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Sample records for cellular resolution volumetric

  1. Cellular resolution volumetric in vivo retinal imaging with adaptive optics–optical coherence tomography◊

    PubMed Central

    Zawadzki, Robert J.; Choi, Stacey S.; Fuller, Alfred R.; Evans, Julia W.; Hamann, Bernd; Werner, John S.

    2009-01-01

    Ultrahigh-resolution adaptive optics–optical coherence tomography (UHR-AO-OCT) instrumentation allowing monochromatic and chromatic aberration correction was used for volumetric in vivo retinal imaging of various retinal structures including the macula and optic nerve head (ONH). Novel visualization methods that simplify AO-OCT data viewing are presented, and include co-registration of AO-OCT volumes with fundus photography and stitching of multiple AO-OCT sub-volumes to create a large field of view (FOV) high-resolution volume. Additionally, we explored the utility of Interactive Science Publishing by linking all presented AO-OCT datasets with the OSA ISP software. PMID:19259248

  2. A model for the volumetric radiation characteristics of cellular ceramics

    SciTech Connect

    Fu, X.; Viskanta, R.; Gore, J.P.

    1997-12-01

    A unit cell based model for cellular ceramics was developed in conjunction with the discrete ordinates method for radiative transfer to predict theoretically the effective volumetric radiation characteristics of the cellular ceramics. Model input parameters include the porosity, pores per centimeter (PPC) and reflectivity of the solid material. Numerical calculations of the extinction coefficients and single scattering albedo are reported over the range of reflectivities from 0 to 1, porosities from 0.6 to 0.95 and PPC from 4 to 26. A comparison between model predictions and spectral emittance data for cellular ceramics reported in the literature shows agreement within 5 to 10% which is within experimental uncertainty.

  3. Computed optical interferometric tomography for high-speed volumetric cellular imaging

    PubMed Central

    Liu, Yuan-Zhi; Shemonski, Nathan D.; Adie, Steven G.; Ahmad, Adeel; Bower, Andrew J.; Carney, P. Scott; Boppart, Stephen A.

    2014-01-01

    Three-dimensional high-resolution imaging methods are important for cellular-level research. Optical coherence microscopy (OCM) is a low-coherence-based interferometry technology for cellular imaging with both high axial and lateral resolution. Using a high-numerical-aperture objective, OCM normally has a shallow depth of field and requires scanning the focus through the entire region of interest to perform volumetric imaging. With a higher-numerical-aperture objective, the image quality of OCM is affected by and more sensitive to aberrations. Interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) are computed imaging techniques that overcome the depth-of-field limitation and the effect of optical aberrations in optical coherence tomography (OCT), respectively. In this work we combine OCM with ISAM and CAO to achieve high-speed volumetric cellular imaging. Experimental imaging results of ex vivo human breast tissue, ex vivo mouse brain tissue, in vitro fibroblast cells in 3D scaffolds, and in vivo human skin demonstrate the significant potential of this technique for high-speed volumetric cellular imaging. PMID:25401012

  4. Computed optical interferometric tomography for high-speed volumetric cellular imaging.

    PubMed

    Liu, Yuan-Zhi; Shemonski, Nathan D; Adie, Steven G; Ahmad, Adeel; Bower, Andrew J; Carney, P Scott; Boppart, Stephen A

    2014-09-01

    Three-dimensional high-resolution imaging methods are important for cellular-level research. Optical coherence microscopy (OCM) is a low-coherence-based interferometry technology for cellular imaging with both high axial and lateral resolution. Using a high-numerical-aperture objective, OCM normally has a shallow depth of field and requires scanning the focus through the entire region of interest to perform volumetric imaging. With a higher-numerical-aperture objective, the image quality of OCM is affected by and more sensitive to aberrations. Interferometric synthetic aperture microscopy (ISAM) and computational adaptive optics (CAO) are computed imaging techniques that overcome the depth-of-field limitation and the effect of optical aberrations in optical coherence tomography (OCT), respectively. In this work we combine OCM with ISAM and CAO to achieve high-speed volumetric cellular imaging. Experimental imaging results of ex vivo human breast tissue, ex vivo mouse brain tissue, in vitro fibroblast cells in 3D scaffolds, and in vivo human skin demonstrate the significant potential of this technique for high-speed volumetric cellular imaging. PMID:25401012

  5. Resolution and noise trade-off analysis for volumetric CT

    SciTech Connect

    Li Baojun; Avinash, Gopal B.; Hsieh, Jiang

    2007-10-15

    Until recently, most studies addressing the trade-off between spatial resolution and quantum noise were performed in the context of single-slice CT. In this study, we extend the theoretical framework of previous works to volumetric CT and further extend it by taking into account the actual shapes of the preferred reconstruction kernels. In the experimental study, we also attempt to explore a three-dimensional approach for spatial resolution measurement, as opposed to the conventional two-dimensional approaches that were widely adopted in previously published studies. By scanning a finite-sized sphere phantom, the MTF was measured from the edge profile along the spherical surface. Cases of different resolutions (and noise levels) were generated by adjusting the reconstruction kernel. To reduce bias, the total photon fluxes were matched: 120 kVp, 200 mA, and 1 s per gantry rotation. All data sets were reconstructed using a modified FDK algorithm under the same condition: Scan field-of-view (SFOV)=10 cm, and slice thickness=0.625 mm. The theoretical analysis indicated that the variance of noise is proportional to >4th power of the spatial resolution. Our experimental results supported this conclusion by showing the relationship is 4.6th (helical) or 5th (axial) power.

  6. A low-resolution 3D holographic volumetric display

    NASA Astrophysics Data System (ADS)

    Khan, Javid; Underwood, Ian; Greenaway, Alan; Halonen, Mikko

    2010-05-01

    A simple low resolution volumetric display is presented, based on holographic volume-segments. The display system comprises a proprietary holographic screen, laser projector, associated optics plus a control unit. The holographic screen resembles a sheet of frosted glass about A4 in size (20x30cm). The holographic screen is rear-illuminated by the laser projector, which is in turn driven by the controller, to produce simple 3D images that appear outside the plane of the screen. A series of spatially multiplexed and interleaved interference patterns are pre-encoded across the surface of the holographic screen. Each illumination pattern is capable of reconstructing a single holographic volume-segment. Up to nine holograms are multiplexed on the holographic screen in a variety of configurations including a series of numeric and segmented digits. The demonstrator has good results under laboratory conditions with moving colour 3D images in front of or behind the holographic screen.

  7. In vivo volumetric imaging of chicken retina with ultrahigh-resolution spectral domain optical coherence tomography

    PubMed Central

    Moayed, Alireza Akhlagh; Hariri, Sepideh; Song, Eun Sun; Choh, Vivian; Bizheva, Kostadinka

    2011-01-01

    The chicken retina is an established animal model for myopia and light-associated growth studies. It has a unique morphology: it is afoveate and avascular; oxygen and nutrition to the inner retina is delivered by a vascular tissue (pecten) that protrudes into the vitreous. Here we present, to the best of our knowledge, the first in vivo, volumetric high-resolution images of the chicken retina. Images were acquired with an ultrahigh-resolution optical coherence tomography (UHROCT) system with 3.5 µm axial resolution in the retina, at the rate of 47,000 A-scans/s. Spatial variations in the thickness of the nerve fiber and ganglion cell layers were mapped by segmenting and measuring the layer thickness with a semi-automatic segmentation algorithm. Volumetric visualization of the morphology and morphometric analysis of the chicken retina could aid significantly studies with chicken retinal models of ophthalmic diseases. PMID:21559138

  8. 3D surface reconstruction and visualization of the Drosophila wing imaginal disc at cellular resolution

    NASA Astrophysics Data System (ADS)

    Bai, Linge; Widmann, Thomas; Jülicher, Frank; Dahmann, Christian; Breen, David

    2013-01-01

    Quantifying and visualizing the shape of developing biological tissues provide information about the morphogenetic processes in multicellular organisms. The size and shape of biological tissues depend on the number, size, shape, and arrangement of the constituting cells. To better understand the mechanisms that guide tissues into their final shape, it is important to investigate the cellular arrangement within tissues. Here we present a data processing pipeline to generate 3D volumetric surface models of epithelial tissues, as well as geometric descriptions of the tissues' apical cell cross-sections. The data processing pipeline includes image acquisition, editing, processing and analysis, 2D cell mesh generation, 3D contourbased surface reconstruction, cell mesh projection, followed by geometric calculations and color-based visualization of morphological parameters. In their first utilization we have applied these procedures to construct a 3D volumetric surface model at cellular resolution of the wing imaginal disc of Drosophila melanogaster. The ultimate goal of the reported effort is to produce tools for the creation of detailed 3D geometric models of the individual cells in epithelial tissues. To date, 3D volumetric surface models of the whole wing imaginal disc have been created, and the apicolateral cell boundaries have been identified, allowing for the calculation and visualization of cell parameters, e.g. apical cross-sectional area of cells. The calculation and visualization of morphological parameters show position-dependent patterns of cell shape in the wing imaginal disc. Our procedures should offer a general data processing pipeline for the construction of 3D volumetric surface models of a wide variety of epithelial tissues.

  9. The spatial resolution of dual-tracer fluorescence thermometry in volumetrically illuminated channels

    NASA Astrophysics Data System (ADS)

    Kim, Myeongsub; Yoda, Minami

    2014-01-01

    This study estimates the spatial resolution and accuracy of dual-tracer fluorescence thermometry (DFT) for measuring water temperature fields in channels where the entire channel is illuminated as is typical in microfluidics. Temperature fields are measured in heated laminar Poiseuille flow through a 1 mm2 channel. The working fluid, an aqueous solution of the temperature-sensitive fluorophores fluorescein (Fl) and sulforhodamine B (SrB), is volumetrically illuminated over the entire channel cross-section at a wavelength of 514 nm, and the temperature of the solution is estimated from images of the longer-wavelength fluorescence from Fl and SrB. These temperature data are compared with numerical simulations of the same flow where the heat transferred to the water is estimated from independent measurements of wall surface temperature to determine the accuracy and the spatial resolution of the DFT results. The results suggest that temperature measurements in the volumetrically illuminated channel are significantly corrupted by the fluorescence emissions from beyond the focal plane. A model based on the point spread function for an aberration-free lens is employed to estimate the effect of the background "noise," i.e., the signal from beyond the object plane, on the accuracy of these DFT measurements. The results show that this background is about 30 times the signal from the focal plane. Further experiments where the channel is illuminated by a light sheet over about 40 % of the channel cross-section give estimates of the water temperature field that are on average within about 0.3 °C of the numerical predictions at an in-plane spatial resolution of 50 μm. The model is used to estimate the signal-to-background ratio for this case, as well as for a variety of commercially available microscope objectives.

  10. Computed tomography part 3: Volumetric, high-resolution x-ray analysis of fatigue crack closure

    NASA Astrophysics Data System (ADS)

    Stock, S. R.; Guvenilir, A.; Breunig, T. M.; Kinney, J. H.; Nichols, M. C.

    1995-01-01

    The study described illustrates how extremely high-resolution volumetric x-ray computed tomography can be applied to a materials problem. The work also gives an example of what choices must be made to tailor an experiment to the capabilities of a computed tomography system. Tomography is used to reconstruct the volume of material enclosing a fatigue crack in Al-Li2090. From the reconstructed volume, the separations of crack faces are quantified as a function of position within the sample, and, through use of a small load frame designed for use in computed tomography, the changing physical crack closure is measured as a function of applied load. In other words, the rate and amounts of physical crack closure are measured at different points of the unloading portion of a fatigue cycle.

  11. Utility of Early Post-operative High Resolution Volumetric MR Imaging after Transsphenoidal Pituitary Tumor Surgery

    PubMed Central

    Patel, Kunal S.; Kazam, Jacob; Tsiouris, Apostolos J.; Anand, Vijay K.; Schwartz, Theodore H.

    2014-01-01

    Objective Controversy exists over the utility of early post-operative magnetic resonance imaging (MRI) after transsphenoidal pituitary surgery for macroadenomas. We investigate whether valuable information can be derived from current higher resolution scans. Methods Volumetric MRI scans were obtained in the early (<10 days) and late (>30 days) post-operative periods in a series of patients undergoing transsphenoidal pituitary surgery. The volume of the residual tumor, resection cavity, and corresponding visual field tests were recorded at each time point. Statistical analyses of changes in tumor volume and cavity size were calculated using the late MRI as the gold standard. Results 40 patients met the inclusion criteria. Pre-operative tumor volume averaged 8.8 cm3. Early postoperative assessment of average residual tumor volume (1.18 cm3) was quite accurate and did not differ statistically from late post-operative volume (1.23 cm3, p=.64), indicating the utility of early scans to measure residual tumor. Early scans were 100% sensitive and 91% specific for predicting ≥ 98% resection (p<.001, Fisher’s exact test). The average percent decrease in cavity volume from pre-operative MRI (tumor volume) to early post-operative imaging was 45% with decreases in all but 3 patients. There was no correlation between the size of the early cavity and the visual outcome. Conclusions Early high resolution volumetric MRI is valuable in determining the presence or absence of residual tumor. Cavity volume almost always decreases after surgery and a lack of decrease should alert the surgeon to possible persistent compression of the optic apparatus that may warrant re-operation. PMID:25045791

  12. In vivo volumetric imaging of the human upper eyelid with ultrahigh-resolution optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Bizheva, Kostadinka; Lee, Patrick; Sorbara, Luigina; Hutchings, Natalie; Simpson, Trefford

    2010-07-01

    The upper eyelid is a biological tissue with complex structure, essential for the maintenance of an optically clear ocular surface due to its physical (blinking) effect. The Meibomian glands (MGs) are structures that lie beneath the surface of the inner eyelid and are partially responsible for the production of the superficial oily layer of the tear film. The MGs are only superficially visible under magnification when the eyelid is everted. We present for the first time in vivo 3-D images of healthy and inflamed human MGs. Tomograms were acquired from the tarsal plate of everted human eyelids with a 1060-nm ultrahigh-resolution optical coherence tomography (UHOCT) system, with ~3 μm×10 μm (axial×lateral) resolution in biological tissue at the rate of 91,911 A-scans/s. Comparison with histology shows that the UHOCT images reveal a spatial distribution of structures that appear to correspond with the MGs' acini and ducts (in healthy subjects), and accumulation of heterogeneous, highly scattering biological material and clear fluids in the visibly blocked glands. Noninvasive, volumetric high-resolution morphological imaging of the human tarsal area could have a significant impact in the clinical diagnosis of inflammatory and noninflammatory lid pathologies.

  13. Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans.

    PubMed

    Nguyen, Jeffrey P; Shipley, Frederick B; Linder, Ashley N; Plummer, George S; Liu, Mochi; Setru, Sagar U; Shaevitz, Joshua W; Leifer, Andrew M

    2016-02-23

    The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. We present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal's position, posture, and locomotion. This instrument provides whole-brain imaging with cellular resolution in an unrestrained and behaving animal. We use spinning-disk confocal microscopy to capture 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s at 6 head-volumes/s. A suite of three cameras monitor neuronal fluorescence and the animal's position and orientation. Custom software tracks the 3D position of the animal's head in real time and two feedback loops adjust a motorized stage and objective to keep the animal's head within the field of view as the animal roams freely. We observe calcium transients from up to 77 neurons for over 4 min and correlate this activity with the animal's behavior. We characterize noise in the system due to animal motion and show that, across worms, multiple neurons show significant correlations with modes of behavior corresponding to forward, backward, and turning locomotion. PMID:26712014

  14. Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

    PubMed Central

    Nguyen, Jeffrey P.; Shipley, Frederick B.; Linder, Ashley N.; Plummer, George S.; Liu, Mochi; Setru, Sagar U.; Shaevitz, Joshua W.

