold to distinguish bone from non-bone material. Minimum and maximum moments of inertia and section moduli were measured in the mid-diaphysis region using both a binary threshold for areal, unit-density measures and a novel technique for density-weighted measures. BMD and geometric strength indices were strongly correlated to ultimate force measured by ex vivo 3-point bending. Geometric indices were more highly correlated to ultimate force than was BMD; bone thickness and density-weighted minimum section modulus had the highest individual correlations to ultimate force. Density-weighted geometric indices explained more variance than their binary analogs. Multiple regression analyses defined models that predicted 85-89% of variance in ultimate force in Met2 and Met3 using bone thickness and minimum section modulus in the mid-diaphysis. These results have implications for future in vivo imaging to non-invasively assess bone strength and metatarsal fracture risk.

  5. Quantitative determination of the mineral distribution in different collagen zones of calcifying tendon using high voltage electron microscopic tomography

    NASA Technical Reports Server (NTRS)

    McEwen, B. F.; Song, M. J.; Landis, W. J.

    1991-01-01

    High voltage electron microscopic tomography was used to make the first quantitative determination of the distribution of mineral between different regions of collagen fibrils undergoing early calcification in normal leg tendons of the domestic turkey, Meleagris gallopavo. The tomographic 3-D reconstruction was computed from a tilt series of 61 different views spanning an angular range of +/- 60 degrees in 2 degrees intervals. Successive applications of an interactive computer operation were used to mask the collagen banding pattern of either hole or overlap zones into separate versions of the reconstruction. In such 3-D volumes, regions specified by the mask retained their original image density while the remaining volume was set to background levels. This approach was also applied to the mineral crystals present in the same volumes to yield versions of the 3-D reconstructions that were masked for both the crystal mass and the respective collagen zones. Density profiles from these volumes contained a distinct peak corresponding only to the crystal mass. A comparison of the integrated density of this peak from each profile established that 64% of the crystals observed were located in the collagen hole zones and 36% were found in the overlap zones. If no changes in crystal stability occur once crystals are formed, this result suggests the possibilities that nucleation of mineral is preferentially and initially associated with the hole zones, nucleation occurs more frequently in the hole zones, the rate of crystal growth is more rapid in the hole zones, or a combination of these alternatives. All lead to the conclusion that the overall accumulation of mineral mass is predominant in the collagen hole zones compared to overlap zones during early collagen fibril calcification.

  6. Optical distortion correction in optical coherence tomography for quantitative ocular anterior segment by three-dimensional imaging.

    PubMed

    Ortiz, Sergio; Siedlecki, Damian; Grulkowski, Ireneusz; Remon, Laura; Pascual, Daniel; Wojtkowski, Maciej; Marcos, Susana

    2010-02-01

    A method for three-dimensional 3-D optical distortion (refraction) correction on anterior segment Optical Coherence Tomography (OCT) images has been developed. The method consists of 3-D ray tracing through the different surfaces, following denoising, segmentation of the surfaces, Delaunay representation of the surfaces, and application of fan distortion correction. The correction has been applied theoretically to realistic computer eye models, and experimentally to OCT images of: an artificial eye with a Polymethyl Methacrylate (PMMA) cornea and an intraocular lens (IOL), an enucleated porcine eye, and a human eye in vivo obtained from two OCT laboratory set-ups (time domain and spectral). Data are analyzed in terms of surface radii of curvature and asphericity. Comparisons are established between the reference values for the surfaces (nominal values in the computer model; non-contact profilometric measurements for the artificial eye; Scheimpflug imaging for the real eyes in vivo and vitro). The results from the OCT data were analyzed following the conventional approach of dividing the optical path by the refractive index, after application of 2-D optical correction, and 3-D optical correction (in all cases after fan distortion correction). The application of 3-D optical distortion correction increased significantly both the accuracy of the radius of curvature estimates and particularly asphericity of the surfaces, with respect to conventional methods of OCT image analysis. We found that the discrepancies of the radii of curvature estimates from 3-D optical distortion corrected OCT images are less than 1% with respect to nominal values. Optical distortion correction in 3-D is critical for quantitative analysis of OCT anterior segment imaging, and allows accurate topography of the internal surfaces of the eye. PMID:20174107

  7. Qualitative and Quantitative Assessment of Adenosine Triphosphate Stress Whole-Heart Dynamic Myocardial Perfusion Imaging Using 256-Slice Computed Tomography

    PubMed Central

    Kurata, Akira; Kawaguchi, Naoto; Kido, Teruhito; Inoue, Katsuji; Suzuki, Jun; Ogimoto, Akiyoshi; Funada, Jun-ichi; Higaki, Jitsuo; Miyagawa, Masao; Vembar, Mani; Mochizuki, Teruhito

    2013-01-01

    Background The aim of this study was to investigate the correlation of the qualitative transmural extent of hypoperfusion areas (HPA) using stress dynamic whole-heart computed tomography perfusion (CTP) imaging by 256-slice CT with CTP-derived myocardial blood flow (MBF) for the estimation of the severity of coronary artery stenosis. Methods and Results Eleven patients underwent adenosine triphosphate (0.16 mg/kg/min, 5 min) stress dynamic CTP by 256-slice CT (coverage: 8 cm, 0.27 s/rotation), and 9 of the 11 patients underwent coronary angiography (CAG). Stress dynamic CTP (whole–heart datasets over 30 consecutive heart beats in systole without spatial and temporal gaps) was acquired with prospective ECG gating (effective radiation dose: 10.4 mSv). The extent of HPAs was visually graded using a 3-point score (normal, subendocardial, transmural). MBF (ml/100g/min) was measured by deconvolution. Differences in MBF (mean ± standard error) according to HPA and CAG results were evaluated. In 27 regions (3 major coronary territories in 9 patients), 11 coronary stenoses (> 50% reduction in diameter) were observed. In 353 myocardial segments, HPA was significantly related to MBF (P < 0.05; normal 295 ± 94; subendocardial 186 ± 67; and transmural 80 ± 53). Coronary territory analysis revealed a significant relationship between coronary stenosis severity and MBF (P < 0.05; non-significant stenosis [< 50%], 284 ± 97; moderate stenosis [50–70%], 184 ± 74; and severe stenosis [> 70%], 119 ± 69). Conclusion The qualitative transmural extent of HPA using stress whole-heart dynamic CTP imaging by 256-slice CT exhibits a good correlation with quantitative CTP-derived MBF and may aid in assessing the hemodynamic significance of coronary artery disease. PMID:24376774

  8. Population-Stratified Analysis of Bone Mineral Density Distribution in Cervical and Lumbar Vertebrae of Chinese from Quantitative Computed Tomography

    PubMed Central

    Zhang, Yong; Zhou, Zhuang; Wu, Cheng'ai; Zhao, Danhui; Wang, Chao; Cai, Wei; Wang, Ling; Duanmu, Yangyang; Zhang, Chenxin; Tian, Wei

    2016-01-01

    Objective To investigate the bone mineral density (BMD) of cervical vertebrae in a population-stratified manner and correlate with that of the lumbar vertebrae. Materials and Methods Five hundred and ninety-eight healthy volunteers (254 males, 344 females), ranging from 20 to 64 years of age, were recruited for volumetric BMD (vBMD) measurements by quantitative computed tomography. Basic information (age, height, weight, waistline, and hipline), and vBMD of the cervical and lumbar vertebrae (C2–7 and L2–4) were recorded. Comparisons among sex, age groups and different levels of vertebrae were analyzed using analysis of variance. Linear regression was performed for relevance of different vertebral levels. Results The vBMD of cervical and lumbar vertebrae was higher in females than males in each age group. The vBMD of the cervical and lumbar vertebrae in males and the vBMD of lumbar vertebrae in females decreased with aging. In each age group, the vBMD of the cervical vertebrae was higher than that of the lumbar vertebrae with gradual decreases from C2 to C7 except for C3; moreover, the vBMD of C6 and C7 was significantly different from that of C2–5. Correlations of vBMD among different cervical vertebrae (females: r = 0.62–0.94; males: r = 0.63–0.94) and lumbar vertebrae (males: r = 0.93–0.98; females: r = 0.82–0.97) were statistically significant at each age group. Conclusion The present study provided normative data of cervical vertebrae in an age- and sex-stratified manner. Sex differences in vBMD prominently vary with age, which can be helpful to design a more comprehensive pre-operative surgical plan. PMID:27587947

  9. Optical distortion correction in optical coherence tomography for quantitative ocular anterior segment by three-dimensional imaging.

    PubMed

    Ortiz, Sergio; Siedlecki, Damian; Grulkowski, Ireneusz; Remon, Laura; Pascual, Daniel; Wojtkowski, Maciej; Marcos, Susana

    2010-02-01

    A method for three-dimensional 3-D optical distortion (refraction) correction on anterior segment Optical Coherence Tomography (OCT) images has been developed. The method consists of 3-D ray tracing through the different surfaces, following denoising, segmentation of the surfaces, Delaunay representation of the surfaces, and application of fan distortion correction. The correction has been applied theoretically to realistic computer eye models, and experimentally to OCT images of: an artificial eye with a Polymethyl Methacrylate (PMMA) cornea and an intraocular lens (IOL), an enucleated porcine eye, and a human eye in vivo obtained from two OCT laboratory set-ups (time domain and spectral). Data are analyzed in terms of surface radii of curvature and asphericity. Comparisons are established between the reference values for the surfaces (nominal values in the computer model; non-contact profilometric measurements for the artificial eye; Scheimpflug imaging for the real eyes in vivo and vitro). The results from the OCT data were analyzed following the conventional approach of dividing the optical path by the refractive index, after application of 2-D optical correction, and 3-D optical correction (in all cases after fan distortion correction). The application of 3-D optical distortion correction increased significantly both the accuracy of the radius of curvature estimates and particularly asphericity of the surfaces, with respect to conventional methods of OCT image analysis. We found that the discrepancies of the radii of curvature estimates from 3-D optical distortion corrected OCT images are less than 1% with respect to nominal values. Optical distortion correction in 3-D is critical for quantitative analysis of OCT anterior segment imaging, and allows accurate topography of the internal surfaces of the eye.

  10. Quantitative measurement of phase variation amplitude of ultrasonic diffraction grating based on diffraction spectral analysis

    SciTech Connect

    Pan, Meiyan Zeng, Yingzhi; Huang, Zuohua

    2014-09-15

    A new method based on diffraction spectral analysis is proposed for the quantitative measurement of the phase variation amplitude of an ultrasonic diffraction grating. For a traveling wave, the phase variation amplitude of the grating depends on the intensity of the zeroth- and first-order diffraction waves. By contrast, for a standing wave, this amplitude depends on the intensity of the zeroth-, first-, and second-order diffraction waves. The proposed method is verified experimentally. The measured phase variation amplitude ranges from 0 to 2π, with a relative error of approximately 5%. A nearly linear relation exists between the phase variation amplitude and driving voltage. Our proposed method can also be applied to ordinary sinusoidal phase grating.

  11. Quantitation of the reconstruction quality of a four-dimensional computed tomography process for lung cancer patients

    SciTech Connect

    Lu Wei; Parikh, Parag J.; El Naqa, Issam M.; Nystrom, Michelle M.; Hubenschmidt, James P.; Wahab, Sasha H.; Mutic, Sasa; Singh, Anurag K.; Christensen, Gary E.; Bradley, Jeffrey D.; Low, Daniel A.

    2005-04-01

    We have developed a four-dimensional computed tomography (4D CT) technique for mapping breathing motion in radiotherapy treatment planning. A multislice CT scanner (1.5 mm slices) operated in cine mode was used to acquire 12 contiguous slices in each couch position for 15 consecutive scans (0.5 s rotation, 0.25 s between scans) while the patient underwent simultaneous quantitative spirometry measurements to provide a sorting metric. The spirometry-sorted scans were used to reconstruct a 4D data set. A critical factor for 4D CT is quantifying the reconstructed data set quality which we measure by correlating the metric used relative to internal-object motion. For this study, the internal air content within the lung was used as a surrogate for internal motion measurements. Thresholding and image morphological operations were applied to delineate the air-containing tissues (lungs, trachea) from each CT slice. The Hounsfield values were converted to the internal air content (V). The relationship between the air content and spirometer-measured tidal volume ({nu}) was found to be quite linear throughout the lungs and was used to estimate the overall accuracy and precision of tidal volume-sorted 4D CT. Inspection of the CT-scan air content as a function of tidal volume showed excellent correlations (typically r>0.99) throughout the lung volume. Because of the discovered linear relationship, the ratio of internal air content to tidal volume was indicative of the fraction of air change in each couch position. Theoretically, due to air density differences within the lung and in room, the sum of these ratios would equal 1.11. For 12 patients, the mean value was 1.08{+-}0.06, indicating the high quality of spirometry-based image sorting. The residual of a first-order fit between {nu} and V was used to estimate the process precision. For all patients, the precision was better than 8%, with a mean value of 5.1%{+-}1.9%. This quantitative analysis highlights the value of using

  12. High-resolution quantitative whole-breast ultrasound: in vivo application using frequency-domain waveform tomography

    NASA Astrophysics Data System (ADS)

    Sandhu, Gursharan Y. S.; Li, Cuiping; Roy, Olivier; Schmidt, Steven; Duric, Neb

    2015-03-01

    Ultrasound tomography is a promising modality for breast imaging. Many current ultrasound tomography imaging algorithms are based on ray theory and assume a homogeneous background which is inaccurate for complex heterogeneous regions. They fail when the size of lesions approaches the wavelength of ultrasound used. Therefore, to accurately image small lesions, wave theory must be used in ultrasound imaging algorithms to properly handle the heterogeneous nature of breast tissue and the diffraction effects that it induces. Using frequency-domain ultrasound waveform tomography, we present sound speed reconstructions of both a tissue-mimicking breast phantom and in vivo data sets. Significant improvements in contrast and resolution are made upon the previous ray based methods. Where it might have been difficult to differentiate a high sound speed tumor from bulk breast parenchyma using ray based methods, waveform tomography improves the shape and margins of a tumor to help more accurately differentiate it from the bulk breast tissue. Waveform tomography sound speed imaging might improve the ability of finding lesions in very dense tissues, a difficult environment for mammography. By comparing the sound speed images produced by waveform tomography to MRI, we see that the complex structures in waveform tomography are consistent with those in MRI. The robustness of the method is established by reconstructing data acquired by two different ultrasound tomography prototypes.

  13. Subduction zones beneath Indonesia imaged by Rayleigh wave phase velocity tomography

    NASA Astrophysics Data System (ADS)

    Liu, F.; Yang, T.; Harmon, N.

    2013-12-01

    Situated at the junction of several tectonic plates including Indian-Australia, Eurasia, and Philippine Sea, the Indonesian archipelago is one of the most tectonically complex regions on earth with subductions, collisions and accretions occurring along and within its boundaries. A high-resolution lithospheric and upper mantle model, therefore, is needed to understand these complex processes beneath this region. We present a phase velocity model derived from teleseismic Rayleigh waves recorded at seismic stations in this region. We use the modified version of the two-plane wave tomography, in which the non-planar effects of surface wave propagation such as multipathing and scattering are accounted for by two plane wave interference and using of finite frequency kernels. We measure the amplitudes and phases at 16 individual periods ranging from 20s to 150s for the fundamental mode of Rayleigh waves at over 30 stations. 254 earthquakes are selected from global events greater than Ms 5.5 in the distance range of 25°- 150°. To account for the wavefield inconsistencies among stations for each earthquake due to the large scale of our study region, we divide the seismic array into 4 groups of stations in the two-plane wave parameter inversion. The phase velocity maps from our preliminary results show coherent features between adjacent periods. The most dominant structure in phase velocity maps for all periods is the strong fast-velocity belts beneath Sunda Trench, Java Trench, Timor Trough and the trenches around Celebes Sea, which shift gradually toward the subduction directions. The strength of the high velocity anomaly varies among trenches, likely suggesting the different age of subducting slabs. In addition, a velocity contrast in the middle of Borneo appears to mark the Lupar Line, a boundary between the stable Sundaland continental core and fragments of ophiolitic and Asian continental material accreted to Borneo during the Cretaceous. The 3-D shear wave structure

  14. Dual-modality wide-field photothermal quantitative phase microscopy and depletion of cell populations

    NASA Astrophysics Data System (ADS)

    Turko, Nir A.; Barnea, Itay; Blum, Omry; Korenstein, Rafi; Shaked, Natan T.