    2016-01-01

    The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. We present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal’s position, posture, and locomotion. This instrument provides whole-brain imaging with cellular resolution in an unrestrained and behaving animal. We use spinning-disk confocal microscopy to capture 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s at 6 head-volumes/s. A suite of three cameras monitor neuronal fluorescence and the animal’s position and orientation. Custom software tracks the 3D position of the animal’s head in real time and two feedback loops adjust a motorized stage and objective to keep the animal’s head within the field of view as the animal roams freely. We observe calcium transients from up to 77 neurons for over 4 min and correlate this activity with the animal’s behavior. We characterize noise in the system due to animal motion and show that, across worms, multiple neurons show significant correlations with modes of behavior corresponding to forward, backward, and turning locomotion. PMID:26712014

  15. Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution.

    PubMed

    Sylwestrak, Emily Lauren; Rajasethupathy, Priyamvada; Wright, Matthew Arnot; Jaffe, Anna; Deisseroth, Karl

    2016-02-11

    In recently developed approaches for high-resolution imaging within intact tissue, molecular characterization over large volumes has been largely restricted to labeling of proteins. But volumetric nucleic acid labeling may represent a far greater scientific and clinical opportunity, enabling detection of not only diverse coding RNA variants but also non-coding RNAs. Moreover, scaling immunohistochemical detection to large tissue volumes has limitations due to high cost, limited renewability/availability, and restricted multiplexing capability of antibody labels. With the goal of versatile, high-content, and scalable molecular phenotyping of intact tissues, we developed a method using carbodiimide-based chemistry to stably retain RNAs in clarified tissue, coupled with amplification tools for multiplexed detection. The resulting technology enables robust measurement of activity-dependent transcriptional signatures, cell-identity markers, and diverse non-coding RNAs in rodent and human tissue volumes. The growing set of validated probes is deposited in an online resource for nucleating related developments from across the scientific community. PMID:26871636

  16. VolRoverN: Enhancing surface and volumetric reconstruction for realistic dynamical simulation of cellular and subcellular function

    PubMed Central

    Edwards, John; Daniel, Eric; Kinney, Justin; Bartol, Tom; Sejnowski, Terrence; Johnston, Daniel; Harris, Kristen; Bajaj, Chandrajit

    2014-01-01

    Establishing meaningful relationships between cellular structure and function requires accurate morphological reconstructions. In particular, there is an unmet need for high quality surface reconstructions to model subcellular and synaptic interactions among neurons at nanometer resolution. We address this need with VolRoverN, a software package that produces accurate, efficient, and automated 3D surface reconstructions from stacked 2D contour tracings. While many techniques and tools have been developed in the past for 3D visualization of cellular structure, the reconstructions from VolRoverN meet specific quality criteria that are important for dynamical simulations. These criteria include manifoldness, water-tightness, lack of self- and object-object-intersections, and geometric accuracy. These enhanced surface reconstructions are readily extensible to any cell type (including glia) and are used here on complex spiny dendrites and axons from mature rat hippocampal area CA1. Both spatially realistic surface reconstructions and reduced skeletonizations are produced and formatted by VolRoverN for easy input into analysis software packages for neurophysiological simulations at multiple spatial and temporal scales ranging from ion electro-diffusion to electrical cable models. PMID:24100964

  17. Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans

    NASA Astrophysics Data System (ADS)

    Nguyen, Jeffrey; Shipley, Frederick; Linder, Ashley; Plummer, George; Liu, Mochi; Setru, Sagar; Shaevitz, Joshua; Leifer, Andrew

    The ability to acquire large-scale recordings of neuronal activity in awake and unrestrained animals is needed to provide new insights into how populations of neurons generate animal behavior. Acquiring this data, however, is challenging because it is difficult to track and image individual neurons as an animal deforms its posture and moves many body lengths. Here, we present an instrument capable of recording intracellular calcium transients from the majority of neurons in the head of a freely behaving Caenorhabditis elegans with cellular resolution while simultaneously recording the animal's position, posture, and locomotion. 3D volumetric fluorescent images of neurons expressing the calcium indicator GCaMP6s are recorded at 6 head-volumes/s using spinning disk confocal microscopy. At the same time, we record low magnification images of the animal to measure the animals behavior and track its head as it moves. We develop a time independent neuronal matching algorithm that uses non-rigid point set registration and machine learning to correctly match neurons across time. Using this method, we are able to observe calcium transients from up to 90 neurons for over 4 min and correlate the neural activity with the animal's behavior.

  18. Volumetric quantification of in vitro sonothrombolysis with microbubbles using high-resolution optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Kim, Jong S.; Leeman, Jonathan E.; Kagemann, Larry; Yu, Francois T. H.; Chen, Xucai; Pacella, John J.; Schuman, Joel S.; Villanueva, Flordeliza S.; Kim, Kang

    2012-07-01

    Several in vitro and in vivo studies have established accelerated thrombolysis using ultrasound (US) induced microbubble (MB) cavitation. However, the mechanisms underlying MB mediated sonothrombolysis are still not completely elucidated. We performed three-dimensional (3-D) volumetric optical coherence tomography (OCT) imaging before and after the application of contrast US to thrombus. The most dramatic reduction in clot volume was observed with US + MB + recombinant tissue plasminogen activator (rt-PA). Thrombus surface erosion in this group on the side of the thrombus exposed to MB and ultrasound was evident on the OCT images. This technique may assist in clarifying the mechanisms underlying sonothrombolysis, especially regarding the importance of US transducer orientation on lytic efficacy and the effects of MB cavitation on thrombus structure.

  19. Automated Classification of Usual Interstitial Pneumonia using Regional Volumetric Texture Analysis in High-Resolution CT

    PubMed Central

    Depeursinge, Adrien; Chin, Anne S.; Leung, Ann N.; Terrone, Donato; Bristow, Michael; Rosen, Glenn; Rubin, Daniel L.

    2014-01-01

    Objectives We propose a novel computational approach for the automated classification of classic versus atypical usual interstitial pneumonia (UIP). Materials and Methods 33 patients with UIP were enrolled in this study. They were classified as classic versus atypical UIP by a consensus of two thoracic radiologists with more than 15 years of experience using the American Thoracic Society evidence–based guidelines for CT diagnosis of UIP. Two cardiothoracic fellows with one year of subspecialty training provided independent readings. The system is based on regional characterization of the morphological tissue properties of lung using volumetric texture analysis of multiple detector CT images. A simple digital atlas with 36 lung subregions is used to locate texture properties, from which the responses of multi-directional Riesz wavelets are obtained. Machine learning is used to aggregate and to map the regional texture attributes to a simple score that can be used to stratify patients with UIP into classic and atypical subtypes. Results We compared the predictions based on regional volumetric texture analysis with the ground truth established by expert consensus. The area under the receiver operating characteristic curve of the proposed score was estimated to be 0.81 using a leave-one-patient-out cross-validation, with high specificity for classic UIP. The performance of our automated method was found to be similar to that of the two fellows and to the agreement between experienced chest radiologists reported in the literature. However, the errors of our method and the fellows occurred on different cases, which suggests that combining human and computerized evaluations may be synergistic. Conclusions Our results are encouraging and suggest that an automated system may be useful in routine clinical practice as a diagnostic aid for identifying patients with complex lung disease such as classic UIP, obviating the need for invasive surgical lung biopsy and its

  20. Microscopic high-resolution digital volumetric imaging of human hair fibers.

    PubMed

    Gruber, J V; Kerschman, R

    2004-01-01

    Methods for examining cationic polymer deposition on hair are well known and polymers such as Polyquaternium-10 have enjoyed a significant commercial impact on shampoos and body washes as unique conditioning materials. It was recently reported that hair can be examined using a new microscopic called Digital Volumetric Imaging or DVI (10). By employing fluorescent dyes, deposition of cationic oligosaccharides onto damaged blond hair fibers was discussed. Because hair auto-fluorescences, the microscope allows for examination of hair fibers directly including viewing of the cuticle, cortex and melanin within the cortex and careful imaging even distinguishes the medulla of the hair fiber. In this paper, examination of six virgin hair types including: 1) Afro-American, 2) Asian, 3) European brown, 4) red, 5) blond and 6) gray was conducted looking for differences that each hair type brings to the visualizing technique. Digital manipulation of the fluorescent data allows for examination of interior hair fiber structures as well as the development of animated movies of three dimensional hair fiber structures. PMID:15645100

  1. Assessment of volumetric noise and resolution performance for linear and nonlinear CT reconstruction methods

    SciTech Connect

    Chen, Baiyu; Christianson, Olav; Wilson, Joshua M.; Samei, Ehsan

    2014-07-15

    Purpose: For nonlinear iterative image reconstructions (IR), the computed tomography (CT) noise and resolution properties can depend on the specific imaging conditions, such as lesion contrast and image noise level. Therefore, it is imperative to develop a reliable method to measure the noise and resolution properties under clinically relevant conditions. This study aimed to develop a robust methodology to measure the three-dimensional CT noise and resolution properties under such conditions and to provide guidelines to achieve desirable levels of accuracy and precision. Methods: The methodology was developed based on a previously reported CT image quality phantom. In this methodology, CT noise properties are measured in the uniform region of the phantom in terms of a task-based 3D noise-power spectrum (NPS{sub task}). The in-plane resolution properties are measured in terms of the task transfer function (TTF) by applying a radial edge technique to the rod inserts in the phantom. The z-direction resolution properties are measured from a supplemental phantom, also in terms of the TTF. To account for the possible nonlinearity of IR, the NPS{sub task} is measured with respect to the noise magnitude, and the TTF with respect to noise magnitude and edge contrast. To determine the accuracy and precision of the methodology, images of known noise and resolution properties were simulated. The NPS{sub task} and TTF were measured on the simulated images and compared to the truth, with criteria established to achieve NPS{sub task} and TTF measurements with <10% error. To demonstrate the utility of this methodology, measurements were performed on a commercial CT system using five dose levels, two slice thicknesses, and three reconstruction algorithms (filtered backprojection, FBP; iterative reconstruction in imaging space, IRIS; and sinogram affirmed iterative reconstruction with strengths of 5, SAFIRE5). Results: To achieve NPS{sub task} measurements with <10% error, the

  2. Accuracy and Resolution of In Vitro Imaging Based Porcine Lens Volumetric Measurements

    PubMed Central

    Wendt, Mark; Bockhorst, Kurt; He, Lin; Glasser, Adrian

    2013-01-01

    There is considerable interest in determining lens volume in the living eye. Lens volume is of interest to understand accommodative changes in the lens and to size accommodative IOLs (A-IOLs) to fit the capsular bag. Some studies have suggested lens volume change during accommodation. Magnetic Resonance Imaging (MRI) is the only method available to determine lens volume in vivo. MRI is, by its nature, relatively low in temporal and spatial resolution. Therefore analysis often requires determining lens volume from single image slices with relatively low resolution on which only simple image analysis methods can be used and without repeated measures. In this study, 7T MRI scans encompassing the full lens volume were performed on 19 enucleated pig eyes. The eyes were then dissected to isolate and photograph the lens in profile and the lens volumes were measured empirically using a fluid displacement method. Lens volumes were calculated from two- and three-dimensional (2D & 3D) MR and 2D photographic profile images of the isolated lenses using several different analysis methods. Image based and actual measured lens volumes were compared. The average image-based volume of all lenses varied from the average measured volume of all lenses by 0.6% to 6.4% depending on the image analysis method. Image analysis methods that use gradient based edge detection showed higher precision with actual volumes (r2: 0.957 to 0.990), while threshold based segmentation had poorer correlations (r2: 0.759 to 0.828). The root-mean-square (RMS) difference between image analysis based volumes and fluid displacement measured volumes ranged from 8.51 µl to 25.79 µl. This provides an estimate of the error of previously published methods used to calculate lens volume. Immobilized, enucleated porcine eyes permit improved MR image resolution relative to living eyes and therefore improved image analysis methods to calculate lens volume. The results show that some of the accommodative changes in

  3. Localization-Based Super-Resolution Imaging of Cellular Structures

    PubMed Central

    Kanchanawong, Pakorn; Waterman, Clare M.

    2013-01-01

    Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures. PMID:23868582

  4. Volumetric analysis of syringomyelia following hindbrain decompression for Chiari malformation Type I: syringomyelia resolution follows exponential kinetics

    PubMed Central

    Coumans, Jean-Valery; Walcott, Brian P.; Butler, William E.; Nahed, Brian V.; Kahle, Kristopher T.

    2013-01-01

    Object Resolution of syringomyelia is common following hindbrain decompression for Chiari malformation, yet little is known about the kinetics governing this process. The authors sought to establish the volumetric rate of syringomyelia resolution. Methods A retrospective cohort of patients undergoing hindbrain decompression for a Chiari malformation Type I with preoperative cervical or thoracic syringomyelia was identified. Patients were included in the study if they had at least 3 neuroimaging studies that detailed the entirety of their preoperative syringomyelia over a minimum of 6 months postoperatively. The authors reconstructed the MR images in 3 dimensions and calculated the volume of the syringomyelia. They plotted the syringomyelia volume over time and constructed regression models using the method of least squares. The Akaike information criterion and Bayesian information criterion were used to calculate the relative goodness of fit. The coefficients of determination R2 (unadjusted and adjusted) were calculated to describe the proportion of variability in each individual data set accounted for by the statistical model. Results Two patients were identified as meeting inclusion criteria. Plots of the least-squares best fit were identified as 4.01459e−0.0180804x and 13.2556e−0.00615859x. Decay of the syringomyelia followed an exponential model in both patients (R2 = 0.989582 and 0.948864). Conclusions Three-dimensional analysis of syringomyelia resolution over time enables the kinetics to be estimated. This technique is yet to be validated in a large cohort. Because syringomyelia is the final common pathway for a number of different pathological processes, it is possible that this exponential only applies to syringomyelia related to treatment of Chiari malformation Type I. PMID:21882909

  5. High-resolution imaging of cellular processes in Caenorhabditis elegans.

    PubMed

    Maddox, Amy S; Maddox, Paul S

    2012-01-01

    Differential interference contrast (DIC) imaging of Caenorhabditis elegans embryogenesis led to a Nobel Prize in Physiology or Medicine (Sulston et al., 1983) as did the first use of green fluorescent protein (GFP) in a transgenic C. elegans (Chalfie et al., 1994). Given that C. elegans is free living, does not require exceptional environmental control, and is optically clear, live imaging is a powerful tool in for this model system. Combining genetics with high-resolution imaging has continued to make important contributions to many fields. In this chapter, we discuss how certain aspects of high-resolution microscopy are implemented. This is not an exhaustive review of microscopy; it is meant to be a helpful guide and point of reference for some basic concepts in imaging. While these concepts are largely true for all biological imaging, they are chosen as particularly important for C. elegans. PMID:22226519

  6. Towards a High Resolution Cellular Model for Coastal Simulation (CEMCOS)

    NASA Astrophysics Data System (ADS)

    Dearing, J.; Plater, A. J.; Richmond, N. C.

    2004-12-01

    The aim of this research is to develop a cellular model for coastal simulation in response to changing climate and sea-level, as a contribution to the UK Tyndall Centre's Research Theme 4: Sustaining the Coastal Zone. The modelling approach uses simple cell-based rules of sediment erosion, transport and deposition operating between adjacent cells. This enables the model to include the full range of processes and properties of the coastal environment, including nonlinear behaviour, using only local interactions at discrete time intervals. Tide propagation and wave action drive sediment transport, which is further conditioned by erosion thresholds related to grain size and vegetation growth. Here, we report an overview of this one-year project and details on model design and validation. This includes tide and wave parameterisation, resulting in sediment transport over a 3-D grid of cells representing estuary morphology and bathymetry. The model (CEMCOS) is being designed to be fully generic and exportable to different coastal areas, with initial testing and validation being conducted using published bathymetric and cartographic data over the last c.150 years for the Blackwater Estuary in eastern England.

  7. Astroglia in Thick Tissue with Super Resolution and Cellular Reconstruction

    PubMed Central

    Miller, Sean J.; Rothstein, Jeffrey D.

    2016-01-01

    We utilized the recently published method of passive CLARITY to explore brain astrocytes for the first time with our optimized method. Astrocytes are the fundamental cells in the brain that act to maintain the synaptic activity of neurons, support metabolism of all neurons, and communicate through extensive networks throughout the CNS. They are the defining cell that differentiates lower organisms from humans. From a disease vantage point they are the principal cause of brain tumors and the propagator of neurodegenerative diseases like amyotrophic lateral sclerosis. New methods to study these cells is paramount. Our modified use of CLARITY provides a new way to study these brain cells. To reduce cost, speed up tissue clearing process, reduce human handling error, and to retrieve quantifiable data from single confocal and pseudo-super resolution microscopy we modified and optimized the original protocol. PMID:27494718

  8. Influence of fat-water separation and spatial resolution on automated volumetric MRI measurements of fibroglandular breast tissue.

    PubMed

    Wengert, Georg J; Pinker-Domenig, Katja; Helbich, Thomas H; Vogl, Wolf-Dieter; Clauser, Paola; Bickel, Hubert; Marino, Maria-Adele; Magometschnigg, Heinrich F; Baltzer, Pascal A

    2016-06-01

    The aim of this study was to investigate the influence of fat-water separation and spatial resolution in MRI on the results of automated quantitative measurements of fibroglandular breast tissue (FGT). Ten healthy volunteers (age range, 28-71 years; mean, 39.9 years) were included in this Institutional Review Board-approved prospective study. All measurements were performed on a 1.5-T scanner (Siemens, AvantoFit) using an 18-channel breast coil. The protocols included isotropic (Di) [TR/TE1 /TE2  = 6.00 ms/2.45 ms/2.67 ms; flip angle, 6.0°; 256 slices; matrix, 360 × 360; 1 mm isotropic; field of view, 360°; acquisition time (TA) = 3 min 38 s] and anisotropic (Da) (TR/TE1 /TE2  = 10.00 ms/2.39 ms/4.77 ms; flip angle, 24.9°; 80 slices; matrix 360 × 360; voxel size, 0.7 × 0.7 × 2.0 mm(3) ; field of view, 360°; TA = 1 min 25 s) T1 three-dimensional (3D) fast low-angle shot (FLASH) Dixon sequences, and a T1 3D FLASH sequence with the same resolution (T1 ) without (TR/TE = 11.00 ms/4.76 ms; flip angle, 25.0°; 80 slices; matrix, 360 × 360; voxel size, 0.7 × 0.7 × 2.0 mm(3) ; field of view, 360°; TA = 50 s) and with (TR/TE = 29.00 ms/4.76 ms; flip angle, 25.0°; 80 slices; matrix, 360 × 360; voxel size, 0.7 × 0.7 × 2.0 mm(3) ; field of view, 360°; TA = 2 min 35 s) fat saturation. Repeating volunteer measurements after 20 min and repositioning were used to assess reproducibility. An automated and quantitative volumetric breast density measurement system was used for FGT calculation. FGT with Di, Da and T1 measured 4.6-63.0% (mean, 30.6%), 3.2-65.3% (mean, 32.5%) and 1.7-66.5% (mean, 33.7%), respectively. The highest correlation between different MRI sequences was found with the Di and Da sequences (R(2)  = 0.976). Coefficients of variation (CVs) for FGT calculation were higher in T1 (CV = 21.5%) compared with Dixon (Di, CV = 5

  9. High Resolution Quantification of Cellular Forces for Rigidity Sensing

    NASA Astrophysics Data System (ADS)

    Liu, Shuaimin

    density of CUs decrease with time after spreading on stiff substrate. However addition of EGF dramatically increased local contraction activity such that about 30% of the total contractility was in the contraction units. This stimulatory effect was only observed on stiff substrate not on soft. Moreover, we find that in the early interactions of cells with rigid substrates that EGFR activity is needed for normal spreading and the assembly of local contraction units in media lacking serum and any soluble EGF. In Chapter 5, we performed high temporal- and spatial-resolution tracking of contractile forces exerted by cells on sub-micron elastomeric pillars. We found that actomyosin-based sarcomere-like CUs simultaneously moved opposing pillars in net steps of ˜2.5 nm, independent of rigidity. What correlated with rigidity was the number of steps taken to reach a force level that activated recruitment of alpha-actinin to the CUs. When we removed actomyosin restriction by depleting tropomyosin 2.1, we observed larger steps and higher forces that resulted in aberrant rigidity sensing and growth of non-transformed cells on soft matrices. Thus, we conclude that tropomyosin 2.1 acts as a suppressor of growth on soft matrices by supporting proper rigidity sensing.

  10. One-micron resolution optical coherence tomography (OCT) in vivo for cellular level imaging

    NASA Astrophysics Data System (ADS)

    Cui, Dongyao; Liu, Xinyu; Zhang, Jing; Yu, Xiaojun; Sun, Ding; Luo, Yuemei; Gu, Jun; Shum, Ping; Liu, Linbo

    2015-03-01

    We developed a spectral domain OCT system combining two NIR, CW light sources of different spectral range. Its resolving power is validated by visualizing the cellular structures of zebra fish larvae in vivo. An NIR extended illumination from 755-1100 nm is achieved. The axial resolution is 1.27 μm in air, corresponding to 0.93μm in tissue (n=1.36), which is the highest axial resolution using NIR, CW laser sources up to date to the best of our knowledge. In vivo imaging is conducted to demonstrate the resolving power of proposed one-micron resolution OCT system. The top and bottom surfaces of individual disk-like red blood cell is reliably visualized, as well as flat, spindle shaped endothelial cells lining along the luminal surface of the blood vessel wall. This study provides a viable solution for cellular and subcellular level OCT imaging system which is also very competitive in cost.

  11. Volumetric feature extraction and visualization of tomographic molecular imaging.

    PubMed

    Bajaj, Chandrajit; Yu, Zeyun; Auer, Manfred

    2003-01-01

    Electron tomography is useful for studying large macromolecular complex within their cellular context. The associate problems include crowding and complexity. Data exploration and 3D visualization of complexes require rendering of tomograms as well as extraction of all features of interest. We present algorithms for fully automatic boundary segmentation and skeletonization, and demonstrate their applications in feature extraction and visualization of cell and molecular tomographic imaging. We also introduce an interactive volumetric exploration and visualization tool (Volume Rover), which encapsulates implementations of the above volumetric image processing algorithms, and additionally uses efficient multi-resolution interactive geometry and volume rendering techniques for interactive visualization. PMID:14643216

  12. Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos.

    PubMed

    Stapel, L Carine; Lombardot, Benoit; Broaddus, Coleman; Kainmueller, Dagmar; Jug, Florian; Myers, Eugene W; Vastenhouw, Nadine L

    2016-02-01

    Analysis of differential gene expression is crucial for the study of cell fate and behavior during embryonic development. However, automated methods for the sensitive detection and quantification of RNAs at cellular resolution in embryos are lacking. With the advent of single-molecule fluorescence in situ hybridization (smFISH), gene expression can be analyzed at single-molecule resolution. However, the limited availability of protocols for smFISH in embryos and the lack of efficient image analysis pipelines have hampered quantification at the (sub)cellular level in complex samples such as tissues and embryos. Here, we present a protocol for smFISH on zebrafish embryo sections in combination with an image analysis pipeline for automated transcript detection and cell segmentation. We use this strategy to quantify gene expression differences between different cell types and identify differences in subcellular transcript localization between genes. The combination of our smFISH protocol and custom-made, freely available, analysis pipeline will enable researchers to fully exploit the benefits of quantitative transcript analysis at cellular and subcellular resolution in tissues and embryos. PMID:26700682

  13. Real-time GPU-accelerated processing and volumetric display for wide-field laser-scanning optical-resolution photoacoustic microscopy.

    PubMed

    Kang, Heesung; Lee, Sang-Won; Lee, Eun-Soo; Kim, Se-Hwa; Lee, Tae Geol

    2015-12-01

    Fast signal processing and real-time displays are essential for practical imaging modality in various fields of applications. However, the imaging speed in optical-resolution photoacoustic microscopy (OR-PAM), in particular, depends on factors such as the pulse repetition rate of the laser, scanning method, field of view (FOV), and signal processing time. In the past, efforts to increase acquisition speed either focused on developing new scanning methods or using lasers with higher pulse repetition rates. However, high-speed signal processing is also important for real-time volumetric display in OR-PAM. In this study, we carried out parallel signal processing using a graphics processing unit (GPU) to enable fast signal processing and wide-field real-time displays in laser-scanning OR-PAM. The average total GPU processing time for a B-mode PAM image was approximately 1.35 ms at a display speed of 480 fps when the data samples were acquired with 736 (axial) × 500 (lateral) points/B-mode-frame at a pulse repetition rate of 300 kHz. In addition, we successfully displayed maximum amplitude projection images of a mouse's ear as volumetric images with an FOV of 3 mm × 3 mm (500 × 500 pixels) at 1.02 s, corresponding to 0.98 fps. PMID:26713184

  14. Real-time GPU-accelerated processing and volumetric display for wide-field laser-scanning optical-resolution photoacoustic microscopy

    PubMed Central

    Kang, Heesung; Lee, Sang-Won; Lee, Eun-Soo; Kim, Se-Hwa; Lee, Tae Geol

    2015-01-01

    Fast signal processing and real-time displays are essential for practical imaging modality in various fields of applications. However, the imaging speed in optical-resolution photoacoustic microscopy (OR-PAM), in particular, depends on factors such as the pulse repetition rate of the laser, scanning method, field of view (FOV), and signal processing time. In the past, efforts to increase acquisition speed either focused on developing new scanning methods or using lasers with higher pulse repetition rates. However, high-speed signal processing is also important for real-time volumetric display in OR-PAM. In this study, we carried out parallel signal processing using a graphics processing unit (GPU) to enable fast signal processing and wide-field real-time displays in laser-scanning OR-PAM. The average total GPU processing time for a B-mode PAM image was approximately 1.35 ms at a display speed of 480 fps when the data samples were acquired with 736 (axial) × 500 (lateral) points/B-mode-frame at a pulse repetition rate of 300 kHz. In addition, we successfully displayed maximum amplitude projection images of a mouse’s ear as volumetric images with an FOV of 3 mm × 3 mm (500 × 500 pixels) at 1.02 s, corresponding to 0.98 fps. PMID:26713184

  15. Label-free imaging of cellular malformation using high resolution photoacoustic microscopy

    NASA Astrophysics Data System (ADS)

    Chen, Zhongjiang; Li, Bingbing; Yang, Sihua

    2014-09-01

    A label-free high resolution photoacoustic microscopy (PAM) system for imaging cellular malformation is presented. The carbon fibers were used to testify the lateral resolution of the PAM. Currently, the lateral resolution is better than 2.7 μm. The human normal red blood cells (RBCs) were used to prove the imaging capability of the system, and a single red blood cell was mapped with high contrast. Moreover, the iron deficiency anemia RBCs were clearly distinguished from the cell morphology by using the PAM. The experimental results demonstrate that the photoacoustic microscopy system can accomplish label-free photoacoustic imaging and that it has clinical potential for use in the detection of erythrocytes and blood vessels malformation.

  16. Building quantitative, three dimensional atlases of gene expression and morphology at cellular resolution

    PubMed Central

    Knowles, David W.; Biggin, Mark D.

    2013-01-01

    Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy based approaches to establish permanent, quantitative datasets—atlases—that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization and quantitative analysis. PMID:24123936

  17. Three-dimensional super-resolution protein localization correlated with vitrified cellular context

    PubMed Central

    Liu, Bei; Xue, Yanhong; Zhao, Wei; Chen, Yan; Fan, Chunyan; Gu, Lusheng; Zhang, Yongdeng; Zhang, Xiang; Sun, Lei; Huang, Xiaojun; Ding, Wei; Sun, Fei; Ji, Wei; Xu, Tao

    2015-01-01

    We demonstrate the use of cryogenic super-resolution correlative light and electron microscopy (csCLEM) to precisely determine the spatial relationship between proteins and their native cellular structures. Several fluorescent proteins (FPs) were found to be photoswitchable and emitted far more photons under our cryogenic imaging condition, resulting in higher localization precision which is comparable to ambient super-resolution imaging. Vitrified specimens were prepared by high pressure freezing and cryo-sectioning to maintain a near-native state with better fluorescence preservation. A 2-3-fold improvement of resolution over the recent reports was achieved due to the photon budget performance of screening out Dronpa and optimized imaging conditions, even with thin sections which is at a disadvantage when calculate the structure resolution from label density. We extended csCLEM to mammalian cells by introducing cryo-sectioning and observed good correlation of a mitochondrial protein with the mitochondrial outer membrane at nanometer resolution in three dimensions. PMID:26462878

  18. Three-dimensional super-resolution protein localization correlated with vitrified cellular context.

    PubMed

    Liu, Bei; Xue, Yanhong; Zhao, Wei; Chen, Yan; Fan, Chunyan; Gu, Lusheng; Zhang, Yongdeng; Zhang, Xiang; Sun, Lei; Huang, Xiaojun; Ding, Wei; Sun, Fei; Ji, Wei; Xu, Tao

    2015-01-01

    We demonstrate the use of cryogenic super-resolution correlative light and electron microscopy (csCLEM) to precisely determine the spatial relationship between proteins and their native cellular structures. Several fluorescent proteins (FPs) were found to be photoswitchable and emitted far more photons under our cryogenic imaging condition, resulting in higher localization precision which is comparable to ambient super-resolution imaging. Vitrified specimens were prepared by high pressure freezing and cryo-sectioning to maintain a near-native state with better fluorescence preservation. A 2-3-fold improvement of resolution over the recent reports was achieved due to the photon budget performance of screening out Dronpa and optimized imaging conditions, even with thin sections which is at a disadvantage when calculate the structure resolution from label density. We extended csCLEM to mammalian cells by introducing cryo-sectioning and observed good correlation of a mitochondrial protein with the mitochondrial outer membrane at nanometer resolution in three dimensions. PMID:26462878

  19. Automated analysis of embryonic gene expression with cellular resolution in C. elegans

    PubMed Central

    Murray, John Isaac; Bao, Zhirong; Boyle, Thomas J.; Boeck, Max E.; Mericle, Barbara L.; Nicholas, Thomas J.; Zhao, Zhongying; Sandel, Matthew J.; Waterston, Robert H.

    2008-01-01

    We describe a system that permits the automated analysis of reporter gene expression in Caenorhabditis elegans with cellular resolution continuously during embryogenesis and demonstrate its utility by defining the expression patterns of reporters for several embryonically expressed transcription factors. The invariant cell lineage permits the automated alignment of multiple expression profiles, allowing the direct comparison of the expression of different genes' reporters. We have also used the system to monitor perturbations to normal development involving changes both in cell division timing and in cell fate. Systematic application could reveal the gene activity of each cell throughout development. PMID:18587405

  20. Spatial Mapping of Lipids at Cellular Resolution in Embryos of Cotton[W][OA

    PubMed Central

    Horn, Patrick J.; Korte, Andrew R.; Neogi, Purnima B.; Love, Ebony; Fuchs, Johannes; Strupat, Kerstin; Borisjuk, Ljudmilla; Shulaev, Vladimir; Lee, Young-Jin; Chapman, Kent D.