    2015-03-01

    We review our dual-modality technique for quantitative imaging and selective depletion of populations of cells based on wide-field photothermal (PT) quantitative phase imaging and simultaneous PT cell extermination. The cells are first labeled by plasmonic gold nanoparticles, which evoke local plasmonic resonance when illuminated by light in a wavelength corresponding to their specific plasmonic resonance peak. This reaction creates changes of temperature, resulting in changes of phase. This phase changes are recorded by a quantitative phase microscope (QPM), producing specific imaging contrast, and enabling bio-labeling in phase microscopy. Using this technique, we have shown discrimination of EGFR over-expressing (EGFR+) cancer cells from EGFR under-expressing (EGFR-) cancer cells. Then, we have increased the excitation power in order to evoke greater temperatures, which caused specific cell death, all under real-time phase acquisition using QPM. Close to 100% of all EGFR+ cells were immediately exterminated when illuminated with the strong excitation beam, while all EGFR- cells survived. For the second experiment, in order to simulate a condition where circulating tumor cells (CTCs) are present in blood, we have mixed the EGFR+ cancer cells with white blood cells (WBCs) from a healthy donor. Here too, we have used QPM to observe and record the phase of the cells as they were excited for selective visualization and then exterminated. The WBCs survival rate was over 95%, while the EGFR+ survival rate was under 5%. The technique may be the basis for real-time detection and controlled treatment of CTCs.

  15. Total internal reflection holographic microscopy (TIRHM) for quantitative phase characterization of cell-substrate adhesion

    NASA Astrophysics Data System (ADS)

    Ash, William Mason, III

    Total Internal Reflection Holographic Microscopy (TIRHM) combines near-field microscopy with digital holography to produce a new form of near-field phase microscopy. Using a prism in TIR as a near-field imager, the presence of microscopic organisms, cell-substrate interfaces, and adhesions, causes relative refractive index (RRI) and frustrated TIR (f-TIR) to modulate the object beam's evanescent wave phase front. Quantitative phase images of test specimens such as Amoeba proteus, Dictyostelium Discoideum and cells such as SKOV-3 ovarian cancer and 3T3 fibroblasts are produced without the need to introduce stains or fluorophores. The angular spectrum method of digital holography to compensate for tilt anamorphism due to the inclined TIR plane is also discussed. The results of this work conclusively demonstrate, for the first time, the integration of near-field microscopy with digital holography. The cellular images presented show a correlation between the physical extent of the Amoeba proteus plasma membrane and the adhesions that are quantitatively profiled by phase cross-sectioning of the holographic images obtained by digital holography. With its ability to quantitatively characterise cellular adhesion and motility, it is anticipated that TIRHM can be a tool for characterizing and combating cancer metastasis, as well as improving our understanding of morphogenesis and embryogenesis itself.

  16. Atomic-scale phase composition through multivariate statistical analysis of atom probe tomography data.

    PubMed

    Keenan, Michael R; Smentkowski, Vincent S; Ulfig, Robert M; Oltman, Edward; Larson, David J; Kelly, Thomas F

    2011-06-01

    We demonstrate for the first time that multivariate statistical analysis techniques can be applied to atom probe tomography data to estimate the chemical composition of a sample at the full spatial resolution of the atom probe in three dimensions. Whereas the raw atom probe data provide the specific identity of an atom at a precise location, the multivariate results can be interpreted in terms of the probabilities that an atom representing a particular chemical phase is situated there. When aggregated to the size scale of a single atom (∼0.2 nm), atom probe spectral-image datasets are huge and extremely sparse. In fact, the average spectrum will have somewhat less than one total count per spectrum due to imperfect detection efficiency. These conditions, under which the variance in the data is completely dominated by counting noise, test the limits of multivariate analysis, and an extensive discussion of how to extract the chemical information is presented. Efficient numerical approaches to performing principal component analysis (PCA) on these datasets, which may number hundreds of millions of individual spectra, are put forward, and it is shown that PCA can be computed in a few seconds on a typical laptop computer.

  17. Shear wave pulse compression for dynamic elastography using phase-sensitive optical coherence tomography

    PubMed Central

    Nguyen, Thu-Mai; Song, Shaozhen; Arnal, Bastien; Wong, Emily Y.; Huang, Zhihong; Wang, Ruikang K.; O’Donnell, Matthew

    2014-01-01

    Abstract. Assessing the biomechanical properties of soft tissue provides clinically valuable information to supplement conventional structural imaging. In the previous studies, we introduced a dynamic elastography technique based on phase-sensitive optical coherence tomography (PhS-OCT) to characterize submillimetric structures such as skin layers or ocular tissues. Here, we propose to implement a pulse compression technique for shear wave elastography. We performed shear wave pulse compression in tissue-mimicking phantoms. Using a mechanical actuator to generate broadband frequency-modulated vibrations (1 to 5 kHz), induced displacements were detected at an equivalent frame rate of 47 kHz using a PhS-OCT. The recorded signal was digitally compressed to a broadband pulse. Stiffness maps were then reconstructed from spatially localized estimates of the local shear wave speed. We demonstrate that a simple pulse compression scheme can increase shear wave detection signal-to-noise ratio (>12  dB gain) and reduce artifacts in reconstructing stiffness maps of heterogeneous media. PMID:24441876

  18. Interior tomography in x-ray differential phase contrast CT imaging.

    PubMed

    Lauzier, Pascal Thériault; Qi, Zhihua; Zambelli, Joseph; Bevins, Nicholas; Chen, Guang-Hong

    2012-05-01

    Differential phase contrast computed tomography (DPC-CT) is an x-ray imaging method that uses the wave properties of imaging photons as the contrast mechanism. It has been demonstrated that DPC images can be obtained using a conventional x-ray tube and a Talbot-Lau-type interferometer. Due to the limited size of the gratings, current data acquisition systems only offer a limited field of view, and thus are prone to data truncation. As a result, the reconstructed DPC-CT image may suffer from image artifacts and increased inaccuracy in the reconstructed image values. In this paper, we demonstrate that a small region of interest (ROI) within a large object can be accurately and stably reconstructed using fully truncated projection datasets provided that a priori information on electron density is known for a small region inside the ROI. The method reconstructs an image iteratively to satisfy a group of physical conditions by using a projection onto convex set (POCS) approach. In this work, this POCS algorithm is validated using both numerical simulations and physical phantom experimental data. In both cases, the root mean square error is reduced by an order of magnitude with respect to the truncated analytic reconstructions. Truncation artifacts observed in the latter reconstructions are eliminated using the POCS algorithm.

  19. Interior tomography in x-ray differential phase contrast CT imaging

    NASA Astrophysics Data System (ADS)

    Thériault Lauzier, Pascal; Qi, Zhihua; Zambelli, Joseph; Bevins, Nicholas; Chen, Guang-Hong

    2012-05-01

    Differential phase contrast computed tomography (DPC-CT) is an x-ray imaging method that uses the wave properties of imaging photons as the contrast mechanism. It has been demonstrated that DPC images can be obtained using a conventional x-ray tube and a Talbot-Lau-type interferometer. Due to the limited size of the gratings, current data acquisition systems only offer a limited field of view, and thus are prone to data truncation. As a result, the reconstructed DPC-CT image may suffer from image artifacts and increased inaccuracy in the reconstructed image values. In this paper, we demonstrate that a small region of interest (ROI) within a large object can be accurately and stably reconstructed using fully truncated projection datasets provided that a priori information on electron density is known for a small region inside the ROI. The method reconstructs an image iteratively to satisfy a group of physical conditions by using a projection onto convex set (POCS) approach. In this work, this POCS algorithm is validated using both numerical simulations and physical phantom experimental data. In both cases, the root mean square error is reduced by an order of magnitude with respect to the truncated analytic reconstructions. Truncation artifacts observed in the latter reconstructions are eliminated using the POCS algorithm.

  20. Virtual unrolling and deciphering of Herculaneum papyri by X-ray phase-contrast tomography

    PubMed Central

    Bukreeva, I.; Mittone, A.; Bravin, A.; Festa, G.; Alessandrelli, M.; Coan, P.; Formoso, V.; Agostino, R. G.; Giocondo, M.; Ciuchi, F.; Fratini, M.; Massimi, L.; Lamarra, A.; Andreani, C.; Bartolino, R.; Gigli, G.; Ranocchia, G.; Cedola, A.

    2016-01-01

    A collection of more than 1800 carbonized papyri, discovered in the Roman ‘Villa dei Papiri’ at Herculaneum is the unique classical library survived from antiquity. These papyri were charred during 79 A.D. Vesuvius eruption, a circumstance which providentially preserved them until now. This magnificent collection contains an impressive amount of treatises by Greek philosophers and, especially, Philodemus of Gadara, an Epicurean thinker of 1st century BC. We read many portions of text hidden inside carbonized Herculaneum papyri using enhanced X-ray phase-contrast tomography non-destructive technique and a new set of numerical algorithms for ‘virtual-unrolling’. Our success lies in revealing the largest portion of Greek text ever detected so far inside unopened scrolls, with unprecedented spatial resolution and contrast, all without damaging these precious historical manuscripts. Parts of text have been decoded and the ‘voice’ of the Epicurean philosopher Philodemus is brought back again after 2000 years from Herculaneum papyri. PMID:27265417

  1. Joint reconstruction of absorption and refractive properties in propagation-based x-ray phase-contrast tomography via a non-linear image reconstruction algorithm

    NASA Astrophysics Data System (ADS)

    Chen, Yujia; Wang, Kun; Gursoy, Doga; Soriano, Carmen; De Carlo, Francesco; Anastasio, Mark A.

    2016-03-01

    Propagation-based X-ray phase-contrast tomography (XPCT) provides the opportunity to image weakly absorbing objects and is being explored actively for a variety of important pre-clinical applications. Quantitative XPCT image reconstruction methods typically involve a phase retrieval step followed by application of an image reconstruction algorithm. Most approaches to phase retrieval require either acquiring multiple images at different object-to-detector distances or introducing simplifying assumptions, such as a single-material assumption, to linearize the imaging model. In order to overcome these limitations, a non-linear image reconstruction method has been proposed previously that jointly estimates the absorption and refractive properties of an object from XPCT projection data acquired at a single propagation distance, without the need to linearize the imaging model. However, the numerical properties of the associated non-convex optimization problem remain largely unexplored. In this study, computer simulations are conducted to investigate the feasibility of the joint reconstruction problem in practice. We demonstrate that the joint reconstruction problem is ill-posed and sensitive to system inconsistencies. Particularly, the method can generate accurate refractive index images only if the object is thin and has no phase-wrapping in the data. However, we also observed that, for weakly absorbing objects, the refractive index images reconstructed by the joint reconstruction method are, in general, more accurate than those reconstructed using methods that simply ignore the object's absorption.

  2. Partially Coherent Quantitative Phase Retrieval with Applications to Extreme Ultraviolet Lithography

    NASA Astrophysics Data System (ADS)

    Claus, Rene Andre

    This dissertation presents a new quantitative phase retrieval algorithm that fully models partially coherent imaging in microscopes. Unlike existing algorithms, our algorithm fully considers the pupil function and illumination by using the Weak Object Transfer Function (WOTF). Using an iterative approach, we extend the applicability of the WOTF beyond weakly scattering objects. This allows almost any measurement to be used during phase retrieval. As an example of how this feature can be used to invent practical new measurement schemes, we present the illumination switched pupil. This measurement uses a phase contrast objective and varied illumination to maximize the sensitivity of the microscope to both the phase and amplitude of the sample. Using only two images, the complex field can be recovered with high sensitivity at almost all spatial frequencies. A complete model of imaging in the microscope enables self-calibration of the measurements and improved phase retrieval. Since all important characteristics of the microscope can be incorporated, an optimization over critical parameters, such as the best focus position and image alignment, can be performed after the images have been captured. This allows errors in the calibration to be corrected after the measurements have been performed, improving the accuracy of the recovered field while simplifying the experiments. To verify and apply the algorithm experimentally, we have performed phase retrieval measurements of Extreme Ultraviolet (EUV) photomasks on the zone plate microscope, SHARP, at Lawrence Berkeley National Laboratory (LBNL). Phase retrieval has enabled the quantitative analysis of multilayer roughness and defects. Experiments, comparing the size of defects measured using phase retrieval to measurements performed by AFM, indicate that AFM consistently underestimates the effective height of the buried multilayer defects by 1 nm. Other measurements of defects, comparing the recovered field extracted from

  3. In vivo imaging of rat cortical bone porosity by synchrotron phase contrast micro computed tomography

    NASA Astrophysics Data System (ADS)

    Pratt, I. V.; Belev, G.; Zhu, N.; Chapman, L. D.; Cooper, D. M. L.

    2015-01-01

    Cortical bone is a dynamic tissue which undergoes adaptive and pathological changes throughout life. Direct longitudinal tracking of this remodeling process holds great promise for improving our understanding of bone development, maintenance and senescence. The application of in vivo micro-computed tomography (micro-CT) has enabled longitudinal tracking of trabecular bone microarchitecture with commercially available scanners generally operating in the 10-20 µm voxel range with absorbed doses reported between 0.5 and 1 Gy. Imaging of cortical bone microarchitecture (porosity) requires higher resolution and thus in vivo imaging of these structures has not been achieved due to excessive radiation dose. In this study we tested the hypothesis that synchrotron propagation phase contrast micro-CT can enable in vivo imaging of cortical porosity in rats at doses comparable to those currently employed for trabecular bone imaging. Synchrotron imaging experiments were conducted at the Canadian Light Source using the bending magnet beamline of the BioMedical Imaging and Therapy (BMIT) facility. Protocol optimization (propagation distance, projection number) was conducted ex vivo on rat (Sprague-Dawley) forelimbs with dose determined by ion chamber and lithium fluoride crystal thermoluminescent dosimeters. Comparative ex vivo imaging was performed using laboratory in vivo scanning systems, identifying a range of doses between 1.2-3.6 Gy for common protocols. A final in vivo synchrotron protocol involving a 2.5 Gy dose was implemented with live rats. The resulting images demonstrated improved delineation of cortical porosity through the improved edge enhancement effect of phase contrast, opening the door to novel experimental studies involving the longitudinal tracking of remodeling.

  4. In vivo imaging of rat cortical bone porosity by synchrotron phase contrast micro computed tomography.

    PubMed

    Pratt, I V; Belev, G; Zhu, N; Chapman, L D; Cooper, D M L

    2015-01-01

    Cortical bone is a dynamic tissue which undergoes adaptive and pathological changes throughout life. Direct longitudinal tracking of this remodeling process holds great promise for improving our understanding of bone development, maintenance and senescence. The application of in vivo micro-computed tomography (micro-CT) has enabled longitudinal tracking of trabecular bone microarchitecture with commercially available scanners generally operating in the 10-20 µm voxel range with absorbed doses reported between 0.5 and 1 Gy. Imaging of cortical bone microarchitecture (porosity) requires higher resolution and thus in vivo imaging of these structures has not been achieved due to excessive radiation dose. In this study we tested the hypothesis that synchrotron propagation phase contrast micro-CT can enable in vivo imaging of cortical porosity in rats at doses comparable to those currently employed for trabecular bone imaging. Synchrotron imaging experiments were conducted at the Canadian Light Source using the bending magnet beamline of the BioMedical Imaging and Therapy (BMIT) facility. Protocol optimization (propagation distance, projection number) was conducted ex vivo on rat (Sprague-Dawley) forelimbs with dose determined by ion chamber and lithium fluoride crystal thermoluminescent dosimeters. Comparative ex vivo imaging was performed using laboratory in vivo scanning systems, identifying a range of doses between 1.2-3.6 Gy for common protocols. A final in vivo synchrotron protocol involving a 2.5 Gy dose was implemented with live rats. The resulting images demonstrated improved delineation of cortical porosity through the improved edge enhancement effect of phase contrast, opening the door to novel experimental studies involving the longitudinal tracking of remodeling. PMID:25489926

  5. Phase-Contrast Optical Coherence Tomography: A New Technique for Non-Invasive Angiography

    PubMed Central

    Schwartz, Daniel M.; Fingler, Jeff; Kim, Dae Yu; Zawadzki, Robert J.; Morse, Lawrence S.; Park, Susanna S.; Fraser, Scott E.; Werner, John S.