    2012-01-01

    Advances in mass spectrometry (MS) have made comprehensive lipidomics analysis of complex tissues relatively commonplace. These compositional analyses, although able to resolve hundreds of molecular species of lipids in single extracts, lose the original cellular context from which these lipids are derived. Recently, high-resolution MS of individual lipid droplets from seed tissues indicated organelle-to-organelle variation in lipid composition, suggesting that heterogeneity of lipid distributions at the cellular level may be prevalent. Here, we employed matrix-assisted laser desorption/ionization–MS imaging (MALDI-MSI) approaches to visualize lipid species directly in seed tissues of upland cotton (Gossypium hirsutum). MS imaging of cryosections of mature cotton embryos revealed a distinct, heterogeneous distribution of molecular species of triacylglycerols and phosphatidylcholines, the major storage and membrane lipid classes in cotton embryos. Other lipids were imaged, including phosphatidylethanolamines, phosphatidic acids, sterols, and gossypol, indicating the broad range of metabolites and applications for this chemical visualization approach. We conclude that comprehensive lipidomics images generated by MALDI-MSI report accurate, relative amounts of lipid species in plant tissues and reveal previously unseen differences in spatial distributions providing for a new level of understanding in cellular biochemistry. PMID:22337917

  1. Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo

    PubMed Central

    Packer, Adam M.; Russell, Lloyd E.; Dalgleish, Henry W.P.; Häusser, Michael

    2016-01-01

    We describe an all-optical strategy for simultaneously manipulating and recording the activity of multiple neurons with cellular resolution in vivo. Concurrent two-photon optogenetic activation and calcium imaging is enabled by coexpression of a red-shifted opsin and a genetically encoded calcium indicator. A spatial light modulator allows tens of user-selected neurons to be targeted for spatiotemporally precise optogenetic activation, while simultaneous fast calcium imaging provides high-resolution network-wide readout of the manipulation with negligible optical crosstalk. Proof-of-principle experiments in mouse barrel cortex demonstrate interrogation of the same neuronal population during different behavioral states, and targeting of neuronal ensembles based on their functional signature. This approach extends the optogenetic toolkit beyond the specificity obtained with genetic or viral approaches, enabling high-throughput, flexible and long-term optical interrogation of functionally defined neural circuits with single-cell and single-spike resolution in the mammalian brain in vivo. PMID:25532138

  2. Optical-Resolution Photoacoustic Microscopy: Auscultation of Biological Systems at the Cellular Level

    PubMed Central

    Hu, Song; Wang, Lihong V.

    2013-01-01

    Photoacoustic microscopy (PAM) offers unprecedented sensitivity to optical absorption and opens a new window to study biological systems at multiple length- and timescales. In particular, optical-resolution PAM (OR-PAM) has pushed the technical envelope to submicron length scales and millisecond timescales. Here, we review the state of the art of OR-PAM in biophysical research. With properly chosen optical wavelengths, OR-PAM can spectrally differentiate a variety of endogenous and exogenous chromophores, unveiling the anatomical, functional, metabolic, and molecular information of biological systems. Newly uncovered contrast mechanisms of linear dichroism and Förster resonance energy transfer further distinguish OR-PAM. Integrating multiple contrasts and advanced scanning mechanisms has capacitated OR-PAM to comprehensively interrogate biological systems at the cellular level in real time. Two future directions are discussed, where OR-PAM holds the potential to translate basic biophysical research into clinical healthcare. PMID:23972836

  3. Neurotransmitter Specific, Cellular-Resolution Functional Brain Mapping Using Receptor Coated Nanoparticles: Assessment of the Possibility

    PubMed Central

    Forati, Ebrahim; Sabouni, Abas; Ray, Supriyo; Head, Brian; Schoen, Christian; Sievenpiper, Dan

    2015-01-01

    Receptor coated resonant nanoparticles and quantum dots are proposed to provide a cellular-level resolution image of neural activities inside the brain. The functionalized nanoparticles and quantum dots in this approach will selectively bind to different neurotransmitters in the extra-synaptic regions of neurons. This allows us to detect neural activities in real time by monitoring the nanoparticles and quantum dots optically. Gold nanoparticles (GNPs) with two different geometries (sphere and rod) and quantum dots (QDs) with different sizes were studied along with three different neurotransmitters: dopamine, gamma-Aminobutyric acid (GABA), and glycine. The absorption/emission spectra of GNPs and QDs before and after binding of neurotransmitters and their corresponding receptors are reported. The results using QDs and nanorods with diameter 25nm and aspect rations larger than three were promising for the development of the proposed functional brain mapping approach. PMID:26717196

  4. Magnetic spin imaging under ambient conditions with sub-cellular resolution

    NASA Astrophysics Data System (ADS)

    Steinert, S.; Ziem, F.; Hall, L. T.; Zappe, A.; Schweikert, M.; Götz, N.; Aird, A.; Balasubramanian, G.; Hollenberg, L.; Wrachtrup, J.

    2013-03-01

    The detection of small numbers of magnetic spins is a significant challenge in the life, physical and chemical sciences, especially when room temperature operation is required. Here we show that a proximal nitrogen-vacancy spin ensemble serves as a high precision sensing and imaging array. Monitoring its longitudinal relaxation enables sensing of freely diffusing, unperturbed magnetic ions and molecules in a microfluidic device without applying external magnetic fields. Multiplexed charge-coupled device acquisition and an optimized detection scheme permits direct spin noise imaging of magnetically labelled cellular structures under ambient conditions. Within 20 s we achieve spatial resolutions below 500 nm and experimental sensitivities down to 1,000 statistically polarized spins, of which only 32 ions contribute to a net magnetization. The results mark a major step towards versatile sub-cellular magnetic imaging and real-time spin sensing under physiological conditions providing a minimally invasive tool to monitor ion channels or haemoglobin trafficking inside live cells.

  5. Investigating spatial and volumetric trends in silicic volcanism along the Yellowstone hotspot track using high-resolution thermomechanical numerical models

    NASA Astrophysics Data System (ADS)

    Colon, D.; Bindeman, I. N.; Gerya, T.

    2015-12-01

    Roughly 2 Ma gaps exist between the Picabo and Heise (from ~8.4 to 6.6Ma) and the Heise and Yellowstone (4.40 to 2.1 Ma) centers along the Yellowstone hotspot track, each of which experienced magmatic activity for several million years. We employ high-resolution magmatic-thermomechanical models of the interaction between a mantle plume and thick continental crust to investigate the causes of the spatial and temporal jumps that occur between these eruptive centers, using a stress implementation of magmatic processes, nonlinear temperature-dependent melting, and progressive depletion the rocks from which magmas are extracted. We investigate two possible mechanisms of these jumps in active centers. First, the spacing between eruptive centers is a function of the longevity of amagma conduit in beneath each eruptive center, which must be abandoned when the crust moves too far away from the center of the hotspot, with the distance traveled by the plate in this time determining the spacing between eruptive centers. Alternatively, the cessation of activity at a given eruptive center is controlled by the formation of geochemically depleted "dead zones" which force any new silicic volcanism to occur in a new area of less depleted crust, with the spacing between centers controlled by the size of these dead zones. By varying the speed of the crust over the hotspot, the thickness and composition of the crust, we can determine the relative importance of these two processes for volcanism along the Yellowstone hotspot track has likely changed over time, with implications for changes in average eruptive volumes and repose times between large eruptions over the last 12 Ma. Early results suggest that heating of the crust causes areas of melt accumulation to move upward with time before resetting to a deeper level as the crust moves over the hotspot, a possible additional source of discrete behavior along the hotspot track. We check our results using existing geochemical constraints.

  6. Volumetric magnetic induction tomography

    NASA Astrophysics Data System (ADS)

    Wei, H.-Y.; Ma, L.; Soleimani, M.

    2012-05-01

    Magnetic induction tomography (MIT) is a new and emerging type of tomography technique that is able to map the passive electromagnetic properties (in particular conductivity) of an object. Because of its non-invasive feature, it becomes a suitable technique for many industries, such as metal processing and mining. This paper presents a volumetric MIT (VMIT) system based on an existing measurement setup in our 2D system (MIT Mk-I). By increasing the number of sensors in the axial direction, volumetric imaging can be realized and hence can improve the spatial resolution of the reconstructed images. All of the system control, data acquisition and signal demodulation are accomplished by a commercial data acquisition card and the National Instruments graphical programming language. In this paper, both the system architecture and the forward 3D sensitivity model will be presented. The image reconstruction scheme is modified by introducing a 3D sensitivity map to replace the previous 2D sensitivity map used for the MIT Mk-I system. The iterative Landweber technique was implemented as the inverse solver to reconstruct the images. Several laboratory-based experimental results are demonstrated in this paper, with different shapes of imaging objects. The reconstructed images are satisfactory showing for the first time volumetric conductivity reconstruction using a multi-layer MIT system. The results indicate the high-quality image reconstruction using our novel VMIT system for potential use in industrial applications, such as metal flow imaging.

  7. Boron dipyrromethene (BODIPY) functionalized carbon nano-onions for high resolution cellular imaging

    NASA Astrophysics Data System (ADS)

    Bartelmess, Juergen; de Luca, Elisa; Signorelli, Angelo; Baldrighi, Michele; Becce, Michele; Brescia, Rosaria; Nardone, Valentina; Parisini, Emilio; Echegoyen, Luis; Pompa, Pier Paolo; Giordani, Silvia

    2014-10-01

    Carbon nano-onions (CNOs) are an exciting class of carbon nanomaterials, which have recently demonstrated a facile cell-penetration capability. In the present work, highly fluorescent boron dipyrromethene (BODIPY) dyes were covalently attached to the surface of CNOs. The introduction of this new carbon nanomaterial-based imaging platform, made of CNOs and BODIPY fluorophores, allows for the exploration of synergetic effects between the two building blocks and for the elucidation of its performance in biological applications. The high fluorescence intensity exhibited by the functionalized CNOs translates into an excellent in vitro probe for the high resolution imaging of MCF-7 human breast cancer cells. It was also found that the CNOs, internalized by the cells by endocytosis, localized in the lysosomes and did not show any cytotoxic effects. The presented results highlight CNOs as excellent platforms for biological and biomedical studies due to their low toxicity, efficient cellular uptake and low fluorescence quenching of attached probes.Carbon nano-onions (CNOs) are an exciting class of carbon nanomaterials, which have recently demonstrated a facile cell-penetration capability. In the present work, highly fluorescent boron dipyrromethene (BODIPY) dyes were covalently attached to the surface of CNOs. The introduction of this new carbon nanomaterial-based imaging platform, made of CNOs and BODIPY fluorophores, allows for the exploration of synergetic effects between the two building blocks and for the elucidation of its performance in biological applications. The high fluorescence intensity exhibited by the functionalized CNOs translates into an excellent in vitro probe for the high resolution imaging of MCF-7 human breast cancer cells. It was also found that the CNOs, internalized by the cells by endocytosis, localized in the lysosomes and did not show any cytotoxic effects. The presented results highlight CNOs as excellent platforms for biological and biomedical

  8. High resolution simulations of energy absorption in dynamically loaded cellular structures

    NASA Astrophysics Data System (ADS)

    Winter, R. E.; Cotton, M.; Harris, E. J.; Eakins, D. E.; McShane, G.

    2016-04-01

    Cellular materials have potential application as absorbers of energy generated by high velocity impact. CTH, a Sandia National Laboratories Code which allows very severe strains to be simulated, has been used to perform very high resolution simulations showing the dynamic crushing of a series of two-dimensional, stainless steel metal structures with varying architectures. The structures are positioned to provide a cushion between a solid stainless steel flyer plate with velocities ranging from 300 to 900 m/s, and an initially stationary stainless steel target. Each of the alternative architectures under consideration was formed by an array of identical cells each of which had a constant volume and a constant density. The resolution of the simulations was maximised by choosing a configuration in which one-dimensional conditions persisted for the full period over which the specimen densified, a condition which is most readily met by impacting high density specimens at high velocity. It was found that the total plastic flow and, therefore, the irreversible energy dissipated in the fully densified energy absorbing cell, increase (a) as the structure becomes more rodlike and less platelike and (b) as the impact velocity increases. Sequential CTH images of the deformation processes show that the flow of the cell material may be broadly divided into macroscopic flow perpendicular to the compression direction and jetting-type processes (microkinetic flow) which tend to predominate in rod and rodlike configurations and also tend to play an increasing role at increased strain rates. A very simple analysis of a configuration in which a solid flyer impacts a solid target provides a baseline against which to compare and explain features seen in the simulations. The work provides a basis for the development of energy absorbing structures for application in the 200-1000 m/s impact regime.

  9. The functional micro-organization of grid cells revealed by cellular-resolution imaging

    PubMed Central

    Heys, James G.; Rangarajan, Krsna V.; Dombeck, Daniel A.

    2015-01-01

    Summary Establishing how grid cells are anatomically arranged, on a microscopic scale, in relation to their firing patterns in the environment would facilitate a greater micro-circuit level understanding of the brain’s representation of space. However, all previous grid cell recordings used electrode techniques that provide limited descriptions of fine-scale organization. We therefore developed a technique for cellular-resolution functional imaging of medial entorhinal cortex (MEC) neurons in mice navigating a virtual linear track, enabling a new experimental approach to study MEC. Using these methods, we show that grid cells are physically clustered in MEC compared to non-grid cells. Additionally, we demonstrate that grid cells are functionally micro-organized: The similarity between the environment firing locations of grid cell pairs varies as a function of the distance between them according to a “Mexican Hat” shaped profile. This suggests that, on average, nearby grid cells have more similar spatial firing phases than those further apart. PMID:25467986

  10. Impact of Resolution on Simulation of Closed Mesoscale Cellular Convection Identified by Dynamically Guided Watershed Segmentation

    SciTech Connect

    Martini, Matus N.; Gustafson, William I.; Yang, Qing; Xiao, Heng

    2014-11-18

    Organized mesoscale cellular convection (MCC) is a common feature of marine stratocumulus that forms in response to a balance between mesoscale dynamics and smaller scale processes such as cloud radiative cooling and microphysics. We use the Weather Research and Forecasting model with chemistry (WRF-Chem) and fully coupled cloud-aerosol interactions to simulate marine low clouds during the VOCALS-REx campaign over the southeast Pacific. A suite of experiments with 3- and 9-km grid spacing indicates resolution-dependent behavior. The simulations with finer grid spacing have smaller liquid water paths and cloud fractions, while cloud tops are higher. The observed diurnal cycle is reasonably well simulated. To isolate organized MCC characteristics we develop a new automated method, which uses a variation of the watershed segmentation technique that combines the detection of cloud boundaries with a test for coincident vertical velocity characteristics. This ensures that the detected cloud fields are dynamically consistent for closed MCC, the most common MCC type over the VOCALS-REx region. We demonstrate that the 3-km simulation is able to reproduce the scaling between horizontal cell size and boundary layer height seen in satellite observations. However, the 9-km simulation is unable to resolve smaller circulations corresponding to shallower boundary layers, instead producing invariant MCC horizontal scale for all simulated boundary layers depths. The results imply that climate models with grid spacing of roughly 3 km or smaller may be needed to properly simulate the MCC structure in the marine stratocumulus regions.