    2014-01-01

    Purpose Phase-contrast optical coherence tomography (PC-OCT) provides volumetric imaging of the retinal vasculature without the need for intravenous injection of a fluorophore. Here, we compare images from PC-OCT and fluorescein angiography (FA) for normal individuals and patients with age-related macular degeneration and diabetic retinopathy. Design This is an evaluation of a diagnostic technology. Participants 4 patients underwent comparative retinovascular imaging using FA and PC-OCT. Imaging was performed on 1 normal individual, 1 patient with dry age-related macular degeneration, 1 patient with exudative age-related macular degeneration and 1 patient with non-proliferative diabetic retinopathy. Methods FA imaging was performed using a Topcon (TRC-50IX) camera having resolution of 1280 (H) x 1024 (V) pixels. PC-OCT images were generated by software data processing of the entire cross-sectional image from consecutively acquired B-scans. Bulk axial motion was calculated and corrected for each transverse location, reducing the phase noise introduced from eye motion. Phase contrast was calculated through the variance of the motion-corrected phase changes acquired within multiple B-scans at the same position. Repeating these calculations over the entire volumetric scan produced a three-dimensional PC-OCT representation of the vasculature. Main Outcome Measures Feasibility of rendering retinal and choroidal microvasculature using PC-OCT was compared qualitatively to FA, the current gold standard for retinovascular imaging. Results PC-OCT rendered a two-dimensional depth color-coded vasculature map of the retinal and choroidal vasculature non-invasively. The choriocapillaris was imaged with better resolution of microvascular detail using PC-OCT. Areas of geographic atrophy and choroidal neovascularization imaged by FA were depicted by PC-OCT. Regions of capillary non-perfusion from diabetic retinopathy were shown by both imaging techniques; there was not complete

  6. Quantitative mapping of phase coexistence in Mott-Peierls insulator during electronic and thermally driven phase transition.

    PubMed

    Madan, Himanshu; Jerry, Matthew; Pogrebnyakov, Alexej; Mayer, Theresa; Datta, Suman

    2015-02-24

    Quantitative impedance mapping of the spatially inhomogeneous insulator-to-metal transition (IMT) in vanadium dioxide (VO2) is performed with a lateral resolution of 50 nm through near-field scanning microwave microscopy (SMM) at 16 GHz. SMM is used to measure spatially resolved electronic properties of the phase coexistence in an unstrained VO2 film during the electrically as well as thermally induced IMT. A quantitative impedance map of both the electrically driven filamentary conduction and the thermally induced bulk transition is established. This was modeled as a 2-D heterogeneous resistive network where the distribution function of the IMT temperature across the sample is captured. Applying the resistive network model for the electrically induced IMT case, we reproduce the filamentary nature of electronically induced IMT, which elucidates a cascading avalanche effect triggered by the local electric field across nanoscale insulating and metallic domains.

  7. Flipping interferometry and its application for quantitative phase microscopy in a micro-channel.

    PubMed

    Roitshtain, Darina; Turko, Nir A; Javidi, Bahram; Shaked, Natan T

    2016-05-15

    We present a portable, off-axis interferometric module for quantitative phase microscopy of live cells, positioned at the exit port of a coherently illuminated inverted microscope. The module creates on the digital camera an interference pattern between the image of the sample and its flipped version. The proposed simplified module is based on a retro-reflector modification in an external Michelson interferometer. The module does not contain any lenses, pinholes, or gratings and its alignment is straightforward. Still, it allows full control of the off-axis angle and does not suffer from ghost images. As experimentally demonstrated, the module is useful for quantitative phase microscopy of live cells rapidly flowing in a micro-channel. PMID:27177001

  8. New approaches for the analysis of confluent cell layers with quantitative phase digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Pohl, L.; Kaiser, M.; Ketelhut, S.; Pereira, S.; Goycoolea, F.; Kemper, Björn

    2016-03-01

    Digital holographic microscopy (DHM) enables high resolution non-destructive inspection of technical surfaces and minimally-invasive label-free live cell imaging. However, the analysis of confluent cell layers represents a challenge as quantitative DHM phase images in this case do not provide sufficient information for image segmentation, determination of the cellular dry mass or calculation of the cell thickness. We present novel strategies for the analysis of confluent cell layers with quantitative DHM phase contrast utilizing a histogram based-evaluation procedure. The applicability of our approach is illustrated by quantification of drug induced cell morphology changes and it is shown that the method is capable to quantify reliable global morphology changes of confluent cell layers.

  9. Quantitative x-ray phase imaging at the nanoscale by multilayer Laue lenses.

    PubMed

    Yan, Hanfei; Chu, Yong S; Maser, Jörg; Nazaretski, Evgeny; Kim, Jungdae; Kang, Hyon Chol; Lombardo, Jeffrey J; Chiu, Wilson K S

    2013-01-01

    For scanning x-ray microscopy, many attempts have been made to image the phase contrast based on a concept of the beam being deflected by a specimen, the so-called differential phase contrast imaging (DPC). Despite the successful demonstration in a number of representative cases at moderate spatial resolutions, these methods suffer from various limitations that preclude applications of DPC for ultra-high spatial resolution imaging, where the emerging wave field from the focusing optic tends to be significantly more complicated. In this work, we propose a highly robust and generic approach based on a Fourier-shift fitting process and demonstrate quantitative phase imaging of a solid oxide fuel cell (SOFC) anode by multilayer Laue lenses (MLLs). The high sensitivity of the phase to structural and compositional variations makes our technique extremely powerful in correlating the electrode performance with its buried nanoscale interfacial structures that may be invisible to the absorption and fluorescence contrasts.

  10. Nanoscale topography and spatial light modulator characterization using wide-field quantitative phase imaging.

    PubMed

    Rajshekhar, Gannavarpu; Bhaduri, Basanta; Edwards, Chris; Zhou, Renjie; Goddard, Lynford L; Popescu, Gabriel

    2014-02-10

    We demonstrate an optical technique for large field of view quantitative phase imaging of reflective samples. It relies on a common-path interferometric design, which ensures high stability without the need for active stabilization. The technique provides single-shot, full-field and robust measurement of nanoscale topography of large samples. Further, the inherent stability allows reliable measurement of the temporally varying phase retardation of the liquid crystal cells, and thus enables real-time characterization of spatial light modulators. The technique's application potential is validated through experimental results. PMID:24663633

  11. Quantitative phase imaging of living cells with a swept laser source

    NASA Astrophysics Data System (ADS)

    Chen, Shichao; Zhu, Yizheng

    2016-03-01

    Digital holographic phase microscopy is a well-established quantitative phase imaging technique. However, interference artifacts from inside the system, typically induced by elements whose optical thickness are within the source coherence length, limit the imaging quality as well as sensitivity. In this paper, a swept laser source based technique is presented. Spectra acquired at a number of wavelengths, after Fourier Transform, can be used to identify the sources of the interference artifacts. With proper tuning of the optical pathlength difference between sample and reference arms, it is possible to avoid these artifacts and achieve sensitivity below 0.3nm. Performance of the proposed technique is examined in live cell imaging.

  12. Lab on chip optical imaging of biological sample by quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Memmolo, P.; Miccio, L.; Merola, F.; Gennari, O.; Mugnano, M.; Netti, P. A.; Ferraro, P.

    2015-03-01

    Quantitative imaging and three dimensional (3D) morphometric analysis of flowing and not-adherent cells is an important aspect for diagnostic purposes at Lab on Chip scale. Diagnostics tools need to be quantitative, label-free and, as much as possible, accurate. In recent years digital holography (DH) has been improved to be considered as suitable diagnostic method in several research field. In this paper we demonstrate that DH can be used for retrieving 3D morphometric data for sorting and diagnosis aims. Several techniques exist for 3D morphological study as optical coherent tomography and confocal microscopy, but they are not the best choice in case of dynamic events as flowing samples. Recently, a DH approach, based on shape from silhouette algorithm (SFS), has been developed for 3D shape display and calculation of cells biovolume. Such approach, adopted in combination with holographic optical tweezers (HOT) was successfully applied to cells with convex shape. Unfortunately, it's limited to cells with convex surface as sperm cells or diatoms. Here, we demonstrate an improvement of such procedure. By decoupling thickness information from refractive index ones and combining this with SFS analysis, 3D shape of concave cells is obtained. Specifically, the topography contour map is computed and used to adjust the 3D shape retrieved by the SFS algorithm. We prove the new procedure for healthy red blood cells having a concave surface in their central region. Experimental results are compared with theoretical model.

  13. Noninvasive imaging of hemoglobin concentration and oxygen saturation for detection of osteoarthritis in the finger joints using multispectral three-dimensional quantitative photoacoustic tomography

    NASA Astrophysics Data System (ADS)

    Sun, Yao; Sobel, Eric; Jiang, Huabei

    2013-05-01

    We present quantitative imaging of hemoglobin concentration and oxygen saturation in in vivo finger joints and evaluate the feasibility of detecting osteoarthritis (OA) in the hand using three-dimensional (3D) multispectral quantitative photoacoustic tomography (3D qPAT). The results show that both the anatomical structures and quantitative chromophore concentrations (oxy-hemoglobin and deoxy-hemoglobin) of different joint tissues (hard phalanges and soft cartilage/synovial fluid between phalanges) can be imaged in vivo with the multispectral 3D qPAT. Enhanced hemoglobin concentrations and dropped oxygen saturations in osteoarthritic phalanges and soft joint tissues in joint cavities have been observed. This study indicates that the multispectral 3D qPAT is a promising approach to detect the angiogenesis and hypoxia associated with OA disease and a potential clinical tool for early OA detection in the finger joints.

  14. Real time quantitative phase microscopy based on single-shot transport of intensity equation (ssTIE) method

    NASA Astrophysics Data System (ADS)

    Yu, Wei; Tian, Xiaolin; He, Xiaoliang; Song, Xiaojun; Xue, Liang; Liu, Cheng; Wang, Shouyu

    2016-08-01

    Microscopy based on transport of intensity equation provides quantitative phase distributions which opens another perspective for cellular observations. However, it requires multi-focal image capturing while mechanical and electrical scanning limits its real time capacity in sample detections. Here, in order to break through this restriction, real time quantitative phase microscopy based on single-shot transport of the intensity equation method is proposed. A programmed phase mask is designed to realize simultaneous multi-focal image recording without any scanning; thus, phase distributions can be quantitatively retrieved in real time. It is believed the proposed method can be potentially applied in various biological and medical applications, especially for live cell imaging.

  15. High resolution quantitative phase imaging of live cells with constrained optimization approach

    NASA Astrophysics Data System (ADS)

    Pandiyan, Vimal Prabhu; Khare, Kedar; John, Renu

    2016-03-01

    Quantitative phase imaging (QPI) aims at studying weakly scattering and absorbing biological specimens with subwavelength accuracy without any external staining mechanisms. Use of a reference beam at an angle is one of the necessary criteria for recording of high resolution holograms in most of the interferometric methods used for quantitative phase imaging. The spatial separation of the dc and twin images is decided by the reference beam angle and Fourier-filtered reconstructed image will have a very poor resolution if hologram is recorded below a minimum reference angle condition. However, it is always inconvenient to have a large reference beam angle while performing high resolution microscopy of live cells and biological specimens with nanometric features. In this paper, we treat reconstruction of digital holographic microscopy images as a constrained optimization problem with smoothness constraint in order to recover only complex object field in hologram plane even with overlapping dc and twin image terms. We solve this optimization problem by gradient descent approach iteratively and the smoothness constraint is implemented by spatial averaging with appropriate size. This approach will give excellent high resolution image recovery compared to Fourier filtering while keeping a very small reference angle. We demonstrate this approach on digital holographic microscopy of live cells by recovering the quantitative phase of live cells from a hologram recorded with nearly zero reference angle.

  16. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells.

    PubMed

    Park, Han Sang; Rinehart, Matthew T; Walzer, Katelyn A; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  17. Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells

    PubMed Central

    Park, Han Sang; Rinehart, Matthew T.; Walzer, Katelyn A.; Chi, Jen-Tsan Ashley; Wax, Adam

    2016-01-01

    Malaria detection through microscopic examination of stained blood smears is a diagnostic challenge that heavily relies on the expertise of trained microscopists. This paper presents an automated analysis method for detection and staging of red blood cells infected by the malaria parasite Plasmodium falciparum at trophozoite or schizont stage. Unlike previous efforts in this area, this study uses quantitative phase images of unstained cells. Erythrocytes are automatically segmented using thresholds of optical phase and refocused to enable quantitative comparison of phase images. Refocused images are analyzed to extract 23 morphological descriptors based on the phase information. While all individual descriptors are highly statistically different between infected and uninfected cells, each descriptor does not enable separation of populations at a level satisfactory for clinical utility. To improve the diagnostic capacity, we applied various machine learning techniques, including linear discriminant classification (LDC), logistic regression (LR), and k-nearest neighbor classification (NNC), to formulate algorithms that combine all of the calculated physical parameters to distinguish cells more effectively. Results show that LDC provides the highest accuracy of up to 99.7% in detecting schizont stage infected cells compared to uninfected RBCs. NNC showed slightly better accuracy (99.5%) than either LDC (99.0%) or LR (99.1%) for discriminating late trophozoites from uninfected RBCs. However, for early trophozoites, LDC produced the best accuracy of 98%. Discrimination of infection stage was less accurate, producing high specificity (99.8%) but only 45.0%-66.8% sensitivity with early trophozoites most often mistaken for late trophozoite or schizont stage and late trophozoite and schizont stage most often confused for each other. Overall, this methodology points to a significant clinical potential of using quantitative phase imaging to detect and stage malaria infection

  18. Non-destructive characterisation of polymers and Al-alloys by polychromatic cone-beam phase contrast tomography

    SciTech Connect

    Kastner, Johann; Plank, Bernhard; Requena, Guillermo

    2012-02-15

    X-ray computed tomography (XCT) has become a very important tool for the non-destructive characterisation of materials. Continuous improvements in the quality and performance of X-ray tubes and detectors have led to cone-beam XCT systems that can now achieve spatial resolutions down to 1 {mu}m and even below. Since not only the amplitude but also the phase of an X-ray beam is altered while passing through an object, phase contrast effects can occur even for polychromatic sources when the spatial coherence due to a small focal spot size is high enough. This can lead to significant improvements over conventional attenuation-based X-ray computed tomography. Phase contrast can increase by edge enhancement the visibility of small structures and of features which are only slightly different in attenuation. We report on the possibilities of polychromatic cone-beam phase contrast tomography for non-destructive characterisation of materials. A carbon fibre-reinforced polymer and the Al-alloys AlMg5Si7 and AlSi18 were investigated with high resolution cone-beam X-ray computed tomography with a polychromatic tube source. Under certain conditions strong phase contrast resulting in an upward and downward overshooting of the grey values across edges was observed. The phase effects are much stronger for the polymer than for the Al-alloys. The influence on the phase contrast of the parameters, including source-detector distance, focal spot size and tube acceleration voltage is presented. Maximum phase contrast was observed for a maximum distance between the source and the detector, for a low voltage and a minimum focal spot size at the X-ray source. The detectability of the different phases is improved by the edge enhancement and the resulting improvement of sharpness. Thus, a better segmentation of the carbon fibres in the fibre-reinforced polymer and of the Mg{sub 2}Si-phase in the AlMg5Si7-alloy is achieved. Primary and eutectic Si cannot be detected by attenuation-based X

  19. Quantitative analysis of doped/undoped ZnO nanomaterials using laser assisted atom probe tomography: Influence of the analysis parameters

    SciTech Connect

    Amirifar, Nooshin; Lardé, Rodrigue Talbot, Etienne; Pareige, Philippe; Rigutti, Lorenzo; Mancini, Lorenzo; Houard, Jonathan; Castro, Celia; Sallet, Vincent; Zehani, Emir; Hassani, Said; Sartel, Corine; Ziani, Ahmed; Portier, Xavier

    2015-12-07

    In the last decade, atom probe tomography has become a powerful tool to investigate semiconductor and insulator nanomaterials in microelectronics, spintronics, and optoelectronics. In this paper, we report an investigation of zinc oxide nanostructures using atom probe tomography. We observed that the chemical composition of zinc oxide is strongly dependent on the analysis parameters used for atom probe experiments. It was observed that at high laser pulse energies, the electric field at the specimen surface is strongly dependent on the crystallographic directions. This dependence leads to an inhomogeneous field evaporation of the surface atoms, resulting in unreliable measurements. We show that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.