  11. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics

    PubMed Central

    Keränen, Soile VE; Fowlkes, Charless C; Luengo Hendriks, Cris L; Sudar, Damir; Knowles, David W; Malik, Jitendra; Biggin, Mark D

    2006-01-01

    Background To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos. Results Using automated image analysis methods, we provide the first quantitative description of temporal changes in morphology and gene expression at cellular resolution in whole embryos, using the Drosophila blastoderm as a model. Analyses based on both fixed and live embryos reveal complex, previously undetected three-dimensional changes in nuclear density patterns caused by nuclear movements prior to gastrulation. Gene expression patterns move, in part, with these changes in morphology, but additional spatial shifts in expression patterns are also seen, supporting a previously proposed model of pattern dynamics based on the induction and inhibition of gene expression. We show that mutations that disrupt either the anterior/posterior (a/p) or the dorsal/ventral (d/v) transcriptional cascades alter morphology and gene expression along both the a/p and d/v axes in a way suggesting that these two patterning systems interact via both transcriptional and morphological mechanisms. Conclusion Our work establishes a new strategy for measuring temporal changes in the locations of cells and gene expression patterns that uses fixed cell material and computational modeling. It also provides a coordinate framework for the blastoderm embryo that will allow increasingly accurate spatio-temporal modeling of both the transcriptional control network and morphogenesis. PMID:17184547

  12. Resolution of Infinite-Loop in Hyperincursive and Nonlocal Cellular Automata: Introduction to Slime Mold Computing

    NASA Astrophysics Data System (ADS)

    Aono, Masashi; Gunji, Yukio-Pegio

    2004-08-01

    How can non-algorithmic/non-deterministic computational syntax be computed? "The hyperincursive system" introduced by Dubois is an anticipatory system embracing the contradiction/uncertainty. Although it may provide a novel viewpoint for the understanding of complex systems, conventional digital computers cannot run faithfully as the hyperincursive computational syntax specifies, in a strict sense. Then is it an imaginary story? In this paper we try to argue that it is not. We show that a model of complex systems "Elementary Conflictable Cellular Automata (ECCA)" proposed by Aono and Gunji is embracing the hyperincursivity and the nonlocality. ECCA is based on locality-only type settings basically as well as other CA models, and/but at the same time, each cell is required to refer to globality-dominant regularity. Due to this contradictory locality-globality loop, the time evolution equation specifies that the system reaches the deadlock/infinite-loop. However, we show that there is a possibility of the resolution of these problems if the computing system has parallel and/but non-distributed property like an amoeboid organism. This paper is an introduction to "the slime mold computing" that is an attempt to cultivate an unconventional notion of computation.

  13. Automated Identification of Closed Mesoscale Cellular Convection and Impact of Resolution on Related Mesoscale Dynamics

    NASA Astrophysics Data System (ADS)

    Martini, M.; Gustafson, W. I.; Yang, Q.; Xiao, H.

    2013-12-01

    Organized mesoscale cellular convection (MCC) is a common feature of marine stratocumulus that forms in response to a balance between mesoscale dynamics and smaller scale processes such as cloud radiative cooling and microphysics. Cloud resolving models begin to resolve some, but not all, of these processes with less of the mesoscale dynamics resolved as one progresses from <1 km to 10 km grid spacing. While limited domain cloud resolving models can use high resolution to simulate MCC, global cloud resolving models must resort to using grid spacings closer to 5 to 10 km. This effectively truncates the scales through which the dynamics can act and impacts the MCC characteristics, potentially altering the climate impact of these clouds in climate models. To understand the impact of this truncation, we use the Weather Research and Forecasting model with chemistry (WRF-Chem) and fully coupled cloud-aerosol interactions to simulate marine low clouds during the VOCALS-REx campaign over the Southeast Pacific. A suite of experiments with 1-, 3- and 9-km grid spacing indicates resolution dependent behavior. The simulations with finer grid spacing have lower liquid water paths and cloud fractions, while cloud tops are higher. When compared to observed liquid water paths from GOES and MODIS, the 3-km simulation has better agreement over the coastal regions while the 9-km simulation better agrees over remote regions. The observed diurnal cycle is reasonably well simulated. To isolate organized MCC characteristics we developed a new automated method, which uses a variation of the watershed segmentation technique that combines the detection of cloud boundaries with a test for coincident vertical velocity characteristics. This has the advantage of ensuring that the detected cloud fields are dynamically consistent for closed MCC and helps minimize false detections from secondary circulations. We demonstrate that the 3-km simulation is able to reproduce the scaling between

  14. Snapshot Hyperspectral Volumetric Microscopy.

    PubMed

    Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

    2016-01-01

    The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens. PMID:27103155

  15. Snapshot Hyperspectral Volumetric Microscopy

    NASA Astrophysics Data System (ADS)

    Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

    2016-04-01

    The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens.

  16. Snapshot Hyperspectral Volumetric Microscopy

    PubMed Central

    Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

    2016-01-01

    The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens. PMID:27103155

  17. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline

    PubMed Central

    Luengo Hendriks, Cris L; Keränen, Soile VE; Fowlkes, Charless C; Simirenko, Lisa; Weber, Gunther H; DePace, Angela H; Henriquez, Clara; Kaszuba, David W; Hamann, Bernd; Eisen, Michael B; Malik, Jitendra; Sudar, Damir; Biggin, Mark D; Knowles, David W

    2006-01-01

    Background To model and thoroughly understand animal transcription networks, it is essential to derive accurate spatial and temporal descriptions of developing gene expression patterns with cellular resolution. Results Here we describe a suite of methods that provide the first quantitative three-dimensional description of gene expression and morphology at cellular resolution in whole embryos. A database containing information derived from 1,282 embryos is released that describes the mRNA expression of 22 genes at multiple time points in the Drosophila blastoderm. We demonstrate that our methods are sufficiently accurate to detect previously undescribed features of morphology and gene expression. The cellular blastoderm is shown to have an intricate morphology of nuclear density patterns and apical/basal displacements that correlate with later well-known morphological features. Pair rule gene expression stripes, generally considered to specify patterning only along the anterior/posterior body axis, are shown to have complex changes in stripe location, stripe curvature, and expression level along the dorsal/ventral axis. Pair rule genes are also found to not always maintain the same register to each other. Conclusion The application of these quantitative methods to other developmental systems will likely reveal many other previously unknown features and provide a more rigorous understanding of developmental regulatory networks. PMID:17184546

  18. High-resolution gene expression analysis of the developing mouse kidney defines novel cellular compartments within the nephron progenitor population.

    PubMed

    Mugford, Joshua W; Yu, Jing; Kobayashi, Akio; McMahon, Andrew P

    2009-09-15

    The functional unit of the kidney is the nephron. During its organogenesis, the mammalian metanephric kidney generates thousands of nephrons over a protracted period of fetal life. All nephrons are derived from a population of self-renewing multi-potent progenitor cells, termed the cap mesenchyme. However, our understanding of the molecular and cellular mechanisms underlying nephron development is at an early stage. In order to identify factors involved in nephrogenesis, we performed a high-resolution, spatial profiling of a number of transcriptional regulators expressed within the cap mesenchyme and early developing nephron. Our results demonstrate novel, stereotypic, spatially defined cellular sub-domains within the cap mesenchyme, which may, in part, reflect induction of nephron precursors. These results suggest a hitherto unappreciated complexity of cell states that accompany the assembly of the metanephric kidney, likely reflecting diverse regulatory actions such as the maintenance and induction of nephron progenitors. PMID:19591821

  19. High-resolution gene expression analysis of the developing mouse kidney defines novel cellular compartments within the nephron progenitor population

    PubMed Central

    Mugford, Joshua W.; Yu, Jing; Kobayashi, Akio; McMahon, Andrew P.

    2009-01-01

    The functional unit of the kidney is the nephron. During its organogenesis, the mammalian metanephric kidney generates thousands of nephrons over a protracted period of fetal life. All nephrons are derived from a population of self-renewing multi-potent progenitor cells, termed the cap mesenchyme. However, our understanding of the molecular and cellular mechanisms underlying nephron development is at an early stage. In order to identify factors involved in nephrogenesis, we performed a high-resolution, spatial profiling of a number of transcriptional regulators expressed within the cap mesenchyme and early developing nephron. Our results demonstrate novel, stereotypic, spatially defined cellular sub-domains within the cap mesenchyme, which may, in part, reflect induction of nephron precursors. These results suggest a hitherto unappreciated complexity of cell states that accompany the assembly of the metanephric kidney, likely reflecting diverse regulatory actions such as the maintenance and induction of nephron progenitors. PMID:19591821

  20. Efficient threshold for volumetric segmentation

    NASA Astrophysics Data System (ADS)

    Burdescu, Dumitru D.; Brezovan, Marius; Stanescu, Liana; Stoica Spahiu, Cosmin; Ebanca, Daniel

    2015-07-01

    Image segmentation plays a crucial role in effective understanding of digital images. However, the research on the existence of general purpose segmentation algorithm that suits for variety of applications is still very much active. Among the many approaches in performing image segmentation, graph based approach is gaining popularity primarily due to its ability in reflecting global image properties. Volumetric image segmentation can simply result an image partition composed by relevant regions, but the most fundamental challenge in segmentation algorithm is to precisely define the volumetric extent of some object, which may be represented by the union of multiple regions. The aim in this paper is to present a new method to detect visual objects from color volumetric images and efficient threshold. We present a unified framework for volumetric image segmentation and contour extraction that uses a virtual tree-hexagonal structure defined on the set of the image voxels. The advantage of using a virtual tree-hexagonal network superposed over the initial image voxels is that it reduces the execution time and the memory space used, without losing the initial resolution of the image.

  1. Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison

    PubMed Central

    Wegel, Eva; Göhler, Antonia; Lagerholm, B. Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M.

    2016-01-01

    Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques. PMID:27264341

  2. Revealing the cellular localization of STAT1 during the cell cycle by super-resolution imaging.

    PubMed

    Gao, Jing; Wang, Feng; Liu, Yanhou; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

    2015-01-01

    Signal transducers and activators of transcription (STATs) can transduce cytokine signals and regulate gene expression. The cellular localization and nuclear trafficking of STAT1, a representative of the STAT family with multiple transcriptional functions, is tightly related with transcription process, which usually happens in the interphase of the cell cycle. However, these priority questions regarding STAT1 distribution and localization at the different cell-cycle stages remain unclear. By using direct stochastic optical reconstruction microscopy (dSTORM), we found that the nuclear expression level of STAT1 increased gradually as the cell cycle carried out, especially after EGF stimulation. Furthermore, STAT1 formed clusters in the whole cell during the cell cycle, with the size and the number of clusters also increasing significantly from G1 to G2 phase, suggesting that transcription and other cell-cycle related activities can promote STAT1 to form more and larger clusters for fast response to signals. Our work reveals that the cellular localization and clustering distribution of STAT1 are associated with the cell cycle, and further provides an insight into the mechanism of cell-cycle regulated STAT1 signal transduction. PMID:25762114

  3. Revealing the cellular localization of STAT1 during the cell cycle by super-resolution imaging

    PubMed Central

    Gao, Jing; Wang, Feng; Liu, Yanhou; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

    2015-01-01

    Signal transducers and activators of transcription (STATs) can transduce cytokine signals and regulate gene expression. The cellular localization and nuclear trafficking of STAT1, a representative of the STAT family with multiple transcriptional functions, is tightly related with transcription process, which usually happens in the interphase of the cell cycle. However, these priority questions regarding STAT1 distribution and localization at the different cell-cycle stages remain unclear. By using direct stochastic optical reconstruction microscopy (dSTORM), we found that the nuclear expression level of STAT1 increased gradually as the cell cycle carried out, especially after EGF stimulation. Furthermore, STAT1 formed clusters in the whole cell during the cell cycle, with the size and the number of clusters also increasing significantly from G1 to G2 phase, suggesting that transcription and other cell-cycle related activities can promote STAT1 to form more and larger clusters for fast response to signals. Our work reveals that the cellular localization and clustering distribution of STAT1 are associated with the cell cycle, and further provides an insight into the mechanism of cell-cycle regulated STAT1 signal transduction. PMID:25762114

  4. Revealing the cellular localization of STAT1 during the cell cycle by super-resolution imaging

    NASA Astrophysics Data System (ADS)

    Gao, Jing; Wang, Feng; Liu, Yanhou; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

    2015-03-01

    Signal transducers and activators of transcription (STATs) can transduce cytokine signals and regulate gene expression. The cellular localization and nuclear trafficking of STAT1, a representative of the STAT family with multiple transcriptional functions, is tightly related with transcription process, which usually happens in the interphase of the cell cycle. However, these priority questions regarding STAT1 distribution and localization at the different cell-cycle stages remain unclear. By using direct stochastic optical reconstruction microscopy (dSTORM), we found that the nuclear expression level of STAT1 increased gradually as the cell cycle carried out, especially after EGF stimulation. Furthermore, STAT1 formed clusters in the whole cell during the cell cycle, with the size and the number of clusters also increasing significantly from G1 to G2 phase, suggesting that transcription and other cell-cycle related activities can promote STAT1 to form more and larger clusters for fast response to signals. Our work reveals that the cellular localization and clustering distribution of STAT1 are associated with the cell cycle, and further provides an insight into the mechanism of cell-cycle regulated STAT1 signal transduction.

  5. Cellular resolution circuit mapping with temporal-focused excitation of soma-targeted channelrhodopsin.

    PubMed

    Baker, Christopher A; Elyada, Yishai M; Parra, Andres; Bolton, M McLean

    2016-01-01

    We describe refinements in optogenetic methods for circuit mapping that enable measurements of functional synaptic connectivity with single-neuron resolution. By expanding a two-photon beam in the imaging plane using the temporal focusing method and restricting channelrhodopsin to the soma and proximal dendrites, we are able to reliably evoke action potentials in individual neurons, verify spike generation with GCaMP6s, and determine the presence or absence of synaptic connections with patch-clamp electrophysiological recording. PMID:27525487

  6. The stress response resolution assay. I. Quantitative assessment of environmental agent/condition effects on cellular stress resolution outcomes in epithelium.

    PubMed

    Walker, Dale M; Patrick O'Neill, J; Tyson, Frederick L; Walker, Vernon E

    2013-05-01

    The events or factors that lead from normal cell function to conditions and diseases such as aging or cancer reflect complex interactions between cells and their environment. Cellular stress responses, a group of processes involved in homeostasis and adaptation to environmental change, contribute to cell survival under stress and can be resolved with damage avoidance or damage tolerance outcomes. To investigate the impact of environmental agents/conditions upon cellular stress response outcomes in epithelium, a novel quantitative assay, the "stress response resolution" (SRR) assay, was developed. The SRR assay consists of pretreatment with a test agent or vehicle followed later by a calibrated stress conditions exposure step (here, using 6-thioguanine). Pilot studies conducted with a spontaneously-immortalized murine mammary epithelial cell line pretreated with vehicle or 20 µg N-ethyl-N-nitrososurea/ml medium for 1 hr, or two hTERT-immortalized human bronchial epithelial cell lines pretreated with vehicle or 100 µM zidovudine/lamivudine for 12 days, found minimal alterations in cell morphology, survival, or cell function through 2 weeks post-exposure. However, when these pretreatments were followed 2 weeks later by exposure to calibrated stress conditions of limited duration (for 4 days), significant alterations in stress resolution were observed in pretreated cells compared with vehicle-treated control cells, with decreased damage avoidance survival outcomes in all cell lines and increased damage tolerance outcomes in two of three cell lines. These pilot study results suggest that sub-cytotoxic pretreatments with chemical mutagens have long-term adverse impact upon the ability of cells to resolve subsequent exposure to environmental stressors. PMID:23554083

  7. Cellular resolution circuit mapping with temporal-focused excitation of soma-targeted channelrhodopsin

    PubMed Central

    Baker, Christopher A; Elyada, Yishai M; Parra, Andres; Bolton, M McLean

    2016-01-01

    We describe refinements in optogenetic methods for circuit mapping that enable measurements of functional synaptic connectivity with single-neuron resolution. By expanding a two-photon beam in the imaging plane using the temporal focusing method and restricting channelrhodopsin to the soma and proximal dendrites, we are able to reliably evoke action potentials in individual neurons, verify spike generation with GCaMP6s, and determine the presence or absence of synaptic connections with patch-clamp electrophysiological recording. DOI: http://dx.doi.org/10.7554/eLife.14193.001 PMID:27525487

  8. Exploring Volumetrically Indexed Cups

    ERIC Educational Resources Information Center

    Jones, Dustin L.