  20. Quantitative analysis of doped/undoped ZnO nanomaterials using laser assisted atom probe tomography: Influence of the analysis parameters

    NASA Astrophysics Data System (ADS)

    Amirifar, Nooshin; Lardé, Rodrigue; Talbot, Etienne; Pareige, Philippe; Rigutti, Lorenzo; Mancini, Lorenzo; Houard, Jonathan; Castro, Celia; Sallet, Vincent; Zehani, Emir; Hassani, Said; Sartel, Corine; Ziani, Ahmed; Portier, Xavier

    2015-12-01

    In the last decade, atom probe tomography has become a powerful tool to investigate semiconductor and insulator nanomaterials in microelectronics, spintronics, and optoelectronics. In this paper, we report an investigation of zinc oxide nanostructures using atom probe tomography. We observed that the chemical composition of zinc oxide is strongly dependent on the analysis parameters used for atom probe experiments. It was observed that at high laser pulse energies, the electric field at the specimen surface is strongly dependent on the crystallographic directions. This dependence leads to an inhomogeneous field evaporation of the surface atoms, resulting in unreliable measurements. We show that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.

  1. Quantitative X-ray projection microscopy: phase-contrast and multi-spectral imaging.

    PubMed

    Mayo, S C; Miller, P R; Wilkins, S W; Davis, T J; Gao, D; Gureyev, T E; Paganin, D; Parry, D J; Pogany, A; Stevenson, A W

    2002-08-01

    We outline a new approach to X-ray projection microscopy in a scanning electron microscope (SEM), which exploits phase contrast to boost the quality and information content of images. These developments have been made possible by the combination of a high-brightness field-emission gun (FEG)-based SEM, direct detection CCD technology and new phase retrieval algorithms. Using this approach we have been able to obtain spatial resolution of < 0.2 micro m and have demonstrated novel features such as: (i) phase-contrast enhanced visibility of high spatial frequency image features (e.g. edges and boundaries) over a wide energy range; (ii) energy-resolved imaging to simultaneously produce multiple quasi-monochromatic images using broad-band polychromatic illumination; (iii) easy implementation of microtomography; (iv) rapid and robust phase/amplitude-retrieval algorithms to enable new real-time and quantitative modes of microscopic imaging. These algorithms can also be applied successfully to recover object-plane information from intermediate-field images, unlocking the potentially greater contrast and resolution of the intermediate-field regime. Widespread applications are envisaged for fields such as materials science, biological and biomedical research and microelectronics device inspection. Some illustrative examples are presented. The quantitative methods described here are also very relevant to projection microscopy using other sources of radiation, such as visible light and electrons.

  2. Identification of malaria infected red blood samples by digital holographic quantitative phase microscope

    NASA Astrophysics Data System (ADS)

    Patel, Nimit R.; Chhaniwal, Vani K.; Javidi, Bahram; Anand, Arun

    2015-07-01

    Development of devices for automatic identification of diseases is desired especially in developing countries. In the case of malaria, even today the gold standard is the inspection of chemically treated blood smears through a microscope. This requires a trained technician/microscopist to identify the cells in the field of view, with which the labeling chemicals gets attached. Bright field microscopes provide only low contrast 2D images of red blood cells and cell thickness distribution cannot be obtained. Quantitative phase contrast microscopes can provide both intensity and phase profiles of the cells under study. The phase information can be used to determine thickness profile of the cell. Since cell morphology is available, many parameters pertaining to the 3D shape of the cell can be computed. These parameters in turn could be used to decide about the state of health of the cell leading to disease diagnosis. Here the investigations done on digital holographic microscope, which provides quantitative phase images, for comparison of parameters obtained from the 3D shape profile of objects leading to identification of diseased samples is described.

  3. Seismic attenuation tomography of the Tonga-Fiji region using phase pair methods

    NASA Astrophysics Data System (ADS)

    Roth, Erich G.; Wiens, Douglas A.; Dorman, Leroy M.; Hildebrand, John; Webb, Spahr C.

    1999-03-01

    The anelastic structure of the region surrounding the Tonga slab and Lau back arc spreading center in the southwest Pacific is studied using data from 12 broadband island stations and 30 ocean bottom seismographs. Two differential attenuation methods determine δt* over the frequency band 0.1 to 3.5 Hz for earthquakes in the Tonga slab. The S-P method measures the difference in spectral decay between P and S waves arriving at the same station. The P-P method measures the difference in spectral decay for P waves with different paths through the upper mantle. Eight hundred sixty phase pairs are used to invert for two-dimensional 1/Qα structure using a nonnegative least squares algorithm. A grid search method determines the Qα/Qβ ratio most compatible with both the S-P and P-P differential measurements. The highest attenuation (Qα = 90) is found within the upper 100 km beneath the active portions of the Lau Basin extending westward to the Lau Ridge. These regions probably delineate the source region for the back arc spreading center magmas, expected to be within the upper 100 km based on petrological considerations. The high attenuation regions also correlate well with zones of low P wave velocity determined by regional velocity tomography. Somewhat lower attenuation is found beneath the Fiji Plateau than beneath the Lau Basin. The entire back arc is characterized by a gradual decrease in attenuation to a depth of 300 to 400 km. The slab is imaged as a region of low attenuation (Qα > 900) material. A Qα/Qβ ratio of 1.75 provides the best fit between the S-P and P-P data sets upon inversion. Spectral stacking shows no frequency dependence within the frequency band analyzed.

  4. Quantitative electron phase imaging with high sensitivity and an unlimited field of view.

    PubMed

    Maiden, A M; Sarahan, M C; Stagg, M D; Schramm, S M; Humphry, M J

    2015-01-01

    As it passes through a sample, an electron beam scatters, producing an exit wavefront rich in information. A range of material properties, from electric and magnetic field strengths to specimen thickness, strain maps and mean inner potentials, can be extrapolated from its phase and mapped at the nanoscale. Unfortunately, the phase signal is not straightforward to obtain. It is most commonly measured using off-axis electron holography, but this is experimentally challenging, places constraints on the sample and has a limited field of view. Here we report an alternative method that avoids these limitations and is easily implemented on an unmodified transmission electron microscope (TEM) operating in the familiar selected area diffraction mode. We use ptychography, an imaging technique popular amongst the X-ray microscopy community; recent advances in reconstruction algorithms now reveal its potential as a tool for highly sensitive, quantitative electron phase imaging. PMID:26423558

  5. Analytical evaluation of the signal and noise propagation in x-ray differential phase-contrast computed tomography

    NASA Astrophysics Data System (ADS)

    Raupach, Rainer; Flohr, Thomas G.

    2011-04-01

    We analyze the signal and noise propagation of differential phase-contrast computed tomography (PCT) compared with conventional attenuation-based computed tomography (CT) from a theoretical point of view. This work focuses on grating-based differential phase-contrast imaging. A mathematical framework is derived that is able to analytically predict the relative performance of both imaging techniques in the sense of the relative contrast-to-noise ratio for the contrast of any two materials. Two fundamentally different properties of PCT compared with CT are identified. First, the noise power spectra show qualitatively different characteristics implying a resolution-dependent performance ratio. The break-even point is derived analytically as a function of system parameters such as geometry and visibility. A superior performance of PCT compared with CT can only be achieved at a sufficiently high spatial resolution. Second, due to periodicity of phase information which is non-ambiguous only in a bounded interval statistical phase wrapping can occur. This effect causes a collapse of information propagation for low signals which limits the applicability of phase-contrast imaging at low dose.

  6. The effect of in situ/in vitro three-dimensional quantitative computed tomography image voxel size on the finite element model of human vertebral cancellous bone.

    PubMed

    Lu, Yongtao; Engelke, Klaus; Glueer, Claus-C; Morlock, Michael M; Huber, Gerd

    2014-11-01

    Quantitative computed tomography-based finite element modeling technique is a promising clinical tool for the prediction of bone strength. However, quantitative computed tomography-based finite element models were created from image datasets with different image voxel sizes. The aim of this study was to investigate whether there is an influence of image voxel size on the finite element models. In all 12 thoracolumbar vertebrae were scanned prior to autopsy (in situ) using two different quantitative computed tomography scan protocols, which resulted in image datasets with two different voxel sizes (0.29 × 0.29 × 1.3 mm(3) vs 0.18 × 0.18 × 0.6 mm(3)). Eight of them were scanned after autopsy (in vitro) and the datasets were reconstructed with two voxel sizes (0.32 × 0.32 × 0.6 mm(3) vs. 0.18 × 0.18 × 0.3 mm(3)). Finite element models with cuboid volume of interest extracted from the vertebral cancellous part were created and inhomogeneous bilinear bone properties were defined. Axial compression was simulated. No effect of voxel size was detected on the apparent bone mineral density for both the in situ and in vitro cases. However, the apparent modulus and yield strength showed significant differences in the two voxel size group pairs (in situ and in vitro). In conclusion, the image voxel size may have to be considered when the finite element voxel modeling technique is used in clinical applications.

  7. Treatment of advanced solid tumours with NSAIDs: Correlation of quantitative monitoring of circulating tumour cells and positron emission tomography-computed tomography imaging

    PubMed Central

    Willecke-Hochmuth, Regina; Pachmann, Katharina; Drevs, Joachim

    2016-01-01

    The detection and characterisation of tumour-derived circulating epithelial tumor cells (CETCs) or circulating tumor cells (CTCs) have been a main focus of basic oncological research over previous years. Numerous studies in the past decade have shown that CTCs are a promising tool for the estimation of the risk for metastatic relapse. The present observational study describes treatment results using tumour imaging and the quantification of CTCs. A group of 14 patients with advanced carcinomas was followed during their anticancer treatments. CTC numbers were serially detected and treatment success was estimated by positron emission tomography-computed tomography. A connection was found between tumour remission and a decreasing CTC count in 83%, a connection between stable disease and stable CTC numbers in 78% and a connection between progressive disease (PD) and an increase in CTC count in 50% of cases. In the patients with PD, an incomplete response was observed affecting the CTCs, but not the solid region of the tumour. As a result of this study, it may be concluded that patients with solid tumours benefit from serial quantification of CTCs in addition to imaging, as this combination of techniques provides a more sensitive result than imaging alone. PMID:27588120

  8. Quantitative asymmetric-detection time-stretch optical microscopy (Q-ATOM) for ultrafast quantitative phase imaging flow cytometry (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lau, Andy K. S.; Tang, Anson H. L.; Chung, Bob M. F.; Tsang, Kwok Yeung; Chan, Antony C. S.; Wei, Xiaoming; Wong, Kenneth K.; Lam, Edmund Y.; Cheah, Kathryn S. E.; Shum, Anderson H. C.; Tsia, Kevin K.

    2016-03-01

    Based on the interferometric or holographic approaches, recent QPM techniques provide quantitative-phase information, e.g cell volume, dry mass and optical scattering properties for label-free cellular physical phenotyping. These approaches generally rely on iterative phase-retrieval algorithms to obtain quantitative-phase information, which are computationally intensive. Moreover, current QPM techniques can only offer limited image acquisition rate by using CMOS/CCD image sensors, these two limitations hinder QPM for high-throughput quantitative image-based single-cell analysis in real-time. To this end, we demonstrate an interferometry-free quantitative phase microscopy developed on a new generation of time-stretch microscopy, asymmetric-detection time-stretch optical microscopy (ATOM), which is coined quantitative ATOM (Q-ATOM) - featuring an unprecedented cell measurement throughput together with the assorted intrinsic optical phenotypes (e.g. angular light scattering profile) and the derived physical properties of the cells (e.g. cell size, dry mass density etc.). Based on a similar concept to Schlieren imaging, Q-ATOM retrieves quantitative-phase information through multiple off-axis light-beam detection at a line-scan rate of <10 MHz - a speed unachievable by any existing QPM techniques. Phase retrieval in Q-ATOM relies on a non-iterative method, significantly reducing the computational complexity of the technique. It is a particularly important feature which facilitates real-time continuous label-free single-cell analysis in Q-ATOM. With the use of a non-interferometric configuration, we demonstrate ultrafast Q-ATOM of mouse chondrocytes and hypertrophic chondrocytes in ultrafast microfluidic flow with sub-cellular resolution at an imaging throughput equivalent to ~100,000 cells/sec without image blur. This technique shows a great potential for ultrahigh throughput label-free image-based single-cell biophysical phentotyping.

  9. Quantitative X-ray phase contrast waveguide imaging of bacterial endospores1

    PubMed Central

    Wilke, R. N.; Hoppert, M.; Krenkel, M.; Bartels, M.; Salditt, T.

    2015-01-01

    Quantitative waveguide-based X-ray phase contrast imaging has been carried out on the level of single, unstained, unsliced and freeze-dried bacterial cells of Bacillus thuringiensis and Bacillus subtilis using hard X-rays of 7.9 keV photon energy. The cells have been prepared in the metabolically dormant state of an endospore. The quantitative phase maps obtained by iterative phase retrieval using a modified hybrid input–output algorithm allow for mass and mass density determinations on the level of single individual endospores but include also large field of view investigations. Additionally, a direct reconstruction based on the contrast transfer function is investigated, and the two approaches are compared. Depending on the field of view and method, a resolution down to 65 nm was achieved at a maximum applied dose of below 5 × 105 Gy. Masses in the range of about ∼110–190 (20) fg for isolated endospores have been obtained. PMID:25844079

  10. Measuring the Nonuniform Evaporation Dynamics of Sprayed Sessile Microdroplets with Quantitative Phase Imaging.

    PubMed

    Edwards, Chris; Arbabi, Amir; Bhaduri, Basanta; Wang, Xiaozhen; Ganti, Raman; Yunker, Peter J; Yodh, Arjun G; Popescu, Gabriel; Goddard, Lynford L

    2015-10-13

    We demonstrate real-time quantitative phase imaging as a new optical approach for measuring the evaporation dynamics of sessile microdroplets. Quantitative phase images of various droplets were captured during evaporation. The images enabled us to generate time-resolved three-dimensional topographic profiles of droplet shape with nanometer accuracy and, without any assumptions about droplet geometry, to directly measure important physical parameters that characterize surface wetting processes. Specifically, the time-dependent variation of the droplet height, volume, contact radius, contact angle distribution along the droplet's perimeter, and mass flux density for two different surface preparations are reported. The studies clearly demonstrate three phases of evaporation reported previously: pinned, depinned, and drying modes; the studies also reveal instances of partial pinning. Finally, the apparatus is employed to investigate the cooperative evaporation of the sprayed droplets. We observe and explain the neighbor-induced reduction in evaporation rate, that is, as compared to predictions for isolated droplets. In the future, the new experimental methods should stimulate the exploration of colloidal particle dynamics on the gas-liquid-solid interface.

  11. Analyzing the texture changes in the quantitative phase maps of adipocytes

    NASA Astrophysics Data System (ADS)

    Roitshtain, Darina; Sharabani-Yosef, Orna; Gefen, Amit; Shaked, Natan T.

    2016-03-01

    We present a new analysis tool for studying texture changes in the quantitative phase maps of live cells acquired by wide-field interferometry. The sensitivity of wide-field interferometry systems to small changes in refractive index enables visualizing cells and inner cell organelles without the using fluorescent dyes or other cell-invasive approaches, which may affect the measurement and require external labeling. Our label-free texture-analysis tool is based directly on the optical path delay profile of the sample and does not necessitate decoupling refractive index and thickness in the cell quantitative phase profile; thus, relevant parameters can be calculated using a single-frame acquisition. Our experimental system includes low-coherence wide-field interferometer, combined with simultaneous florescence microscopy system for validation. We used this system and analysis tool for studying lipid droplets formation in adipocytes. The latter demonstration is relevant for various cellular functions such as lipid metabolism, protein storage and degradation to viral replication. These processes are functionally linked to several physiological and pathological conditions, including obesity and metabolic diseases. Quantification of these biological phenomena based on the texture changes in the cell phase map has a potential as a new cellular diagnosis tool.