    2011-01-01

    This article was inspired by a set of 12 cylindrical cups, which are volumetrically indexed; that is to say, the volume of cup "n" is equal to "n" times the volume of cup 1. Various sets of volumetrically indexed cylindrical cups are explored. I demonstrate how this children's toy is ripe for mathematical investigation, with connections to…

  9. Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian

    PubMed Central

    Yin, Zongjun; Zhu, Maoyan; Davidson, Eric H.; Bottjer, David J.; Zhao, Fangchen; Tafforeau, Paul

    2015-01-01

    An extraordinarily well preserved, 600-million-year (Myr)-old, three-dimensionally phosphatized fossil displaying multiple independent characters of modern adult sponges has been analyzed by SEM and synchrotron X-ray tomography. The fossilized animal (Eocyathispongia qiania gen. et sp. nov.) is slightly more than 1.2 mm wide and 1.1 mm tall, is composed of hundreds of thousands of cells, and has a gross structure consisting of three adjacent hollow tubes sharing a common base. The main tube is crowned with a large open funnel, and the others end in osculum-like openings to the exterior. The external surface is densely covered with flat tile-like cells closely resembling sponge pinacocytes, and this layer is punctuated with smaller pores. A dense patch of external structures that display the form of a lawn of sponge papillae has also survived. Within the main funnel, an area where features of the inner surface are preserved displays a regular pattern of uniform pits. Many of them are surrounded individually by distinct collars, mounted in a supporting reticulum. The possibility cannot be excluded that these pits are the remains of a field of choanocytes. The character set evinced by this specimen, ranging from general anatomy to cell type, uniquely indicates that this specimen is a fossil of probable poriferan affinity. So far, we have only this single specimen, and although its organized and complex cellular structure precludes any reasonable interpretation that its origin is abiogenic, confirmation that it is indeed a fossilized sponge will clearly require discovery of additional specimens. PMID:25775601

  10. Sponge grade body fossil with cellular resolution dating 60 Myr before the Cambrian.

    PubMed

    Yin, Zongjun; Zhu, Maoyan; Davidson, Eric H; Bottjer, David J; Zhao, Fangchen; Tafforeau, Paul

    2015-03-24

    An extraordinarily well preserved, 600-million-year (Myr)-old, three-dimensionally phosphatized fossil displaying multiple independent characters of modern adult sponges has been analyzed by SEM and synchrotron X-ray tomography. The fossilized animal (Eocyathispongia qiania gen. et sp. nov.) is slightly more than 1.2 mm wide and 1.1 mm tall, is composed of hundreds of thousands of cells, and has a gross structure consisting of three adjacent hollow tubes sharing a common base. The main tube is crowned with a large open funnel, and the others end in osculum-like openings to the exterior. The external surface is densely covered with flat tile-like cells closely resembling sponge pinacocytes, and this layer is punctuated with smaller pores. A dense patch of external structures that display the form of a lawn of sponge papillae has also survived. Within the main funnel, an area where features of the inner surface are preserved displays a regular pattern of uniform pits. Many of them are surrounded individually by distinct collars, mounted in a supporting reticulum. The possibility cannot be excluded that these pits are the remains of a field of choanocytes. The character set evinced by this specimen, ranging from general anatomy to cell type, uniquely indicates that this specimen is a fossil of probable poriferan affinity. So far, we have only this single specimen, and although its organized and complex cellular structure precludes any reasonable interpretation that its origin is abiogenic, confirmation that it is indeed a fossilized sponge will clearly require discovery of additional specimens. PMID:25775601

  11. Cellular resolution maps of X chromosome inactivation: implications for neural development, function, and disease.

    PubMed

    Wu, Hao; Luo, Junjie; Yu, Huimin; Rattner, Amir; Mo, Alisa; Wang, Yanshu; Smallwood, Philip M; Erlanger, Bracha; Wheelan, Sarah J; Nathans, Jeremy

    2014-01-01

    Female eutherian mammals use X chromosome inactivation (XCI) to epigenetically regulate gene expression from ∼4% of the genome. To quantitatively map the topography of XCI for defined cell types at single cell resolution, we have generated female mice that carry X-linked, Cre-activated, and nuclear-localized fluorescent reporters--GFP on one X chromosome and tdTomato on the other. Using these reporters in combination with different Cre drivers, we have defined the topographies of XCI mosaicism for multiple CNS cell types and of retinal vascular dysfunction in a model of Norrie disease. Depending on cell type, fluctuations in the XCI mosaic are observed over a wide range of spatial scales, from neighboring cells to left versus right sides of the body. These data imply a major role for XCI in generating female-specific, genetically directed, stochastic diversity in eutherian mammals on spatial scales that would be predicted to affect CNS function within and between individuals. PMID:24411735

  12. Cellular resolution maps of X-chromosome inactivation: implications for neural development, function, and disease

    PubMed Central

    Wu, Hao; Luo, Junjie; Yu, Huimin; Rattner, Amir; Mo, Alisa; Wang, Yanshu; Smallwood, Philip M.; Erlanger, Bracha; Wheelan, Sarah J.; Nathans, Jeremy

    2014-01-01

    Female eutherian mammals use X-chromosome inactivation (XCI) to epigenetically regulate gene expression from ~4% of genes. To quantitatively map the topography of XCI for defined cell types at single cell resolution, we have generated female mice that carry X-linked, Cre-activated, and nuclear-localized fluorescent reporters – GFP on one X-chromosome and tdTomato on the other. Using these reporters in combination with different Cre drivers we have defined the topographies of XCI mosaicism for multiple CNS cell types and of retinal vascular dysfunction in a model of Norrie Disease. Depending on cell type, fluctuations in the XCI mosaic are observed over a wide range of spatial scales, from neighboring cells to left vs. right sides of the body. These data imply a major role for XCI in generating female-specific, genetically directed, stochastic diversity in eutherian mammals on spatial scales that would be predicted to affect CNS function within and between individuals. PMID:24411735

  13. In vivo near-realtime volumetric optical-resolution photoacoustic microscopy using a high-repetition-rate nanosecond fiber-laser

    NASA Astrophysics Data System (ADS)

    Shi, Wei; Hajireza, Parsin; Shao, Peng; Forbrich, Alexander; Zemp, Roger J.

    2011-08-01

    Optical-resolution photoacoustic microscopy (OR-PAM) is capable of achieving optical-absorption-contrast images with micron-scale spatial resolution. Previous OR-PAM systems have been frame-rate limited by mechanical scanning speeds and laser pulse repetition rate (PRR). We demonstrate OR-PAM imaging using a diode-pumped nanosecond-pulsed Ytterbium-doped 532-nm fiber laser with PRR up to 600 kHz. Combined with fast-scanning mirrors, our proposed system provides C-scan and 3D images with acquisition frame rate of 4 frames per second (fps) or higher, two orders of magnitude faster than previously published systems. High-contrast images of capillary-scale microvasculature in a live Swiss Webster mouse ear with ~6-μm optical lateral spatial resolution are demonstrated.

  14. High-resolution FTIR imaging of colon tissues for elucidation of individual cellular and histopathological features.

    PubMed

    Nallala, Jayakrupakar; Lloyd, Gavin Rhys; Shepherd, Neil; Stone, Nick

    2016-01-21

    Novel technologies that could complement current histopathology based cancer diagnostic methods are under examination. In this endeavour mid-infrared spectroscopic imaging is a promising candidate that can provide valuable bio-molecular information from unstained cells and tissues in a rapid and a non-destructive manner. With this imaging technique, the biochemical information obtained from smaller areas of the tissues can be of clinical significance and hence the measured pixel size. Until recently it was difficult to obtain spectral data from pixels below around 5 microns square. High NA objectives have been utilised to reduce the ideal diffraction limit, enabling for the first time elucidation of subcellular features. In this context, the ability of high-resolution imaging, obtained using novel high-magnification optics retro-fitted onto a bench top FTIR imaging system, to characterise histopathological features in colonic tissues has been tested. Formalin fixed paraffin embedded colon tissues from three different pathologies were imaged directly using the conventional and the high-magnification imaging set-ups. To circumvent chemical de-paraffinization protocols, an extended multiplicative signal correction (EMSC) based electronic de-paraffinization was carried out on all the infrared images. Multivariate analysis of the high-magnification infrared imaging data showed a detailed information of the histological features of the colon tissue in comparison to conventional imaging. Furthermore, high-magnification imaging has enabled a label-free characterization of the mucin rich goblet cell features in an unprecedented manner. The current study demonstrates the applicability of high-magnification FTIR imaging to characterise complex tissues on a smaller scale that could be of clinical significance. PMID:26549223

  15. Exploring volumetrically indexed cups

    NASA Astrophysics Data System (ADS)

    Jones, Dustin L.

    2011-03-01

    This article was inspired by a set of 12 cylindrical cups, which are volumetrically indexed; that is to say, the volume of cup n is equal to n times the volume of cup 1. Various sets of volumetrically indexed cylindrical cups are explored. I demonstrate how this children's toy is ripe for mathematical investigation, with connections to geometry, algebra and differential calculus. Students with an understanding of these topics should be able to complete the analysis and related exercises contained herein.

  16. AFM-based Mapping of the Elastic Properties of Cell Walls: at Tissue, Cellular, and Subcellular Resolutions

    PubMed Central

    Peaucelle, Alexis

    2014-01-01

    We describe a recently developed method to measure mechanical properties of the surfaces of plant tissues using atomic force microscopy (AFM) micro/nano-indentations, for a JPK AFM. Specifically, in this protocol we measure the apparent Young’s modulus of cell walls at subcellular resolutions across regions of up to 100 µm x 100 µm in floral meristems, hypocotyls, and roots. This requires careful preparation of the sample, the correct selection of micro-indenters and indentation depths. To account for cell wall properties only, measurements are performed in highly concentrated solutions of mannitol in order to plasmolyze the cells and thus remove the contribution of cell turgor pressure. In contrast to other extant techniques, by using different indenters and indentation depths, this method allows simultaneous multiscale measurements, i.e. at subcellular resolutions and across hundreds of cells comprising a tissue. This means that it is now possible to spatially-temporally characterize the changes that take place in the mechanical properties of cell walls during development, enabling these changes to be correlated with growth and differentiation. This represents a key step to understand how coordinated microscopic cellular changes bring about macroscopic morphogenetic events. However, several limitations remain: the method can only be used on fairly small samples (around 100 µm in diameter) and only on external tissues; the method is sensitive to tissue topography; it measures only certain aspects of the tissue’s complex mechanical properties. The technique is being developed rapidly and it is likely that most of these limitations will be resolved in the near future. PMID:25080133

  17. A medaka model of cancer allowing direct observation of transplanted tumor cells in vivo at a cellular-level resolution.

    PubMed

    Hasegawa, Sumitaka; Maruyama, Kouichi; Takenaka, Hikaru; Furukawa, Takako; Saga, Tsuneo

    2009-08-18

    The recent success with small fish as an animal model of cancer with the aid of fluorescence technique has attracted cancer modelers' attention because it would be possible to directly visualize tumor cells in vivo in real time. Here, we report a medaka model capable of allowing the observation of various cell behaviors of transplanted tumor cells, such as cell proliferation and metastasis, which were visualized easily in vivo. We established medaka melanoma (MM) cells stably expressing GFP and transplanted them into nonirradiated and irradiated medaka. The tumor cells were grown at the injection sites in medaka, and the spatiotemporal changes were visualized under a fluorescence stereoscopic microscope at a cellular-level resolution, and even at a single-cell level. Tumor dormancy and metastasis were also observed. Interestingly, in irradiated medaka, accelerated tumor growth and metastasis of the transplanted tumor cells were directly visualized. Our medaka model provides an opportunity to visualize in vivo tumor cells "as seen in a culture dish" and would be useful for in vivo tumor cell biology. PMID:19666513

  18. A medaka model of cancer allowing direct observation of transplanted tumor cells in vivo at a cellular-level resolution

    PubMed Central

    Hasegawa, Sumitaka; Maruyama, Kouichi; Takenaka, Hikaru; Furukawa, Takako; Saga, Tsuneo

    2009-01-01

    The recent success with small fish as an animal model of cancer with the aid of fluorescence technique has attracted cancer modelers' attention because it would be possible to directly visualize tumor cells in vivo in real time. Here, we report a medaka model capable of allowing the observation of various cell behaviors of transplanted tumor cells, such as cell proliferation and metastasis, which were visualized easily in vivo. We established medaka melanoma (MM) cells stably expressing GFP and transplanted them into nonirradiated and irradiated medaka. The tumor cells were grown at the injection sites in medaka, and the spatiotemporal changes were visualized under a fluorescence stereoscopic microscope at a cellular-level resolution, and even at a single-cell level. Tumor dormancy and metastasis were also observed. Interestingly, in irradiated medaka, accelerated tumor growth and metastasis of the transplanted tumor cells were directly visualized. Our medaka model provides an opportunity to visualize in vivo tumor cells “as seen in a culture dish” and would be useful for in vivo tumor cell biology. PMID:19666513

  19. The iRoCS Toolbox--3D analysis of the plant root apical meristem at cellular resolution.

    PubMed

    Schmidt, Thorsten; Pasternak, Taras; Liu, Kun; Blein, Thomas; Aubry-Hivet, Dorothée; Dovzhenko, Alexander; Duerr, Jasmin; Teale, William; Ditengou, Franck A; Burkhardt, Hans; Ronneberger, Olaf; Palme, Klaus

    2014-03-01

    To achieve a detailed understanding of processes in biological systems, cellular features must be quantified in the three-dimensional (3D) context of cells and organs. We described use of the intrinsic root coordinate system (iRoCS) as a reference model for the root apical meristem of plants. iRoCS enables direct and quantitative comparison between the root tips of plant populations at single-cell resolution. The iRoCS Toolbox automatically fits standardized coordinates to raw 3D image data. It detects nuclei or segments cells, automatically fits the coordinate system, and groups the nuclei/cells into the root's tissue layers. The division status of each nucleus may also be determined. The only manual step required is to mark the quiescent centre. All intermediate outputs may be refined if necessary. The ability to learn the visual appearance of nuclei by example allows the iRoCS Toolbox to be easily adapted to various phenotypes. The iRoCS Toolbox is provided as an open-source software package, licensed under the GNU General Public License, to make it accessible to a broad community. To demonstrate the power of the technique, we measured subtle changes in cell division patterns caused by modified auxin flux within the Arabidopsis thaliana root apical meristem. PMID:24417645

  20. Volumetric retinal imaging with ultrahigh-resolution spectral-domain optical coherence tomography and adaptive optics using two broadband light sources◊

    PubMed Central

    Cense, Barry; Koperda, Eric; Brown, Jeffrey M.; Kocaoglu, Omer P.; Gao, Weihua; Jonnal, Ravi S.; Miller, Donald T.

    2009-01-01

    Ultrabroadband sources, such as multiplexed superluminescent diodes (SLDs) and femtosecond lasers, have been successfully employed in adaptive optics optical coherence tomography (AO-OCT) systems for ultrahigh resolution retinal imaging. The large cost differential of these sources, however, motivates the need for a performance comparison. Here, we compare the performance of a Femtolasers Integral Ti:Sapphire laser and a Superlum BroadLighter T840, using the same AO-OCT system and the same subject. In addition, we investigate the capability of our instrument equipped with the Integral to capture volume images of the fovea and adjacent regions on a second subject using the AO to control focus in the retina and custom and freeware image registration software to reduce eye motion artifacts. Monochromatic ocular aberrations were corrected with a woofer-tweeter AO system. Coherence lengths of the Integral and BroadLighter were measured in vivo at 3.2 μm and 3.3 μm, respectively. The difference in dynamic range was 5 dB, close to the expected variability of the experiment. Individual cone photoreceptors, retinal capillaries and nerve fiber bundles were distinguished in all three dimensions with both sources. The acquired retinal volumes are provided for viewing in OSA ISP, allowing the reader to data mine at the microscope level. PMID:19259249

  1. Volumetric structured illumination microscopy enabled by tunable focus lens (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Hinsdale, Taylor; Malik, Bilal; Olsovsky, Cory; Jo, Javier A.; Maitland, Kristen C.

    2016-03-01

    We present a volumetric imaging method for biological tissue that is free of mechanically scanning components. The optical sectioning in the system is obtained by structured illumination microscopy (SIM) with the depth of focus being varied by the use of an electronic tunable-focus lens (ETL). The performance of the axial scanning mechanism was evaluated and characterized in conjunction with SIM to ensure volumetric images could be recorded and reconstructed without significant losses in optical section thickness and lateral resolution over the full desired scan range. It was demonstrated that sub-cellular image resolutions were obtainable in both microsphere films and in ex vivo oral mucosa, spanning multiple cell layers, without significant losses in image quality. The mechanism proposed here has the ability to be integrated into any wide-field microscopy system to convert it into a three-dimensional imaging platform without the need for axial scanning of the sample or imaging optics. The ability to axially scan independent of mechanical movement also provides the opportunity for the development of endoscopic systems which can create volumetric images of tissue in vivo.

  2. Mapping whole-brain activity with cellular resolution by light-sheet microscopy and high-throughput image analysis (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Silvestri, Ludovico; Rudinskiy, Nikita; Paciscopi, Marco; Müllenbroich, Marie Caroline; Costantini, Irene; Sacconi, Leonardo; Frasconi, Paolo; Hyman, Bradley T.; Pavone, Francesco S.

    2016-03-01

    Mapping neuronal activity patterns across the whole brain with cellular resolution is a challenging task for state-of-the-art imaging methods. Indeed, despite a number of technological efforts, quantitative cellular-resolution activation maps of the whole brain have not yet been obtained. Many techniques are limited by coarse resolution or by a narrow field of view. High-throughput imaging methods, such as light sheet microscopy, can be used to image large specimens with high resolution and in reasonable times. However, the bottleneck is then moved from image acquisition to image analysis, since many TeraBytes of data have to be processed to extract meaningful information. Here, we present a full experimental pipeline to quantify neuronal activity in the entire mouse brain with cellular resolution, based on a combination of genetics, optics and computer science. We used a transgenic mouse strain (Arc-dVenus mouse) in which neurons which have been active in the last hours before brain fixation are fluorescently labelled. Samples were cleared with CLARITY and imaged with a custom-made confocal light sheet microscope. To perform an automatic localization of fluorescent cells on the large images produced, we used a novel computational approach called semantic deconvolution. The combined approach presented here allows quantifying the amount of Arc-expressing neurons throughout the whole mouse brain. When applied to cohorts of mice subject to different stimuli and/or environmental conditions, this method helps finding correlations in activity between different neuronal populations, opening the possibility to infer a sort of brain-wide 'functional connectivity' with cellular resolution.

  3. Volumetric Muscle Loss.

    PubMed

    Pollot, Beth E; Corona, Benjamin T

    2016-01-01

    Volumetric muscle loss (VML) injury is prevalent in severe extremity trauma and is an emerging focus area among orthopedic and regenerative medicine fields. VML injuries are the result of an abrupt, frank loss of tissue and therefore of different etiology from other standard rodent injury models to include eccentric contraction, ischemia reperfusion, crush, and freeze injury. The current focus of many VML-related research efforts is to regenerate the lost muscle tissue and thereby improve muscle strength. Herein, we describe a VML model in the anterior compartment of the hindlimb that is permissible to repeated neuromuscular strength assessments and is validated in mouse, rat, and pig. PMID:27492162

  4. Flexible Volumetric Structure

    NASA Technical Reports Server (NTRS)

    Cagle, Christopher M. (Inventor); Schlecht, Robin W. (Inventor)

    2014-01-01

    A flexible volumetric structure has a first spring that defines a three-dimensional volume and includes a serpentine structure elongatable and compressible along a length thereof. A second spring is coupled to at least one outboard edge region of the first spring. The second spring is a sheet-like structure capable of elongation along an in-plane dimension thereof. The second spring is oriented such that its in-plane dimension is aligned with the length of the first spring's serpentine structure.

  5. Fluorescent scanning laser ophthalmoscopy for cellular resolution in vivo mouse retinal imaging: benefits and drawbacks of implementing adaptive optics (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Zhang, Pengfei; Goswami, Mayank; Pugh, Edward N.; Zawadzki, Robert J.

    2016-03-01

    Scanning Laser Ophthalmoscopy (SLO) is a very important imaging tool in ophthalmology research. By combing with Adaptive Optics (AO) technique, AO-SLO can correct for ocular aberrations resulting in cellular level resolution, allowing longitudinal studies of single cells morphology in the living eyes. The numerical aperture (NA) sets the optical resolution that can be achieve in the "classical" imaging systems. Mouse eye has more than twice NA of the human eye, thus offering theoretically higher resolution. However, in most SLO based imaging systems the imaging beam size at mouse pupil sets the NA of that instrument, while most of the AO-SLO systems use almost the full NA of the mouse eye. In this report, we first simulated the theoretical resolution that can be achieved in vivo for different imaging beam sizes (different NA), assumingtwo cases: no aberrations and aberrations based on published mouse ocular wavefront data. Then we imaged mouse retinas with our custom build SLO system using different beam sizes to compare these results with theory. Further experiments include comparison of the SLO and AO-SLO systems for imaging different type of fluorescently labeled cells (microglia, ganglion, photoreceptors, etc.). By comparing those results and taking into account systems complexity and ease of use, the benefits and drawbacks of two imaging systems will be discussed.

  6. GPU-based computational adaptive optics for volumetric optical coherence microscopy

    NASA Astrophysics Data System (ADS)

    Tang, Han; Mulligan, Jeffrey A.; Untracht, Gavrielle R.; Zhang, Xihao; Adie, Steven G.

    2016-03-01

    Optical coherence tomography (OCT) is a non-invasive imaging technique that measures reflectance from within biological tissues. Current higher-NA optical coherence microscopy (OCM) technologies with near cellular resolution have limitations on volumetric imaging capabilities due to the trade-offs between resolution vs. depth-of-field and sensitivity to aberrations. Such trade-offs can be addressed using computational adaptive optics (CAO), which corrects aberration computationally for all depths based on the complex optical field measured by OCT. However, due to the large size of datasets plus the computational complexity of CAO and OCT algorithms, it is a challenge to achieve high-resolution 3D-OCM reconstructions at speeds suitable for clinical and research OCM imaging. In recent years, real-time OCT reconstruction incorporating both dispersion and defocus correction has been achieved through parallel computing on graphics processing units (GPUs). We add to these methods by implementing depth-dependent aberration correction for volumetric OCM using plane-by-plane phase deconvolution. Following both defocus and aberration correction, our reconstruction algorithm achieved depth-independent transverse resolution of 2.8 um, equal to the diffraction-limited focal plane resolution. We have translated the CAO algorithm to a CUDA code implementation and tested the speed of the software in real-time using two GPUs - NVIDIA Quadro K600 and Geforce TITAN Z. For a data volume containing 4096×256×256 voxels, our system's processing speed can keep up with the 60 kHz acquisition rate of the line-scan camera, and takes 1.09 seconds to simultaneously update the CAO correction for 3 en face planes at user-selectable depths.

  7. High resolution light-sheet based high-throughput imaging cytometry system enables visualization of intra-cellular organelles

    NASA Astrophysics Data System (ADS)

    Regmi, Raju; Mohan, Kavya; Mondal, Partha Pratim

    2014-09-01

    Visualization of intracellular organelles is achieved using a newly developed high throughput imaging cytometry system. This system interrogates the microfluidic channel using a sheet of light rather than the existing point-based scanning techniques. The advantages of the developed system are many, including, single-shot scanning of specimens flowing through the microfluidic channel at flow rate ranging from micro- to nano- lit./min. Moreover, this opens-up in-vivo imaging of sub-cellular structures and simultaneous cell counting in an imaging cytometry system. We recorded a maximum count of 2400 cells/min at a flow-rate of 700 nl/min, and simultaneous visualization of fluorescently-labeled mitochondrial network in HeLa cells during flow. The developed imaging cytometry system may find immediate application in biotechnology, fluorescence microscopy and nano-medicine.

  8. A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis

    PubMed Central

    Castro-González, Carlos; Luengo-Oroz, Miguel A.; Duloquin, Louise; Savy, Thierry; Rizzi, Barbara; Desnoulez, Sophie; Doursat, René; Kergosien, Yannick L.; Ledesma-Carbayo, María J.; Bourgine, Paul

    2014-01-01

    A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages. PMID:24945246

  9. Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures.

    PubMed

    Silvaroli, Josie A; Arne, Jason M; Chelstowska, Sylwia; Kiser, Philip D; Banerjee, Surajit; Golczak, Marcin

    2016-04-15

    Important in regulating the uptake, storage, and metabolism of retinoids, cellular retinol-binding protein 1 (CRBP1) is essential for trafficking vitamin A through the cytoplasm. However, the molecular details of ligand uptake and targeted release by CRBP1 remain unclear. Here we report the first structure of CRBP1 in a ligand-free form as well as ultra-high resolution structures of this protein bound to either all-trans-retinol or retinylamine, the latter a therapeutic retinoid that prevents light-induced retinal degeneration. Superpositioning of human apo- and holo-CRBP1 revealed major differences within segments surrounding the entrance to the retinoid-binding site. These included α-helix II and hairpin turns between β-strands βC-βD and βE-βF as well as several side chains, such as Phe-57, Tyr-60, and Ile-77, that change their orientations to accommodate the ligand. Additionally, we mapped hydrogen bond networks inside the retinoid-binding cavity and demonstrated their significance for the ligand affinity. Analyses of the crystallographic B-factors indicated several regions with higher backbone mobility in the apoprotein that became more rigid upon retinoid binding. This conformational flexibility of human apo-CRBP1 facilitates interaction with the ligands, whereas the more rigid holoprotein structure protects the labile retinoid moiety during vitamin A transport. These findings suggest a mechanism of induced fit upon ligand binding by mammalian cellular retinol-binding proteins. PMID:26900151

  10. Three-Dimensional Analysis of Syncytial-Type Cell Plates during Endosperm Cellularization Visualized by High Resolution Electron Tomography W⃞

    PubMed Central

    Otegui, Marisa S.; Mastronarde, David N.; Kang, Byung-Ho; Bednarek, Sebastian Y.; Staehelin, L. Andrew

    2001-01-01

    The three-dimensional architecture of syncytial-type cell plates in the endosperm of Arabidopsis has been analyzed at ∼6-nm resolution by means of dual-axis high-voltage electron tomography of high-pressure frozen/freeze-substituted samples. Mini-phragmoplasts consisting of microtubule clusters assemble between sister and nonsister nuclei. Most Golgi-derived vesicles appear connected to these microtubules by two molecules that resemble kinesin-like motor proteins. These vesicles fuse with each other to form hourglass-shaped intermediates, which become wide (∼45 nm in diameter) tubules, the building blocks of wide tubular networks. New mini-phragmoplasts also are generated de novo around the margins of expanding wide tubular networks, giving rise to new foci of cell plate growth, which later become integrated into the main cell plate. Spiral-shaped rings of the dynamin-like protein ADL1A constrict but do not fission the wide tubules at irregular intervals. These rings appear to maintain the tubular geometry of the network. The wide tubular network matures into a convoluted fenestrated sheet in a process that involves increases of 45 and 130% in relative membrane surface area and volume, respectively. The proportionally larger increase in volume appears to reflect callose synthesis. Upon fusion with the parental plasma membrane, the convoluted fenestrated sheet is transformed into a planar fenestrated sheet. This transformation involves clathrin-coated vesicles that reduce the relative membrane surface area and volume by ∼70%. A ribosome-excluding matrix encompasses the cell plate membranes from the fusion of the first vesicles until the onset of the planar fenestrated sheet formation. We postulate that this matrix contains the molecules that mediate cell plate assembly. PMID:11549762

  11. Imaging of cellular spread on a three-dimensional scaffold by means of a novel cell-labeling technique for high-resolution computed tomography.

    PubMed

    Thimm, Benjamin W; Hofmann, Sandra; Schneider, Philipp; Carretta, Roberto; Müller, Ralph

    2012-03-01

    Computed tomography (CT) represents a truly three-dimensional (3D) imaging technique that can provide high-resolution images on the cellular level. Thus, one approach to detect single cells is X-ray absorption-based CT, where cells are labeled with a dense, opaque material providing the required contrast for CT imaging. Within the present work, a novel cell-labeling method has been developed showing the feasibility of labeling fixed cells with iron oxide (FeO) particles for subsequent CT imaging and quantitative morphometry. A biotin-streptavidin detection system was exploited to bind FeO particles to its target endothelial cells. The binding of the particles was predominantly close to the cell centers on 2D surfaces as shown by light microscopy, scanning electron microscopy, and CT. When cells were cultured on porous, 3D polyurethane surfaces, significantly more FeO particles were detected compared with surfaces without cells and FeO particle labeling using CT. Here, we report on the implementation and evaluation of a novel cell detection method based on high-resolution CT. This system has potential in cell tracking for 3D in vitro imaging in the future. PMID:21951168

  12. Adaptive optics optical coherence tomography at 120,000 depth scans/s for non-invasive cellular phenotyping of the living human retina

    PubMed Central

    Torti, Cristiano; Považay, Boris; Hofer, Bernd; Unterhuber, Angelika; Carroll, Joseph; Ahnelt, Peter Kurt; Drexler, Wolfgang

    2012-01-01

    This paper presents a successful combination of ultra-high speed (120,000 depth scans/s), ultra-high resolution optical coherence tomography with adaptive optics and an achromatizing lens for compensation of monochromatic and longitudinal chromatic ocular aberrations, respectively, allowing for non-invasive volumetric imaging in normal and pathologic human retinas at cellular resolution. The capability of this imaging system is demonstrated here through preliminary studies by probing cellular intraretinal structures that have not been accessible so far with in vivo, non-invasive, label-free imaging techniques, including pigment epithelial cells, micro-vasculature of the choriocapillaris, single nerve fibre bundles and collagenous plates of the lamina cribrosa in the optic nerve head. In addition, the volumetric extent of cone loss in two colour-blinds could be quantified for the first time. This novel technique provides opportunities to enhance the understanding of retinal pathogenesis and early diagnosis of retinal diseases. PMID:19997159

  13. Volumetric Light-Field Excitation.

    PubMed

    Schedl, David C; Bimber, Oliver

    2016-01-01

    We explain how to concentrate light simultaneously at multiple selected volumetric positions by means of a 4D illumination light field. First, to select target objects, a 4D imaging light field is captured. A light field mask is then computed automatically for this selection to avoid illumination of the remaining areas. With one-photon illumination, simultaneous generation of complex volumetric light patterns becomes possible. As a full light-field can be captured and projected simultaneously at the desired exposure and excitation times, short readout and lighting durations are supported. PMID:27363565

  14. Volumetric Light-Field Excitation

    PubMed Central

    Schedl, David C.; Bimber, Oliver

    2016-01-01

    We explain how to concentrate light simultaneously at multiple selected volumetric positions by means of a 4D illumination light field. First, to select target objects, a 4D imaging light field is captured. A light field mask is then computed automatically for this selection to avoid illumination of the remaining areas. With one-photon illumination, simultaneous generation of complex volumetric light patterns becomes possible. As a full light-field can be captured and projected simultaneously at the desired exposure and excitation times, short readout and lighting durations are supported. PMID:27363565

  15. Rapid mapping of volumetric errors

    SciTech Connect

    Krulewich, D.; Hale, L.; Yordy, D.