  12. Quantitative investigation of cellular growth in directional solidification by phase-field simulation.

    PubMed

    Wang, Zhijun; Wang, Jincheng; Li, Junjie; Yang, Gencang; Zhou, Yaohe

    2011-10-01

    Using a quantitative phase-field model, a systematic investigation of cellular growth in directional solidification is carried out with emphasis on the selection of cellular tip undercooling, tip radius, and cellular spacing. Previous analytical models of cellular growth are evaluated according to the phase-field simulation results. The results show that cellular tip undercooling and tip radius not only depend on the pulling velocity and thermal gradient, but also depend on the cellular interaction related to the cellular spacing. The cellular interaction results in a finite stable range of cellular spacing. The lower limit is determined by the submerging mechanism while the upper limit comes from the tip splitting instability corresponding to the absence of the cellular growth solution, both of which can be obtained from phase-field simulation. Further discussions on the phase-field results also present an analytical method to predict the lower limit. Phase-field simulations on cell elimination between cells with equal spacing validate the finite range of cellular spacing and give deep insight into the cellular doublon and oscillatory instability between cell elimination and tip splitting.

  13. Mapping biological composition through quantitative phase and absorption X-ray ptychography

    NASA Astrophysics Data System (ADS)

    Jones, Michael W. M.; Elgass, Kirstin; Junker, Mark D.; Luu, Mac B.; Ryan, Michael T.; Peele, Andrew G.; van Riessen, Grant A.

    2014-10-01

    Isolating compositional information in biological X-ray imaging can be problematic as such information is conflated with thickness and density variations when viewing in projection through a sample. We demonstrate an effective method for identifying variations in material composition by simultaneously using the quantitative phase and magnitude images provided through soft X-ray ptychography. Using this approach we show significantly increased contrast and improved reliability of the identification of intracellular features from uncharacterised samples. While demonstrated for X-ray ptychography, this method is immediately applicable to electron and optical microscopy methods where the complex transmission function of the sample is recovered.

  14. Quantitative phase and refractive index measurements with point-source digital in-line holographic microscopy.

    PubMed

    Jericho, M H; Kreuzer, H J; Kanka, M; Riesenberg, R

    2012-04-01

    Point-source digital in-line holographic microscopy with numerical reconstruction is ideally suited for quantitative phase measurements to determine optical path lengths and to extract changes in refractive index within accuracy close to 0.001 on the submicrometer length scale. This is demonstrated with simulated holograms and with detailed measurements on a number of different micrometer-sized samples such as suspended drops, optical fibers, as well as organisms of biological interest such as E. coli bacteria, HeLa cells, and fibroblast cells.

  15. Spatially resolved quantitative mapping of thermomechanical properties and phase transition temperatures using scanning probe microscopy

    DOEpatents

    Jesse, Stephen; Kalinin, Sergei V; Nikiforov, Maxim P

    2013-07-09

    An approach for the thermomechanical characterization of phase transitions in polymeric materials (polyethyleneterephthalate) by band excitation acoustic force microscopy is developed. This methodology allows the independent measurement of resonance frequency, Q factor, and oscillation amplitude of a tip-surface contact area as a function of tip temperature, from which the thermal evolution of tip-surface spring constant and mechanical dissipation can be extracted. A heating protocol maintained a constant tip-surface contact area and constant contact force, thereby allowing for reproducible measurements and quantitative extraction of material properties including temperature dependence of indentation-based elastic and loss moduli.

  16. Quantitative phase imaging of biological cells using spatially low and temporally high coherent light source.

    PubMed

    Ahmad, Azeem; Dubey, Vishesh; Singh, Gyanendra; Singh, Veena; Mehta, Dalip Singh

    2016-04-01

    In this Letter, we demonstrate quantitative phase imaging of biological samples, such as human red blood cells (RBCs) and onion cells using narrow temporal frequency and wide angular frequency spectrum light source. This type of light source was synthesized by the combined effect of spatial, angular, and temporal diversity of speckle reduction technique. The importance of using low spatial and high temporal coherence light source over the broad band and narrow band light source is that it does not require any dispersion compensation mechanism for biological samples. Further, it avoids the formation of speckle or spurious fringes which arises while using narrow band light source. PMID:27192285

  17. Prostate cancer diagnosis using quantitative phase imaging and machine learning algorithms

    NASA Astrophysics Data System (ADS)

    Nguyen, Tan H.; Sridharan, Shamira; Macias, Virgilia; Balla, Andre K.; Do, Minh N.; Popescu, Gabriel

    2015-03-01

    We report, for the first time, the use of Quantitative Phase Imaging (QPI) images to perform automatic prostate cancer diagnosis. A machine learning algorithm is implemented to learn textural behaviors of prostate samples imaged under QPI and produce labeled maps of different regions for testing biopsies (e.g. gland, stroma, lumen etc.). From these maps, morphological and textural features are calculated to predict outcomes of the testing samples. Current performance is reported on a dataset of more than 300 cores of various diagnosis results.

  18. Intensity-based modified Doppler variance algorithm: application to phase instable and phase stable optical coherence tomography systems.

    PubMed

    Liu, Gangjun; Chou, Lidek; Jia, Wangcun; Qi, Wenjuan; Choi, Bernard; Chen, Zhongping

    2011-06-01

    The traditional phase-resolved Doppler method demonstrates great success for in-vivo imaging of blood flow and blood vessels. However, the phase-resolved method always requires high phase stability of the system. In phase instable situations, the performance of the phase-resolved methods will be degraded. We propose a modified Doppler variance algorithm that is based on the intensity or amplitude value. Performances of the proposed algorithm are compared with traditional phase-resolved Doppler variance and color Doppler methods for both phase stable and phase instable systems. For the phase instable situation, the proposed algorithm demonstrates images without phase instability induced artifacts. In-vivo imaging of window-chamber hamster skin is demonstrated for phase instable situation with a spectrometer-based Fourier domain OCT system. A microelectromechanical systems (MEMS) based swept source OCT (SSOCT) system is also used to demonstrate the performance of the proposed method in a phase instable situation. The phase stability of the SSOCT system is analyzed. In-vivo imaging of the blood vessel of human skin is demonstrated with the proposed method and the SSOCT system. For the phase stable situation, the proposed algorithm also demonstrates comparable performance with traditional phase-resolved methods. In-vivo imaging of the human choroidal blood vessel network is demonstrated with the proposed method under the phase stable situation. Depth-resolved fine choroidal blood vessel networks are shown.

  19. Quantitation of Binding, Recovery and Desalting Efficiency in Solid Phase Extraction Micropipette Tips

    SciTech Connect

    Palmblad, M N; Vogel, J S

    2004-08-02

    Micropipette-tip solid phase extraction systems are common in proteomic analyses for desalting and concentrating samples for mass spectrometry, removing interferences, and increasing sensitivity. These systems are inexpensive, disposable, and highly efficient. Here we show micropipette-tip solid phase extraction is a direct sample preparation method for {sup 14}C-accelerator mass spectrometry (AMS), removing salts or reagent from labeled macromolecules. We compared loading, recovery and desalting efficiency in commercially available SPE micro-tips using {sup 14}C-labeled peptides and proteins, AMS, and alpha spectrometry ion energy loss quantitation. The polypropylene in the tips was nearly {sup 14}C-free and simultaneously provided low-background carrier for AMS. The silica material did not interfere with the analysis. Alpha spectrometry provided an absolute measurement of desalting efficiency.

  20. Full quantitative phase analysis of hydrated lime using the Rietveld method

    SciTech Connect

    Lassinantti Gualtieri, Magdalena

    2012-09-15

    Full quantitative phase analysis (FQPA) using X-ray powder diffraction and Rietveld refinements is a well-established method for the characterization of various hydraulic binders such as Portland cement and hydraulic limes. In this paper, the Rietveld method is applied to hydrated lime, a non-hydraulic traditional binder. The potential presence of an amorphous phase in this material is generally ignored. Both synchrotron radiation and a conventional X-ray source were used for data collection. The applicability of the developed control file for the Rietveld refinements was investigated using samples spiked with glass. The results were cross-checked by other independent methods such as thermal and chemical analyses. The sample microstructure was observed by transmission electron microscopy. It was found that the consistency between the different methods was satisfactory, supporting the validity of FQPA for this material. For the samples studied in this work, the amount of amorphous material was in the range 2-15 wt.%.

  1. Quantitative evaluation of mask phase defects from through-focus EUV aerial images

    SciTech Connect

    Mochi, Iacopo; Yamazoe, Kenji; Neureuther, Andrew; Goldberg, Kenneth A.

    2011-02-21

    Mask defects inspection and imaging is one of the most important issues for any pattern transfer lithography technology. This is especially true for EUV lithography where the wavelength-specific properties of masks and defects necessitate actinic inspection for a faithful prediction of defect printability and repair performance. In this paper we will present a technique to obtain a quantitative characterization of mask phase defects from EUV aerial images. We apply this technique to measure the aerial image phase of native defects on a blank mask, measured with the SEMATECH Berkeley Actinic Inspection Tool (AIT) an EUV zoneplate microscope that operates at Lawrence Berkeley National Laboratory. The measured phase is compared with predictions made from AFM top-surface measurements of those defects. While amplitude defects are usually easy to recognize and quantify with standard inspection techniques like scanning electron microscopy (SEM), defects or structures that have a phase component can be much more challenging to inspect. A phase defect can originate from the substrate or from any level of the multilayer. In both cases its effect on the reflected field is not directly related to the local topography of the mask surface, but depends on the deformation of the multilayer structure. Using the AIT, we have previously showed that EUV inspection provides a faithful and reliable way to predict the appearance of mask defect on the printed wafer; but to obtain a complete characterization of the defect we need to evaluate quantitatively its phase component. While aerial imaging doesn't provide a direct measurement of the phase of the object, this information is encoded in the through focus evolution of the image intensity distribution. Recently we developed a technique that allows us to extract the complex amplitude of EUV mask defects using two aerial images from different focal planes. The method for the phase reconstruction is derived from the Gerchberg-Saxton (GS

  2. Synchronization Tomography: A Method for Three-Dimensional Localization of Phase Synchronized Neuronal Populations in the Human Brain using Magnetoencephalography

    NASA Astrophysics Data System (ADS)

    Tass, P. A.; Fieseler, T.; Dammers, J.; Dolan, K.; Morosan, P.; Majtanik, M.; Boers, F.; Muren, A.; Zilles, K.; Fink, G. R.

    2003-02-01

    We present a noninvasive technique which allows the anatomical localization of phase synchronized neuronal populations in the human brain with magnetoencephalography. We study phase synchronization between the reconstructed current source density (CSD) of different brain areas as well as between the CSD and muscular activity. We asked four subjects to tap their fingers in synchrony with a rhythmic tone, and to continue tapping at the same rate after the tone was switched off. The phase synchronization behavior of brain areas relevant for movement coordination, inner voice, and time estimation changes drastically when the transition to internal pacing occurs, while their averaged amplitudes remain unchanged. Information of this kind cannot be derived with standard neuroimaging techniques like functional magnetic resonance imaging or positron emission tomography.

  3. Polarization-sensitive optical coherence tomography measurements with different phase modulation amplitude when using continuous polarization modulation

    NASA Astrophysics Data System (ADS)

    Lu, Zenghai; Kasaragod, Deepa K.; Matcher, Stephen J.

    2012-01-01

    We demonstrate theoretically and experimentally that the phase retardance and relative optic-axis orientation of a sample can be calculated without prior knowledge of the actual value of the phase modulation amplitude when using a polarization-sensitive optical coherence tomography system based on continuous polarization modulation (CPM-PS-OCT). We also demonstrate that the sample Jones matrix can be calculated at any values of the phase modulation amplitude in a reasonable range depending on the system effective signal-to-noise ratio. This has fundamental importance for the development of clinical systems by simplifying the polarization modulator drive instrumentation and eliminating its calibration procedure. This was validated on measurements of a three-quarter waveplate and an equine tendon sample by a fiber-based swept-source CPM-PS-OCT system.

  4. Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast.

    PubMed

    Kumar, Ravinder; Srivastava, Sanjeeva

    2016-01-01

    Most of the microbial cells on earth under natural conditions exist in a dormant condition, commonly known as quiescent state. Quiescent cells exhibit low rates of transcription and translation suggesting that cellular abundance of proteins may be similar in quiescent cells. Therefore, this study aim to compare the proteome of budding yeast cells from two quiescent states viz. stationary phase/G0 and tetrads. Using iTRAQ (isobaric tag for relative and absolute quantitation) based quantitative proteomics we identified 289 proteins, among which around 40 proteins exhibited ±1.5 fold change consistently from the four biological replicates. Proteomics data was validated by western blot and denstiometric analysis of Hsp12 and Spg4. Level of budding yeast 14-3-3 proteins was found to be similar in both the quiescent states, whereas Hsp12 and Spg4 expressed only during stress. FACS (fluorescence-activated cell sorting) analysis showed that budding yeast cells were arrested at G1 stages both in tetrads as well as in stationary phase. We also observed that quiescent states did not express Ime1 (inducer of meiosis). Taken together, our present study demonstrates that the cells in quiescent state may have similar proteome, and accumulation of proteins like Hsp12, Hsp26, and Spg4 may play an important role in retaining viability of the cells during dormancy. PMID:27558777

  5. Studying the relationship between redox and cell growth using quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Sridharan, Shamira; Leslie, Matthew T.; Bapst, Natalya; Smith, John; Gaskins, H. Rex; Popescu, Gabriel

    2016-03-01

    Quantitative phase imaging has been used in the past to study the dry mass of cells and study cell growth under various treatment conditions. However, the relationship between cellular redox and growth rates has not yet been studied in this context. This study employed the recombinant Glrx-roGFP2 redox biosensor targeted to the mitochondrial matrix or cytosolic compartments of A549 lung epithelial carcinoma cells. The Glrx-roGFP2s biosensor consists of a modified GFP protein containing internal cysteine residues sensitive to the local redox environment. The formation/dissolution of sulfide bridges contorts the internal chromophore, dictating corresponding changes in florescence emission that provide direct measures of the local redox potential. Combining 2-channel florescent imaging of the redox sensor with quantitative phase imaging allowed observation of redox homeostasis alongside measurements of cellular mass during full cycles of cellular division. The results indicate that mitochondrial redox showed a stronger inverse correlation with cell growth than cytoplasmic redox states; although redox changes are restricted to a 5% range. We are now studying the relationship between mitochondrial redox and cell growth in an isogenic series of breast cell lines built upon the MCF-10A genetic background that vary both in malignancy and metastatic potential.

  6. Digital Holographic Microscopy: Quantitative Phase Imaging and Applications in Live Cell Analysis

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Langehanenberg, Patrik; Kosmeier, Sebastian; Schlichthaber, Frank; Remmersmann, Christian; von Bally, Gert; Rommel, Christina; Dierker, Christian; Schnekenburger, Jürgen

    The analysis of complex processes in living cells creates a high demand for fast and label-free methods for online monitoring. Widely used fluorescence methods require specific labeling and are often restricted to chemically fixated samples. Thus, methods that offer label-free and minimally invasive detection of live cell processes and cell state alterations are of particular interest. In combination with light microscopy, digital holography provides label-free, multi-focus quantitative phase imaging of living cells. In overview, several methods for digital holographic microscopy (DHM) are presented. First, different experimental setups for the recording of digital holograms and the modular integration of DHM into common microscopes are described. Then the numerical processing of digitally captured holograms is explained. This includes the description of spatial and temporal phase shifting techniques, spatial filtering based reconstruction, holographic autofocusing, and the evaluation of self-interference holograms. Furthermore, the usage of partial coherent light and multi-wavelength approaches is discussed. Finally, potentials of digital holographic microscopy for quantitative cell imaging are illustrated by results from selected applications. It is shown that DHM can be used for automated tracking of migrating cells and cell thickness monitoring as well as for refractive index determination of cells and particles. Moreover, the use of DHM for label-free analysis in fluidics and micro-injection monitoring is demonstrated. The results show that DHM is a highly relevant method that allows novel insights in dynamic cell biology, with applications in cancer research and for drugs and toxicity testing.

  7. Quantitative proteomic comparison of stationary/G0 phase cells and tetrads in budding yeast

    PubMed Central

    Kumar, Ravinder; Srivastava, Sanjeeva

    2016-01-01

    Most of the microbial cells on earth under natural conditions exist in a dormant condition, commonly known as quiescent state. Quiescent cells exhibit low rates of transcription and translation suggesting that cellular abundance of proteins may be similar in quiescent cells. Therefore, this study aim to compare the proteome of budding yeast cells from two quiescent states viz. stationary phase/G0 and tetrads. Using iTRAQ (isobaric tag for relative and absolute quantitation) based quantitative proteomics we identified 289 proteins, among which around 40 proteins exhibited ±1.5 fold change consistently from the four biological replicates. Proteomics data was validated by western blot and denstiometric analysis of Hsp12 and Spg4. Level of budding yeast 14-3-3 proteins was found to be similar in both the quiescent states, whereas Hsp12 and Spg4 expressed only during stress. FACS (fluorescence-activated cell sorting) analysis showed that budding yeast cells were arrested at G1 stages both in tetrads as well as in stationary phase. We also observed that quiescent states did not express Ime1 (inducer of meiosis). Taken together, our present study demonstrates that the cells in quiescent state may have similar proteome, and accumulation of proteins like Hsp12, Hsp26, and Spg4 may play an important role in retaining viability of the cells during dormancy. PMID:27558777

  8. Deciphering the internal complexity of living cells with quantitative phase microscopy: a multiscale approach

    NASA Astrophysics Data System (ADS)

    Martinez-Torres, Cristina; Laperrousaz, Bastien; Berguiga, Lotfi; Boyer-Provera, Elise; Elezgaray, Juan; Nicolini, Franck E.; Maguer-Satta, Veronique; Arneodo, Alain; Argoul, Françoise

    2015-09-01

    The distribution of refractive indices (RIs) of a living cell contributes in a nonintuitive manner to its optical phase image and quite rarely can be inverted to recover its internal structure. The interpretation of the quantitative phase images of living cells remains a difficult task because (1) we still have very little knowledge on the impact of its internal macromolecular complexes on the local RI and (2) phase changes produced by light propagation through the sample are mixed with diffraction effects by the internal cell bodies. We propose to implement a two-dimensional wavelet-based contour chain detection method to distinguish internal boundaries based on their greatest optical path difference gradients. These contour chains correspond to the highest image phase contrast and follow the local RI inhomogeneities linked to the intracellular structural intricacy. Their statistics and spatial distribution are the morphological indicators suited for comparing cells of different origins and/or to follow their transformation in pathologic situations. We use this method to compare nonadherent blood cells from primary and laboratory culture origins and to assess the internal transformation of hematopoietic stem cells by the transduction of the BCR-ABL oncogene responsible for the chronic myelogenous leukemia.

  9. Addressing the amorphous content issue in quantitative phase analysis : the certification of NIST SRM 676a.

    SciTech Connect

    Cline, J. P.; Von Dreele, R. B.; Winburn, R.; Stephens, P. W.; Filliben, J. J.

    2011-07-01

    A non-diffracting surface layer exists at any boundary of a crystal and can comprise a mass fraction of several percent in a finely divided solid. This has led to the long-standing issue of amorphous content in standards for quantitative phase analysis (QPA). NIST standard reference material (SRM) 676a is a corundum ({alpha}-Al{sub 2}O{sub 3}) powder, certified with respect to phase purity for use as an internal standard in powder diffraction QPA. The amorphous content of SRM 676a is determined by comparing diffraction data from mixtures with samples of silicon powders that were engineered to vary their specific surface area. Under the (supported) assumption that the thickness of an amorphous surface layer on Si was invariant, this provided a method to control the crystalline/amorphous ratio of the silicon components of 50/50 weight mixtures of SRM 676a with silicon. Powder diffraction experiments utilizing neutron time-of-flight and 25 keV and 67 keV X-ray energies quantified the crystalline phase fractions from a series of specimens. Results from Rietveld analyses, which included a model for extinction effects in the silicon, of these data were extrapolated to the limit of zero amorphous content of the Si powder. The certified phase purity of SRM 676a is 99.02% {+-} 1.11% (95% confidence interval). This novel certification method permits quantification of amorphous content for any sample of interest, by spiking with SRM 676a.

  10. In-focus quantitative intensity and phase imaging with the numerical focusing transport of intensity equation method

    NASA Astrophysics Data System (ADS)

    Tian, Xiaolin; Meng, Xin; Yu, Wei; Song, Xiaojun; Xue, Liang; Liu, Cheng; Wang, Shouyu

    2016-10-01

    Microscopy combined with the transport of intensity equation is capable of retrieving both intensity and phase distributions of samples from both in-focus and defocus intensities. However, during measurements, the focal plane is often decided artificially and the improper choice may induce errors in quantitative intensity and phase retrieval. In order to obtain accurate in-focus information, quantitative intensity and phase imaging with the numerical focusing transport of intensity equation method combined with cellular duty ratio criterion and numerical wavefront propagation is introduced in this paper. Both numerical simulations and experimental measurements are provided proving this designed method can increase both retrieved in-focus intensity and phase accuracy and reduce dependence of focal plane determination in transport of intensity equation measurements. It is believed that the proposed method can be potentially applied in various fields as in-focus compensation for quantitative phase imaging and automatic focal plane determination, etc.

  11. Visualizing ultrasonically-induced shear wave propagation using phase-sensitive optical coherence tomography for dynamic elastography

    PubMed Central

    Song, Shaozhen; Arnal, Bastien; Huang, Zhihong; O’Donnell, Matthew; Wang, Ruikang K.

    2015-01-01

    We report on the use of phase-sensitive optical coherence tomography (PhS-OCT) to detect and track temporally and spatially shear wave propagation within tissue induced by ultrasound radiation force. Kilohertz-range shear waves are remotely generated in sample using focused ultrasound emission and their propagation is tracked using PhS-OCT. Cross-sectional maps of the local shear modulus are reconstructed from local estimates of shear wave speed in tissue-mimicking phantoms. We demonstrate the feasibility of combining ultrasound radiation force and PhS-OCT to perform high-resolution mapping of the shear modulus. PMID:24562220

  12. X-ray microdiffraction as a tool for quantitative phase analysis

    NASA Astrophysics Data System (ADS)

    Medici, L.; Belviso, C.; Fiore, S.

    2009-04-01

    This work aims to verify if data obtained via laboratory-based X-ray microdiffraction are suitable for mineralogical quantitative analyses and to determine the best instrumental parameters for quantitative phase analyses using powder diffraction. A X-ray microdiffractometer needs few milligrams of powder material to obtain a complete X-ray spectrum and can directly work on thin sections and bulk matrices; this routine technique could satisfy the claims of a lot of experiments where small samples are used and mineralogical quantitative determinations are required. Different ratios of solid binary mixtures of quartz, calcite, kaolinite, and illite were prepared by analytical balance: 5/95, 25/75, 50/50, 75/25, 95/5. These powder mixtures were analyzed using a Rigaku Rint 2200 instrument with a conventional Bragg-Brentano geometry equipped with a copper tube and a graphite crystal monochromator. The data were collected in the angular range 3-100˚ 2Î& cedil;with steps of 0.02˚ and 5 s/step. The data collections were converted into GSAS files for EXPGUI software and quantitatively refined by Rietveld method. These refinements and weight amounts were used as references for the following data collections. The same powder mixtures were analyzed by a X-ray microdiffractometer Rigaku D-Max Rapid, equipped with an image plate detector, a flat graphite monochromator, a microscope for the positioning of the sample in the path of the X-ray beam, operating at 40 kV and 30 mA with CuKα radiation. Each powder sample was collected with different beam collimators (beam diameters: 0.03, 0.05, 0.10, 0.30 mm), different collection times, two fixed values of omega angle (3˚ and 6˚ ), five angular ranges of rotation of phi angle (0˚ , 30˚ , 90˚ , 180˚ , 360˚ ). The XRD data were collected as two-dimensional images and converted into 2Î& cedil;- I profiles; further conversions into GSAS files for EXPGUI software were carried out, and the data were

  13. Nanoparticles as contrast-enhancing agents in optical coherence tomography imaging of the structural components of skin: Quantitative evaluation

    SciTech Connect

    Kirillin, M Yu; Agrba, P D; Kamenskii, V A; Sirotkina, M A; Shiryamova, M V; Zagainova, E V

    2010-08-27

    This work examines the effect of gold nanoshells and titania nanoparticles on the imaging contrast of structural components of skin in optical coherence tomography (OCT). Experimental data are compared to Monte Carlo (MC) simulation results. In experiments with pig skin in vivo, the epidermis - dermis contrast is improved from 0.78 {+-} 0.03 to 0.92 {+-} 0.04 by gold nanoshells applied to the skin surface and from 0.78 {+-} 0.03 to 0.86 {+-} 0.04 by titania nanoparticles. The contrast of glands is enhanced by titania from 0.68 {+-} 0.12 to 0.84 {+-} 0.07. The highest contrast is reached 120 - 150 min after applying gold nanoshells and 160 - 200 min after applying titania. According to the MC simulation results, the contrast of inclusions increases from zero to 0.85 and 0.65, respectively. (optical tomography)

  14. Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs.

    PubMed

    Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P; Schrooten, Jan; Geris, Liesbet

    2015-01-01

    To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial 'design of experiments' approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology. PMID:26076131

  15. Quantifying dynamic rheology, phase interactions and strain localisation in deforming three phase magmas using high-speed x-ray tomography

    NASA Astrophysics Data System (ADS)

    Dobson, Katherine; Pistone, Mattia; Fife, Julie; Cordonnier, Benoit; Blundy, Jon; Dingwell, Don; Lee, Peter

    2015-04-01

    The crystal and bubble cargoes of magmas are critical to controlling magma mobility and rheology. These cargos vary in both time and space and the local, and bulk, rheological behaviour are correspondingly heterogeneous. Tracking how these heterogeneous cargoes evolve, and how crystals and bubbles interact with each other in deforming systems is a critical challenge in volcanology, as these processes control both the chemical and physical evolution of the magma, including phenomena such as melt-crystal segregation, strain localisation, and fragmentation. The only methodology available to track these processes in real time, and at the scale of individual melt-crystal-bubble interactions is high speed x-ray tomography. This non-destructive imaging technique allows the rapid acquisition of sequential 3D images that capture the physical, and to some degree chemical, microstructure of the sample during a deformation cycle. We utilise in situ tomographic methods developed in materials science to perfume magmatic deformation experiments on synthesized three phase systems at magmatic temperatures. Through a novel combination of a high temperature laser heating system [1] in situ micro-precision deformation apparatus [2] and the temporal and spatial resolution available at the TOMCAT beam line at the Swiss Light Source synchrotron facility we performed in situ observations of the microstructural evolution of a synthesized anhydrous borosilicate melt seeded with a variable concentration of non-reactive rutile crystals and air bubbles (30-70 volume %). The experiments were conducted at 800-1000C, under constant deformation rates of 0.25-5.00 microns/second. Each 3D image has 2D and 3D spatial resolution of approximately 3 microns per pixel, and each 3D image took ~3 seconds to acquire. Here we present this innovative high speed, high temperature, syn-deformation tomographic data , and show how it can be used to trace the location and local distribution of each crystal and

  16. Synthesis and purification of iodoaziridines involving quantitative selection of the optimal stationary phase for chromatography.

    PubMed

    Boultwood, Tom; Affron, Dominic P; Bull, James A

    2014-05-16

    The highly diastereoselective preparation of cis-N-Ts-iodoaziridines through reaction of diiodomethyllithium with N-Ts aldimines is described. Diiodomethyllithium is prepared by the deprotonation of diiodomethane with LiHMDS, in a THF/diethyl ether mixture, at -78 °C in the dark. These conditions are essential for the stability of the LiCHI2 reagent generated. The subsequent dropwise addition of N-Ts aldimines to the preformed diiodomethyllithium solution affords an amino-diiodide intermediate, which is not isolated. Rapid warming of the reaction mixture to 0 °C promotes cyclization to afford iodoaziridines with exclusive cis-diastereoselectivity. The addition and cyclization stages of the reaction are mediated in one reaction flask by careful temperature control. Due to the sensitivity of the iodoaziridines to purification, assessment of suitable methods of purification is required. A protocol to assess the stability of sensitive compounds to stationary phases for column chromatography is described. This method is suitable to apply to new iodoaziridines, or other potentially sensitive novel compounds. Consequently this method may find application in range of synthetic projects. The procedure involves firstly the assessment of the reaction yield, prior to purification, by (1)H NMR spectroscopy with comparison to an internal standard. Portions of impure product mixture are then exposed to slurries of various stationary phases appropriate for chromatography, in a solvent system suitable as the eluent in flash chromatography. After stirring for 30 min to mimic chromatography, followed by filtering, the samples are analyzed by (1)H NMR spectroscopy. Calculated yields for each stationary phase are then compared to that initially obtained from the crude reaction mixture. The results obtained provide a quantitative assessment of the stability of the compound to the different stationary phases; hence the optimal can be selected. The choice of basic alumina, modified to

  17. Quantitation of lipid phases in phospholipid vesicles by the generalized polarization of Laurdan fluorescence.

    PubMed Central

    Parasassi, T; De Stasio, G; Ravagnan, G; Rusch, R M; Gratton, E

    1991-01-01

    The sensitivity of Laurdan (6-dodecanoyl-2-dimethylaminonaphthalene) excitation and emission spectra to the physical state of the membrane arises from dipolar relaxation processes in the membrane region surrounding the Laurdan molecule. Experiments performed using phospholipid vesicles composed of phospholipids with different polar head groups show that this part of the molecule is not responsible for the observed effects. Also, pH titration in the range from pH 4 to 10 shows that the spectral variations are independent of the charge of the polar head. A two-state model of dipolar relaxation is used to qualitatively explain the behavior of Laurdan. It is concluded that the presence of water molecules in the phospholipid matrix are responsible for the spectral properties of Laurdan in the gel phase. In the liquid crystalline phase there is a relaxation process that we attribute to water molecules that can reorientate during the few nanoseconds of the excited state lifetime. The quantitation of lipid phases is obtained using generalized polarization which, after proper choice of excitation and emission wavelengths, satisfies a simple addition rule. PMID:1883937

  18. Quantitative tracking of tumor cells in phase-contrast microscopy exploiting halo artifact pattern

    NASA Astrophysics Data System (ADS)

    Kang, Mi-Sun; Song, Soo-Min; Lee, Hana; Kim, Myoung-Hee

    2012-03-01

    Tumor cell morphology is closely related to its invasiveness characteristics and migratory behaviors. An invasive tumor cell has a highly irregular shape, whereas a spherical cell is non-metastatic. Thus, quantitative analysis of cell features is crucial to determine tumor malignancy or to test the efficacy of anticancer treatment. We use phase-contrast microscopy to analyze single cell morphology and to monitor its change because it enables observation of long-term activity of living cells without photobleaching and phototoxicity, which is common in other fluorescence-labeled microscopy. Despite this advantage, there are image-level drawbacks to phase-contrast microscopy, such as local light effect and contrast interference ring, among others. Thus, we first applied a local filter to compensate for non-uniform illumination. Then, we used intensity distribution information to detect the cell boundary. In phase-contrast microscopy images, the cell normally appears as a dark region surrounded by a bright halo. As the halo artifact around the cell body is minimal and has an asymmetric diffusion pattern, we calculated the cross-sectional plane that intersected the center of each cell and was orthogonal to the first principal axis. Then, we extracted the dark cell region by level set. However, a dense population of cultured cells still rendered single-cell analysis difficult. Finally, we measured roundness and size to classify tumor cells into malignant and benign groups. We validated segmentation accuracy by comparing our findings with manually obtained results.

  19. Establishment of optimal scan delay for multi-phase computed tomography using bolus-tracking technique in canine pancreas.

    PubMed

    Choi, Soo-Young; Choi, Ho-Jung; Lee, Ki-Ja; Lee, Young-Won

    2015-09-01

    To establish a protocol for a multi-phase computed tomography (CT) of the canine pancreas using the bolus-tracking technique, dynamic scan and multi-phase CT were performed in six normal beagle dogs. The dynamic scan was performed for 60 sec at 1-sec intervals after the injection (4 ml/sec) of a contrast medium, and intervals from aortic enhancement appearance to aortic, pancreatic parenchymal and portal vein peaks were measured. The multi-phase CT with 3 phases was performed three times using a bolus-tracking technique. Scan delays were 0, 15 and 30 in first multi-phase scan; 5, 20 and 35 in second multi-phase scan; and 10, 25 and 40 sec in third multi-phase scan, respectively. Attenuation values and contrast enhancement pattern were analyzed from the aorta, pancreas and portal vein. The intervals from aortic enhancement appearance to aortic, pancreatic parenchymal and portal vein peaks were 3.8 ± 0.7, 8.7 ± 0.9 and 13.3 ± 1.5 sec, respectively. The maximum attenuation values of the aorta, pancreatic parenchyma and portal vein were present at scan sections with no scan delay, a 5-sec delay and a 10-sec delay, respectively. When a multi-phase CT of the canine pancreas is triggered at aortic enhancement appearance using a bolus-tracking technique, the recommended optimal delay times of the arterial and pancreatic parenchymal phases are no scan delay and 5 sec, respectively. PMID:25843155

  20. Investigation of noise properties in grating-based x-ray phase tomography with reverse projection method

    NASA Astrophysics Data System (ADS)

    Bao, Yuan; Wang, Yan; Gao, Kun; Wang, Zhi-Li; Zhu, Pei-Ping; Wu, Zi-Yu

    2015-10-01

    The relationship between noise variance and spatial resolution in grating-based x-ray phase computed tomography (PCT) imaging is investigated with reverse projection extraction method, and the noise variances of the reconstructed absorption coefficient and refractive index decrement are compared. For the differential phase contrast method, the noise variance in the differential projection images follows the same inverse-square law with spatial resolution as in conventional absorption-based x-ray imaging projections. However, both theoretical analysis and simulations demonstrate that in PCT the noise variance of the reconstructed refractive index decrement scales with spatial resolution follows an inverse linear relationship at fixed slice thickness, while the noise variance of the reconstructed absorption coefficient conforms with the inverse cubic law. The results indicate that, for the same noise variance level, PCT imaging may enable higher spatial resolution than conventional absorption computed tomography (ACT), while ACT benefits more from degraded spatial resolution. This could be a useful guidance in imaging the inner structure of the sample in higher spatial resolution. Project supported by the National Basic Research Program of China (Grant No. 2012CB825800), the Science Fund for Creative Research Groups, the Knowledge Innovation Program of the Chinese Academy of Sciences (Grant Nos. KJCX2-YW-N42 and Y4545320Y2), the National Natural Science Foundation of China (Grant Nos. 11475170, 11205157, 11305173, 11205189, 11375225, 11321503, 11179004, and U1332109).

  1. Method of optical coherence tomography with parallel depth-resolved signal reception and fibre-optic phase modulators

    SciTech Connect

    Morozov, A N; Turchin, I V

    2013-12-31

    The method of optical coherence tomography with the scheme of parallel reception of the interference signal (P-OCT) is developed on the basis of spatial paralleling of the reference wave by means of a phase diffraction grating producing the appropriate time delay in the Mach–Zehnder interferometer. The absence of mechanical variation of the optical path difference in the interferometer essentially reduces the time required for 2D imaging of the object internal structure, as compared to the classical OCT that uses the time-domain method of the image construction, the sensitivity and the dynamic range being comparable in both approaches. For the resulting field of the interfering object and reference waves an analytical expression is derived that allows the calculation of the autocorrelation function in the plane of photodetectors. For the first time a method of linear phase modulation by 2π is proposed for P-OCT systems, which allows the use of compact high-frequency (a few hundred kHz) piezoelectric cell-based modulators. For the demonstration of the P-OCT method an experimental setup was created, using which the images of the inner structure of biological objects at the depth up to 1 mm with the axial spatial resolution of 12 μm were obtained. (optical coherence tomography)

  2. Quantitative phase-digital holographic microscopy: a new imaging modality to identify original cellular biomarkers of diseases

    NASA Astrophysics Data System (ADS)

    Marquet, P.; Rothenfusser, K.; Rappaz, B.; Depeursinge, C.; Jourdain, P.; Magistretti, P. J.

    2016-03-01

    Quantitative phase microscopy (QPM) has recently emerged as a powerful label-free technique in the field of living cell imaging allowing to non-invasively measure with a nanometric axial sensitivity cell structure and dynamics. Since the phase retardation of a light wave when transmitted through the observed cells, namely the quantitative phase signal (QPS), is sensitive to both cellular thickness and intracellular refractive index related to the cellular content, its accurate analysis allows to derive various cell parameters and monitor specific cell processes, which are very likely to identify new cell biomarkers. Specifically, quantitative phase-digital holographic microscopy (QP-DHM), thanks to its numerical flexibility facilitating parallelization and automation processes, represents an appealing imaging modality to both identify original cellular biomarkers of diseases as well to explore the underlying pathophysiological processes.

  3. Imaging the 3D structure of secondary osteons in human cortical bone using phase-retrieval tomography

    NASA Astrophysics Data System (ADS)

    Arhatari, B. D.; Cooper, D. M. L.; Thomas, C. D. L.; Clement, J. G.; Peele, A. G.

    2011-08-01

    By applying a phase-retrieval step before carrying out standard filtered back-projection reconstructions in tomographic imaging, we were able to resolve structures with small differences in density within a densely absorbing sample. This phase-retrieval tomography is particularly suited for the three-dimensional segmentation of secondary osteons (roughly cylindrical structures) which are superimposed upon an existing cortical bone structure through the process of turnover known as remodelling. The resulting images make possible the analysis of the secondary osteon structure and the relationship between an osteon and the surrounding tissue. Our observations have revealed many different and complex 3D structures of osteons that could not be studied using previous methods. This work was carried out using a laboratory-based x-ray source, which makes obtaining these sorts of images readily accessible.

  4. Propagation based differential phase contrast imaging and tomography of murine tissue with a laser plasma x-ray source

    SciTech Connect

    Laperle, Christopher M.; Wintermeyer, Philip; Wands, Jack R.; Shi, Daxin; Anastasio, Mark A.; Li Xiaodi; Ahr, Brian; Diebold, Gerald J.; Rose-Petruck, Christoph

    2007-10-22

    An ultrafast, laser-driven x-ray source with a liquid mercury target has been used for phase contrast imaging of an excised murine liver and for computed tomography of an electronic component. The x-ray spectrum emitted at 5 kHz repetition rate is found to be similar to that of a 2.5 W, 30 kV microfocus x-ray tube with a tungsten anode. The images of the excised liver show the venous network with approximately 20 {mu}m spatial resolution. Phase contrast features in the tomographic images of the electronic component, transferred to the orthogonal cross sections upon reconstruction, show the internal components of the device with high contrast. Adequate signal-to-noise ratios in the images were achieved with exposure times between 1 and 3 min.

  5. Spectral Domain Optical Coherence Tomography in Glaucoma: Qualitative and Quantitative Analysis of the Optic Nerve Head and Retinal Nerve Fiber Layer (An AOS Thesis)

    PubMed Central

    Chen, Teresa C.

    2009-01-01

    Purpose: To demonstrate that video-rate spectral domain optical coherence tomography (SDOCT) can qualitatively and quantitatively evaluate optic nerve head (ONH) and retinal nerve fiber layer (RNFL) glaucomatous structural changes. To correlate quantitative SDOCT parameters with disc photography and visual fields. Methods: SDOCT images from 4 glaucoma eyes (4 patients) with varying stages of open-angle glaucoma (ie, early, moderate, late) were qualitatively contrasted with 2 age-matched normal eyes (2 patients). Of 61 other consecutive patients recruited in an institutional setting, 53 eyes (33 patients) met inclusion/exclusion criteria for quantitative studies. Images were obtained using two experimental SDOCT systems, one utilizing a superluminescent diode and the other a titanium:sapphire laser source, with axial resolutions of about 6 μm and 3 μm, respectively. Results: Classic glaucomatous ONH and RNFL structural changes were seen in SDOCT images. An SDOCT reference plane 139 μm above the retinal pigment epithelium yielded cup-disc ratios that best correlated with masked physician disc photography cup-disc ratio assessments. The minimum distance band, a novel SDOCT neuroretinal rim parameter, showed good correlation with physician cup-disc ratio assessments, visual field mean deviation, and pattern standard deviation (P values range, .0003–.024). RNFL and retinal thickness maps correlated well with disc photography and visual field testing. Conclusions: To our knowledge, this thesis presents the first comprehensive qualitative and quantitative evaluation of SDOCT images of the ONH and RNFL in glaucoma. This pilot study provides basis for developing more automated quantitative SDOCT-specific glaucoma algorithms needed for future prospective multicenter national trials. PMID:20126502

  6. Robust phase retrieval for high resolution edge illumination x-ray phase-contrast computed tomography in non-ideal environments

    PubMed Central

    Zamir, Anna; Endrizzi, Marco; Hagen, Charlotte K.; Vittoria, Fabio A.; Urbani, Luca; De Coppi, Paolo; Olivo, Alessandro

    2016-01-01

    Edge illumination x-ray phase contrast tomography is a recently developed imaging technique which enables three-dimensional visualisation of low-absorbing materials. Dedicated phase retrieval algorithms can provide separate computed tomography (CT) maps of sample absorption, refraction and scattering properties. In this paper we propose a novel “modified local retrieval” method which is capable of accurately retrieving sample properties in a range of realistic, non-ideal imaging environments. These include system misalignment, defects in the used optical elements and system geometry variations over time due to vibrations or temperature fluctuations. System instabilities were analysed, modelled and incorporated into a simulation study. As a result, an additional modification was introduced to the retrieval procedure to account for changes in the imaging system over time, as well as local variations over the field of view. The performance of the proposed method was evaluated in comparison to a previously used “global retrieval” method by applying both approaches to experimental CT data of a rat’s heart acquired in a non-ideal environment. The use of the proposed method resulted in the removal of major artefacts, leading to a significant improvement in image quality. This method will therefore enable acquiring high-resolution, reliable CT data of large samples in realistic settings. PMID:27502296

  7. Robust phase retrieval for high resolution edge illumination x-ray phase-contrast computed tomography in non-ideal environments.

    PubMed

    Zamir, Anna; Endrizzi, Marco; Hagen, Charlotte K; Vittoria, Fabio A; Urbani, Luca; De Coppi, Paolo; Olivo, Alessandro

    2016-01-01

    Edge illumination x-ray phase contrast tomography is a recently developed imaging technique which enables three-dimensional visualisation of low-absorbing materials. Dedicated phase retrieval algorithms can provide separate computed tomography (CT) maps of sample absorption, refraction and scattering properties. In this paper we propose a novel "modified local retrieval" method which is capable of accurately retrieving sample properties in a range of realistic, non-ideal imaging environments. These include system misalignment, defects in the used optical elements and system geometry variations over time due to vibrations or temperature fluctuations. System instabilities were analysed, modelled and incorporated into a simulation study. As a result, an additional modification was introduced to the retrieval procedure to account for changes in the imaging system over time, as well as local variations over the field of view. The performance of the proposed method was evaluated in comparison to a previously used "global retrieval" method by applying both approaches to experimental CT data of a rat's heart acquired in a non-ideal environment. The use of the proposed method resulted in the removal of major artefacts, leading to a significant improvement in image quality. This method will therefore enable acquiring high-resolution, reliable CT data of large samples in realistic settings. PMID:27502296

  8. Robust phase retrieval for high resolution edge illumination x-ray phase-contrast computed tomography in non-ideal environments

    NASA Astrophysics Data System (ADS)

    Zamir, Anna; Endrizzi, Marco; Hagen, Charlotte K.; Vittoria, Fabio A.; Urbani, Luca; de Coppi, Paolo; Olivo, Alessandro

    2016-08-01

    Edge illumination x-ray phase contrast tomography is a recently developed imaging technique which enables three-dimensional visualisation of low-absorbing materials. Dedicated phase retrieval algorithms can provide separate computed tomography (CT) maps of sample absorption, refraction and scattering properties. In this paper we propose a novel “modified local retrieval” method which is capable of accurately retrieving sample properties in a range of realistic, non-ideal imaging environments. These include system misalignment, defects in the used optical elements and system geometry variations over time due to vibrations or temperature fluctuations. System instabilities were analysed, modelled and incorporated into a simulation study. As a result, an additional modification was introduced to the retrieval procedure to account for changes in the imaging system over time, as well as local variations over the field of view. The performance of the proposed method was evaluated in comparison to a previously used “global retrieval” method by applying both approaches to experimental CT data of a rat’s heart acquired in a non-ideal environment. The use of the proposed method resulted in the removal of major artefacts, leading to a significant improvement in image quality. This method will therefore enable acquiring high-resolution, reliable CT data of large samples in realistic settings.

  9. Integrated scanning laser ophthalmoscopy and optical coherence tomography for quantitative multimodal imaging of retinal degeneration and autofluorescence

    NASA Astrophysics Data System (ADS)

    Issaei, Ali; Szczygiel, Lukasz; Hossein-Javaheri, Nima; Young, Mei; Molday, L. L.; Molday, R. S.; Sarunic, M. V.

    2011-03-01

    Scanning Laser Ophthalmoscopy (SLO) and Coherence Tomography (OCT) are complimentary retinal imaging modalities. Integration of SLO and OCT allows for both fluorescent detection and depth- resolved structural imaging of the retinal cell layers to be performed in-vivo. System customization is required to image rodents used in medical research by vision scientists. We are investigating multimodal SLO/OCT imaging of a rodent model of Stargardt's Macular Dystrophy which is characterized by retinal degeneration and accumulation of toxic autofluorescent lipofuscin deposits. Our new findings demonstrate the ability to track fundus autofluorescence and retinal degeneration concurrently.

  10. Solid-phase extraction and liquid chromatographic quantitation of quinfamide in biological samples.

    PubMed

    Morales, J M; Jung, C H; Alarcón, A; Barreda, A

    2000-09-15

    This paper describes a high-performance liquid chromatographic method for the assay of quinfamide and its main metabolite, 1-(dichloroacetyl)-1,2,3,4,-tetrahydro-6-quinolinol, in plasma, urine and feces. It requires 1 ml of biological fluid, an extraction using Sep-Pack cartridges and acetonitrile for drug elution. Analysis was performed on a CN column (5 microm) using water-acetonitrile-methanol (40:50:10) as a mobile phase at 269 nm. Results showed that the assay was linear in the range between 0.08 and 2.0 microg/ml. The limit of quantitation was 0.08 microg/ml. Maximum assay coefficient of variation was 14%. Recovery obtained in plasma, urine and feces ranged from 82% to 98%.

  11. Reverse Phase Protein Arrays—Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use

    PubMed Central

    Boellner, Stefanie; Becker, Karl-Friedrich

    2015-01-01

    Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed. PMID:27600215

  12. Single-Shot Smartphone-Based Quantitative Phase Imaging Using a Distorted Grating

    PubMed Central

    Yang, Zhenyu; Zhan, Qiwen

    2016-01-01

    Blood testing has been used as an essential tool to diagnose diseases for decades. Recently, there has been a rapid developing trend in using Quantitative Phase Imaging (QPI) methods for blood cell screening. Compared to traditional blood testing techniques, QPI has the advantage of avoiding dyeing or staining the specimen, which may cause damage to the cells. However, most existing systems are bulky and costly, requiring experienced personnel to operate. This work demonstrates the integration of one QPI method onto a smartphone platform and the application of imaging red blood cells. The adopted QPI method is based on solving the Intensity Transport Equation (ITE) from two de-focused pupil images taken in one shot by the smartphone camera. The device demonstrates a system resolution of about 1 μm, and is ready to be used for 3D morphological study of red blood cells. PMID:27441837

  13. Reverse Phase Protein Arrays—Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use

    PubMed Central

    Boellner, Stefanie; Becker, Karl-Friedrich

    2015-01-01

    Reverse Phase Protein Arrays (RPPA) represent a very promising sensitive and precise high-throughput technology for the quantitative measurement of hundreds of signaling proteins in biological and clinical samples. This array format allows quantification of one protein or phosphoprotein in multiple samples under the same experimental conditions at the same time. Moreover, it is suited for signal transduction profiling of small numbers of cultured cells or cells isolated from human biopsies, including formalin fixed and paraffin embedded (FFPE) tissues. Owing to the much easier sample preparation, as compared to mass spectrometry based technologies, and the extraordinary sensitivity for the detection of low-abundance signaling proteins over a large linear range, RPPA have the potential for characterization of deregulated interconnecting protein pathways and networks in limited amounts of sample material in clinical routine settings. Current aspects of RPPA technology, including dilution curves, spotting, controls, signal detection, antibody validation, and calculation of protein levels are addressed.

  14. Single-Shot Smartphone-Based Quantitative Phase Imaging Using a Distorted Grating.

    PubMed

    Yang, Zhenyu; Zhan, Qiwen

    2016-01-01

    Blood testing has been used as an essential tool to diagnose diseases for decades. Recently, there has been a rapid developing trend in using Quantitative Phase Imaging (QPI) methods for blood cell screening. Compared to traditional blood testing techniques, QPI has the advantage of avoiding dyeing or staining the specimen, which may cause damage to the cells. However, most existing systems are bulky and costly, requiring experienced personnel to operate. This work demonstrates the integration of one QPI method onto a smartphone platform and the application of imaging red blood cells. The adopted QPI method is based on solving the Intensity Transport Equation (ITE) from two de-focused pupil images taken in one shot by the smartphone camera. The device demonstrates a system resolution of about 1 μm, and is ready to be used for 3D morphological study of red blood cells.

  15. Quantitative, comparable coherent anti-Stokes Raman scattering (CARS) spectroscopy: correcting errors in phase retrieval

    NASA Astrophysics Data System (ADS)

    Camp, Charles H., Jr.; Lee, Young Jong; Cicerone, Marcus T.

    2016-04-01

    Coherent anti-Stokes Raman scattering (CARS) microspectroscopy has demonstrated significant potential for biological and materials imaging. To date, however, the primary mechanism of disseminating CARS spectroscopic information is through pseudocolor imagery, which explicitly neglects a vast majority of the hyperspectral data. Furthermore, current paradigms in CARS spectral processing do not lend themselves to quantitative sample-to-sample comparability. The primary limitation stems from the need to accurately measure the so-called nonresonant background (NRB) that is used to extract the chemically-sensitive Raman information from the raw spectra. Measurement of the NRB on a pixel-by-pixel basis is a nontrivial task; thus, reference NRB from glass or water are typically utilized, resulting in error between the actual and estimated amplitude and phase. In this manuscript, we present a new methodology for extracting the Raman spectral features that significantly suppresses these errors through phase detrending and scaling. Classic methods of error-correction, such as baseline detrending, are demonstrated to be inaccurate and to simply mask the underlying errors. The theoretical justification is presented by re-developing the theory of phase retrieval via the Kramers-Kronig relation, and we demonstrate that these results are also applicable to maximum entropy method-based phase retrieval. This new error-correction approach is experimentally applied to glycerol spectra and tissue images, demonstrating marked consistency between spectra obtained using different NRB estimates, and between spectra obtained on different instruments. Additionally, in order to facilitate implementation of these approaches, we have made many of the tools described herein available free for download.

  16. Accuracy in Rietveld quantitative phase analysis: a comparative study of strictly monochromatic Mo and Cu radiations

    PubMed Central

    León-Reina, L.; García-Maté, M.; Álvarez-Pinazo, G.; Santacruz, I.; Vallcorba, O.; De la Torre, A. G.; Aranda, M. A. G.

    2016-01-01

    This study reports 78 Rietveld quantitative phase analyses using Cu Kα1, Mo Kα1 and synchrotron radiations. Synchrotron powder diffraction has been used to validate the most challenging analyses. From the results for three series with increasing contents of an analyte (an inorganic crystalline phase, an organic crystalline phase and a glass), it is inferred that Rietveld analyses from high-energy Mo Kα1 radiation have slightly better accuracies than those obtained from Cu Kα1 radiation. This behaviour has been established from the results of the calibration graphics obtained through the spiking method and also from Kullback–Leibler distance statistic studies. This outcome is explained, in spite of the lower diffraction power for Mo radiation when compared to Cu radiation, as arising because of the larger volume tested with Mo and also because higher energy allows one to record patterns with fewer systematic errors. The limit of detection (LoD) and limit of quantification (LoQ) have also been established for the studied series. For similar recording times, the LoDs in Cu patterns, ∼0.2 wt%, are slightly lower than those derived from Mo patterns, ∼0.3 wt%. The LoQ for a well crystallized inorganic phase using laboratory powder diffraction was established to be close to 0.10 wt% in stable fits with good precision. However, the accuracy of these analyses was poor with relative errors near to 100%. Only contents higher than 1.0 wt% yielded analyses with relative errors lower than 20%. PMID:27275132

  17. High-speed line-scanning confocal holographic microscopy for quantitative phase imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Liu, Changgeng; Knitter, Sebastian; Cong, Zhilong; Sencan, Ikbal; Cao, Hui; Choma, Michael A.

    2016-03-01

    We present a high speed, phase-sensitive, line-scanning reflectance confocal interference microscope. We achieved rapid confocal imaging using a fast line-scan camera and quantitative phase imaging using off-axis digital holography on a 1D, line-by-line basis. In our prototype system, a He-Ne laser (~1.2 mW) was used to demonstrate the principle of operation. Using a 20 kHz line scan rate (1024 pixels per line scan), we achieved a video-rate frame rate of 20 Hz for 1024x500 pixel en-face confocal images (20 MHz total pixel rate). By using an objective lens of a NA 0.65, we achieved an axial and lateral resolution of ~3.5 micrometers and ~0.8 micrometers, respectively. By z-stack imaging of a custom silicon target with a stepped structure, we confirmed that the axial sectioning of the interference microscope is similar to that of a traditional line-scan confocal microscope (our microscope with the reference arm blocked). The utility of phase-sensitive holographic detection in line-scan confocal was demonstrated in two ways. First, using a custom axial height phantom fabricated using chrome deposition, we demonstrated variations in phase corresponding to heights in the 100 nm range with a contrast-to-noise ratio of ~31 dB. Second, we demonstrate digital refocusing of an out-of-focus holographic image. The mechanism of confocality in our line-scan system is 1D physical pinholing. Our ongoing work aims to add an additional mechanism of confocality by using low spatial coherence sources to impose interferometric pinholing.

  18. Accuracy and precision of reconstruction of complex refractive index in near-field single-distance propagation-based phase-contrast tomography

    NASA Astrophysics Data System (ADS)

    Gureyev, Timur; Mohammadi, Sara; Nesterets, Yakov; Dullin, Christian; Tromba, Giuliana

    2013-10-01

    We investigate the quantitative accuracy and noise sensitivity of reconstruction of the 3D distribution of complex refractive index, n(r)=1-δ(r)+iβ(r), in samples containing materials with different refractive indices using propagation-based phase-contrast computed tomography (PB-CT). Our present study is limited to the case of parallel-beam geometry with monochromatic synchrotron radiation, but can be readily extended to cone-beam CT and partially coherent polychromatic X-rays at least in the case of weakly absorbing samples. We demonstrate that, except for regions near the interfaces between distinct materials, the distribution of imaginary part of the refractive index, β(r), can be accurately reconstructed from a single projection image per view angle using phase retrieval based on the so-called homogeneous version of the Transport of Intensity equation (TIE-Hom) in combination with conventional CT reconstruction. In contrast, the accuracy of reconstruction of δ(r) depends strongly on the choice of the "regularization" parameter in TIE-Hom. We demonstrate by means of an instructive example that for some multi-material samples, a direct application of the TIE-Hom method in PB-CT produces qualitatively incorrect results for δ(r), which can be rectified either by collecting additional projection images at each view angle, or by utilising suitable a priori information about the sample. As a separate observation, we also show that, in agreement with previous reports, it is possible to significantly improve signal-to-noise ratio by increasing the sample-to-detector distance in combination with TIE-Hom phase retrieval in PB-CT compared to conventional ("contact") CT, with the maximum achievable gain of the order of 0.3δ /β. This can lead to improved image quality and/or reduction of the X-ray dose delivered to patients in medical imaging.

  19. In vivoimaging of human vasculature in the chorioretinal complex using phase-variance contrast method with phase-stabilized 1 - μ m swept-source optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Poddar, Raju; Kim, Dae Yu; Werner, John S.; Zawadzki, Robert J.

    2014-12-01

    We present a noninvasive phase-variance (pv)-based motion contrast method for depth-resolved imaging of the human chorioretinal complex microcirculation with a newly developed phase-stabilized high speed (100-kHz A-scans/s) 1-μm swept-source optical coherence tomography (SSOCT) system. Compared to our previous spectral-domain (spectrometer based) pv-spectral domain OCT (SDOCT) system, this system has the advantages of higher sensitivity, reduced fringe wash-out for high blood flow speeds and deeper penetration in choroid. High phase stability SSOCT imaging was achieved by using a computationally efficient phase stabilization approach. This process does not require additional calibration hardware and complex numerical procedures. Our phase stabilization method is simple and can be employed in a variety of SSOCT systems. Examples of vasculature in the chorioretinal complex imaged by pv-SSOCT from normal as well as diseased eyes are presented and compared to retinal images of the same subjects acquired with fluorescein angiography and indocyanine green angiography. Observations of morphology of vascular perfusion in chorioretinal complex visualized by our method are listed.

  20. A method for volume determination of the orbit and its contents by high resolution axial tomography and quantitative digital image analysis.

    PubMed Central

    Cooper, W C

    1985-01-01

    The various congenital and acquired conditions which alter orbital volume are reviewed. Previous investigative work to determine orbital capacity is summarized. Since these studies were confined to postmortem evaluations, the need for a technique to measure orbital volume in the living state is presented. A method for volume determination of the orbit and its contents by high-resolution axial tomography and quantitative digital image analysis is reported. This procedure has proven to be accurate (the discrepancy between direct and computed measurements ranged from 0.2% to 4%) and reproducible (greater than 98%). The application of this method to representative clinical problems is presented and discussed. The establishment of a diagnostic system versatile enough to expand the usefulness of computerized axial tomography and polytomography should add a new dimension to ophthalmic investigation and treatment. Images FIGURE 8 FIGURE 9 FIGURE 10 A FIGURE 10 B FIGURE 11 A FIGURE 11 B FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 FIGURE 17 FIGURE 18 FIGURE 19 FIGURE 20 FIGURE 21 FIGURE 22 FIGURE 23 FIGURE 24 FIGURE 25 FIGURE 26 A FIGURE 26 B FIGURE 27 FIGURE 28 FIGURE 29 FIGURE 30 FIGURE 31 FIGURE 32 PMID:3938582

  1. Nondestructive and quantitative characterization of TRU and LLW mixed-waste using active and passive gamma-ray spectrometry and computed tomography

    SciTech Connect

    Camp, D.C.; Martz, H.E.

    1991-11-12

    The technology being proposed by LLNL is an Active and Passive Computed Tomography (A P CT) Drum Scanner for contact-handled (CH) wastes. It combines the advantages offered by two well-developed nondestructive assay technologies: gamma-ray spectrometry and computed tomography (CT). Coupled together, these two technologies offer to nondestructively and quantitatively characterize mixed- wastes forms. Gamma-ray spectroscopy uses one or more external radiation detectors to passively and nondestructively measure the energy spectrum emitted from a closed container. From the resulting spectrum one can identify most radioactivities detected, be they transuranic isotopes, mixed-fission products, activation products or environmental radioactivities. Spectral libraries exist at LLNL for all four. Active (A) or transmission CT is a well-developed, nondestructive medical and industrial technique that uses an external-radiation beam to map regions of varying attenuation within a container. Passive (P) or emission CT is a technique mainly developed for medical application, e.g., single-photon emission CT. Nondestructive industrial uses of PCT are under development and just coming into use. This report discuses work on the A P CT Drum Scanner at LLNL.

  2. Peripheral quantitative computed tomography-derived muscle density and peripheral magnetic resonance imaging-derived muscle adiposity: precision and associations with fragility fractures in women

    PubMed Central

    Wong, A.K.O.; Beattie, K.A.; Min, K.K.H.; Gordon, C.; Pickard, L.; Papaioannou, A.; Adachi, J.D.

    2016-01-01

    Purpose To determine the degree to which muscle density and fractures are explained by inter and intramuscular fat (IMF). Methods Women ≥50 years of age (Hamilton, ON, Canada) had peripheral magnetic resonance imaging and peripheral quantitative computed tomography scans at 66% of the tibial length. Muscle on computed tomography images was segmented from subcutaneous fat and bone using fixed thresholds, computing muscle density. IMF was segmented from muscle within magnetic resonance images using a region-growing algorithm, computing IMF volume. Fracture history over the last 14 years was obtained. Odds ratios for fractures were determined for muscle density, adjusting for IMF volume, total hip BMD, age and body mass index. Results Women with a history of fractures were older (N=32, age:75.6±8.3 years) than those without (N=39, age: 67.0±5.2 years) (<0.01). IMF volume explained 49.3% of variance in muscle density (p<0.001). Odds for fractures were associated with lower muscle density even after adjusting for IMF volume but were attenuated after adjusting for age. Conclusions Muscle adiposity represents only 50% of the muscle density measurement. Properties of muscle beyond its adiposity may be related to fractures, but larger and prospective studies are needed to confirm these associations. PMID:25524965

  3. Effect of nitroglycerin on coronary collateral function during exercise evaluated by quantitative analysis of thallium-201 single photon emission computed tomography

    SciTech Connect

    Aoki, M.; Sakai, K.; Koyanagi, S.; Takeshita, A.; Nakamura, M. )

    1991-05-01

    A noninfarcted, entirely collateral-dependent myocardial region provides an opportunity to assess the effect of nitroglycerin on coronary collateral function during exercise. Stress thallium-201 computed tomography was performed in seven patients with effort angina and no history of myocardial infarction, both before and after nitroglycerin (0.3 mg). All patients had single-vessel disease with total or subtotal (99% with delay) occlusion of proximal left anterior descending coronary artery and well-developed collaterals. The pressure-rate product, mean blood pressure, and heart rate at peak exercise did not differ before and after nitroglycerin. The size of the perfusion defect and the severity of ischemia during exercise estimated by quantitative analysis of thallium-201 single photon emission computed tomography were significantly less after nitroglycerin administration (extent score: 23 +/- 17 vs 7 +/- 9, p less than 0.01; severity score: 20 +/- 22 vs 3 +/- 4, p less than 0.05). The pressure-rate products at peak exercise did not differ before and after nitroglycerin, which suggested that the reduction in perfusion defect size was unlikely to be the result of decreased myocardial oxygen consumption. These results suggest that nitroglycerin improved coronary collateral function during exercise and thus prevented exercise-induced myocardial ischemia.

  4. Effects of propranolol and nifedipine on exercise-induced attack in patients variant angina: assessment by exercise thallium-201 myocardial scintigraphy with quantitative rotational tomography

    SciTech Connect

    Kugiyama, K.; Yasue, H.; Horio, Y.; Morikami, Y.; Fujii, H.; Koga, Y.; Kojima, A.; Takahashi, M.

    1986-08-01

    To examine the effects of propranolol and nifedipine on exercise-induced attack in patients with variant angina, exercise /sup 201/Tl myocardial scintigraphy with quantitative analysis by emission-computed tomography was performed in 20 patients with variant angina after oral propranolol (80 mg), nifedipine (20 mg), and placebo. Exercise-induced attack occurred in 11 patients on placebo, in 14 on propranolol, and in none on nifedipine. The exercise duration was significantly shorter in those on propranolol (p less than .05), but significantly longer in patients on nifedipine (p less than .05) than in those on placebo. The peak rate-pressure product was significantly lower in patients on propranolol (p less than .01), but did not change in those on nifedipine, as compared with that in patients on placebo. The size of the perfusion defect as measured by /sup 201/Tl tomography was significantly greater in patients on propranolol (p less than .05), but significantly less in those on nifedipine (p less than .01) than in those on placebo. In conclusion, propranolol does not suppress but rather may aggravate exercise-induced attack in patients with variant angina, while nifedipine suppresses it. This unfavorable effect of propranolol on exercise-induced attack in patients with variant angina is likely to be due to a reduction of regional myocardial blood flow.

  5. Quantitative comparison of contrast and imaging depth of ultrahigh-resolution optical coherence tomography images in 800–1700 nm wavelength region

    PubMed Central

    Ishida, Shutaro; Nishizawa, Norihiko

    2012-01-01

    We investigated the wavelength dependence of imaging depth and clearness of structure in ultrahigh-resolution optical coherence tomography over a wide wavelength range. We quantitatively compared the optical properties of samples using supercontinuum sources at five wavelengths, 800 nm, 1060 nm, 1300 nm, 1550 nm, and 1700 nm, with the same system architecture. For samples of industrially used homogeneous materials with low water absorption, the attenuation coefficients of the samples were fitted using Rayleigh scattering theory. We confirmed that the systems with the longer-wavelength sources had lower scattering coefficients and less dependence on the sample materials. For a biomedical sample, we observed wavelength dependence of the attenuation coefficient, which can be explained by absorption by water and hemoglobin. PMID:22312581

  6. X–ray absorption, phase and dark–field tomography through a beam tracking approach