    1995-09-13

    This paper describes a relatively inexpensive, fast, and easy to execute approach to mapping the volumetric errors of a machine tool, coordinate measuring machine, or robot. An error map is used to characterize a machine or to improve its accuracy by compensating for the systematic errors. The method consists of three steps: (1) modeling the relationship between the volumetric error and the current state of the machine; (2) acquiring error data based on length measurements throughout the work volume; and (3) optimizing the model to the particular machine.

  16. Multiple site optical recording of transmembrane voltage (MSORTV) in patterned growth heart cell cultures: assessing electrical behavior, with microsecond resolution, on a cellular and subcellular scale.

    PubMed Central

    Rohr, S; Salzberg, B M

    1994-01-01

    We have applied multiple site optical recording of transmembrane voltage (MSORTV) to patterned growth cultures of heart cells to analyze the effect of geometry per se on impulse propagation in excitable tissue, with cellular and subcellular resolution. Extensive dye screening led to the choice of di-8-ANEPPS as the most suitable voltage-sensitive dye for this application; it is internalized slowly and permits optical recording with signal-to-noise ratios as high as 40:1 (measured peak-to-peak) and average fractional fluorescence changes of 15% per 100 mV. Using a x 100 objective and a fast data acquisition system, we could resolve impulse propagation on a microscopic scale (15 microns) with high temporal resolution (uncertainty of +/- 5 microseconds). We could observe the decrease in conduction velocity of an impulse propagating along a narrow cell strand as it enters a region of abrupt expansion, and we could explain this phenomenon in terms of the micro-architecture of the tissue. In contrast with the elongated and aligned cells forming the narrow strands, the cells forming the expansions were aligned at random and presented 2.5 times as many cell-to-cell appositions per unit length. If the decrease in conduction velocity results entirely from this increased number of cell-to-cell boundaries per unit length, the mean activation delay introduced by each boundary can be estimated to be 70 microseconds. Using this novel experimental system, we could also demonstrate the electrical coupling of fibroblasts and endotheloid cells to myocytes in culture. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 FIGURE 7 FIGURE 8 PMID:7811945

  17. Combined Volumetric and Surface Registration

    PubMed Central

    Zöllei, Lilla; Fischl, Bruce

    2009-01-01

    In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that aligns cortical folding patterns. This warp field is then refined with an intensity driven optical flow procedure that registers noncortical regions, while preserving the cortical alignment. The result is a combined surface and volume morph (CVS) that accurately registers both cortical and subcortical regions, establishing a single coordinate system suitable for the entire brain. PMID:19273000

  18. Resolution of the cellular proteome of the nucleocapsid protein from a highly pathogenic isolate of porcine reproductive and respiratory syndrome virus identifies PARP-1 as a cellular target whose interaction is critical for virus biology.

    PubMed

    Liu, Long; Lear, Zoe; Hughes, David J; Wu, Weining; Zhou, En-min; Whitehouse, Adrian; Chen, Hongying; Hiscox, Julian A

    2015-03-23

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to the swine industry and food security worldwide. The nucleocapsid (N) protein is a major structural protein of PRRSV. The primary function of this protein is to encapsidate the viral RNA genome, and it is also thought to participate in the modulation of host cell biology and recruitment of cellular factors to facilitate virus infection. In order to the better understand these latter roles the cellular interactome of PRRSV N protein was defined using label free quantitative proteomics. This identified several cellular factors that could interact with the N protein including poly [ADP-ribose] polymerase 1 (PARP-1), a cellular protein, which can add adenosine diphosphate ribose to a protein. Use of the PARP-1 small molecule inhibitor, 3-AB, in PRRSV infected cells demonstrated that PARP-1 was required and acted as an enhancer factor for virus biology. Serial growth of PRRSV in different concentrations of 3-AB did not yield viruses that were able to grow with wild type kinetics, suggesting that by targeting a cellular protein crucial for virus biology, resistant phenotypes did not emerge. This study provides further evidence that cellular proteins, which are critical for virus biology, can also be targeted to ablate virus growth and provide a high barrier for the emergence of drug resistance. PMID:25614100

  19. PSF engineering in multifocus microscopy for increased depth volumetric imaging.

    PubMed

    Hajj, Bassam; El Beheiry, Mohamed; Dahan, Maxime

    2016-03-01

    Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 µm as well as for the tracking of diffusing beads in a fluid environment over 8 µm. PMID:27231584

  20. PSF engineering in multifocus microscopy for increased depth volumetric imaging

    PubMed Central

    Hajj, Bassam; El Beheiry, Mohamed; Dahan, Maxime

    2016-01-01

    Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 µm as well as for the tracking of diffusing beads in a fluid environment over 8 µm. PMID:27231584

  1. Continuous volumetric imaging via an optical phase-locked ultrasound lens

    PubMed Central

    Kong, Lingjie; Tang, Jianyong; Little, Justin P.; Yu, Yang; Lämmermann, Tim; Lin, Charles P.; Germain, Ronald N.; Cui, Meng

    2015-01-01

    In vivo imaging at high spatiotemporal resolution holds the key to the fundamental understanding of complex biological systems. Integrating an optical phase-locked ultrasound lens into a conventional two-photon fluorescence microscope, we achieved microsecond scale axial scanning, which enabled high-speed volumetric imaging. We applied this system to multicolor volumetric imaging of fast processes, including calcium dynamics in the cerebral cortex of behaving mice, and transient morphology changes and trafficking of immune cells. PMID:26167641

  2. Continuous volumetric imaging via an optical phase-locked ultrasound lens.

    PubMed

    Kong, Lingjie; Tang, Jianyong; Little, Justin P; Yu, Yang; Lämmermann, Tim; Lin, Charles P; Germain, Ronald N; Cui, Meng

    2015-08-01

    In vivo imaging at high spatiotemporal resolution is key to the understanding of complex biological systems. We integrated an optical phase-locked ultrasound lens into a two-photon fluorescence microscope and achieved microsecond-scale axial scanning, thus enabling volumetric imaging at tens of hertz. We applied this system to multicolor volumetric imaging of processes sensitive to motion artifacts, including calcium dynamics in behaving mouse brain and transient morphology changes and trafficking of immune cells. PMID:26167641

  3. Volumetric Acoustic Vector Intensity Probe

    NASA Technical Reports Server (NTRS)

    Klos, Jacob

    2006-01-01

    A new measurement tool capable of imaging the acoustic intensity vector throughout a large volume is discussed. This tool consists of an array of fifty microphones that form a spherical surface of radius 0.2m. A simultaneous measurement of the pressure field across all the microphones provides time-domain near-field holograms. Near-field acoustical holography is used to convert the measured pressure into a volumetric vector intensity field as a function of frequency on a grid of points ranging from the center of the spherical surface to a radius of 0.4m. The volumetric intensity is displayed on three-dimensional plots that are used to locate noise sources outside the volume. There is no restriction on the type of noise source that can be studied. The sphere is mobile and can be moved from location to location to hunt for unidentified noise sources. An experiment inside a Boeing 757 aircraft in flight successfully tested the ability of the array to locate low-noise-excited sources on the fuselage. Reference transducers located on suspected noise source locations can also be used to increase the ability of this device to separate and identify multiple noise sources at a given frequency by using the theory of partial field decomposition. The frequency range of operation is 0 to 1400Hz. This device is ideal for the study of noise sources in commercial and military transportation vehicles in air, on land and underwater.

  4. Seismic volumetric flattening and segmentation

    NASA Astrophysics Data System (ADS)

    Lomask, Jesse

    Two novel algorithms provide seismic interpretation solutions that use the full dimensionality of the data. The first is volumetric flattening and the second is image segmentation for tracking salt boundaries. Volumetric flattening is an efficient full-volume automatic dense-picking method applied to seismic data. First local dips (step-outs) are calculated over the entire seismic volume. The dips are then resolved into time shifts (or depth shifts) in a least-squares sense. To handle faults (discontinuous reflections), I apply a weighted inversion scheme. Additional information is incorporated in this flattening algorithm as geological constraints. The method is tested successfully on both synthetic and field data sets of varying degrees of complexity including salt piercements, angular unconformities, and laterally limited faults. The second full-volume interpretation method uses normalized cuts image segmentation to track salt interfaces. I apply a modified version of the normalized cuts image segmentation (NCIS) method to partition seismic images along salt interfaces. The method is capable of tracking interfaces that are not continuous, where conventional horizon tracking algorithms may fail. This method partitions the seismic image into two groups. One group is inside the salt body and the other is outside. Where the two groups meet is the salt boundary. By imposing bounds and by distributing the algorithm on a parallel cluster, I significantly increase efficiency and robustness. This method is demonstrated to be effective on both 2D and 3D seismic data sets.

  5. In vivo real-time volumetric synthetic aperture ultrasound imaging

    NASA Astrophysics Data System (ADS)

    Bouzari, Hamed; Rasmussen, Morten F.; Brandt, Andreas H.; Stuart, Matthias B.; Nikolov, Svetoslav; Jensen, Jørgen A.

    2015-03-01

    Synthetic aperture (SA) imaging can be used to achieve real-time volumetric ultrasound imaging using 2-D array transducers. The sensitivity of SA imaging is improved by maximizing the acoustic output, but one must consider the limitations of an ultrasound system, both technical and biological. This paper investigates the in vivo applicability and sensitivity of volumetric SA imaging. Utilizing the transmit events to generate a set of virtual point sources, a frame rate of 25 Hz for a 90° × 90° field-of-view was achieved. data were obtained using a 3.5 MHz 32 × 32 elements 2-D phased array transducer connected to the experimental scanner (SARUS). Proper scaling is applied to the excitation signal such that intensity levels are in compliance with the U.S. Food and Drug Administration regulations for in vivo ultrasound imaging. The measured Mechanical Index and spatial-peak-temporal-average intensity for parallel beam-forming (PB) are 0.83 and 377.5mW/cm2, and for SA are 0.48 and 329.5mW/cm2. A human kidney was volumetrically imaged with SA and PB techniques simultaneously. Two radiologists for evaluation of the volumetric SA were consulted by means of a questionnaire on the level of details perceivable in the beam-formed images. The comparison was against PB based on the in vivo data. The feedback from the domain experts indicates that volumetric SA images internal body structures with a better contrast resolution compared to PB at all positions in the entire imaged volume. Furthermore, the autocovariance of a homogeneous area in the in vivo SA data, had 23.5% smaller width at the half of its maximum value compared to PB.

  6. Analysis of the relationship between the volumetric soil moisture content and the NDVI from high resolution multi-spectral images for definition of vineyard management zones to improve irrigation

    NASA Astrophysics Data System (ADS)

    Martínez-Casasnovas, J. A.; Ramos, M. C.

    2009-04-01

    As suggested by previous research in the field of precision viticulture, intra-field yield variability is dependent on the variation of soil properties, and in particular the soil moisture content. Since the mapping in detail of this soil property for precision viticulture applications is highly costly, the objective of the present research is to analyse its relationship with the normalised difference vegetation index from high resolution satellite images to the use it in the definition of vineyard zonal management. The final aim is to improve irrigation in commercial vineyard blocks for better management of inputs and to deliver a more homogeneous fruit to the winery. The study was carried out in a vineyard block located in Raimat (NE Spain, Costers del Segre Designation of Origin). This is a semi-arid area with continental Mediterranean climate and a total annual precipitation between 300-400 mm. The vineyard block (4.5 ha) is planted with Syrah vines in a 3x2 m pattern. The vines are irrigated by means of drips under a partial root drying schedule. Initially, the irrigation sectors had a quadrangular distribution, with a size of about 1 ha each. Yield is highly variable within the block, presenting a coefficient of variation of 24.9%. For the measurement of the soil moisture content a regular sampling grid of 30 x 40 m was defined. This represents a sample density of 8 samples ha-1. At the nodes of the grid, TDR (Time Domain Reflectometer) probe tubes were permanently installed up to the 80 cm or up to reaching a contrasting layer. Multi-temporal measures were taken at different depths (each 20 cm) between November 2006 and December 2007. For each date, a map of the variability of the profile soil moisture content was interpolated by means of geostatistical analysis: from the measured values at the grid points the experimental variograms were computed and modelled and global block kriging (10 m squared blocks) undertaken with a grid spacing of 3 m x 3 m. On the

  7. A reduced volumetric expansion factor plot

    NASA Technical Reports Server (NTRS)

    Hendricks, R. C.

    1979-01-01

    A reduced volumetric expansion factor plot has been constructed for simple fluids which is suitable for engineering computations in heat transfer. Volumetric expansion factors have been found useful in correlating heat transfer data over a wide range of operating conditions including liquids, gases and the near critical region.

  8. A reduced volumetric expansion factor plot

    NASA Technical Reports Server (NTRS)

    Hendricks, R. C.

    1979-01-01

    A reduced volumetric expansion factor plot was constructed for simple fluids which is suitable for engineering computations in heat transfer. Volumetric expansion factors were found useful in correlating heat transfer data over a wide range of operating conditions including liquids, gases and the near critical region.

  9. Volumetric optoacoustic monitoring of endovenous laser treatments

    NASA Astrophysics Data System (ADS)

    Fehm, Thomas F.; Deán-Ben, Xosé L.; Schaur, Peter; Sroka, Ronald; Razansky, Daniel

    2016-03-01

    Chronic venous insufficiency (CVI) is one of the most common medical conditions with reported prevalence estimates as high as 30% in the adult population. Although conservative management with compression therapy may improve the symptoms associated with CVI, healing often demands invasive procedures. Besides established surgical methods like vein stripping or bypassing, endovenous laser therapy (ELT) emerged as a promising novel treatment option during the last 15 years offering multiple advantages such as less pain and faster recovery. Much of the treatment success hereby depends on monitoring of the treatment progression using clinical imaging modalities such as Doppler ultrasound. The latter however do not provide sufficient contrast, spatial resolution and three-dimensional imaging capacity which is necessary for accurate online lesion assessment during treatment. As a consequence, incidence of recanalization, lack of vessel occlusion and collateral damage remains highly variable among patients. In this study, we examined the capacity of volumetric optoacoustic tomography (VOT) for real-time monitoring of ELT using an ex-vivo ox foot model. ELT was performed on subcutaneous veins while optoacoustic signals were acquired and reconstructed in real-time and at a spatial resolution in the order of 200μm. VOT images showed spatio-temporal maps of the lesion progression, characteristics of the vessel wall, and position of the ablation fiber's tip during the pull back. It was also possible to correlate the images with the temperature elevation measured in the area adjacent to the ablation spot. We conclude that VOT is a promising tool for providing online feedback during endovenous laser therapy.

  10. High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching

    PubMed Central

    Xu, Min; Beck, Martin; Alber, Frank

    2013-01-01

    Cryo-electron tomography allows the visualization of macromolecular complexes in their cellular environments in close-to-live conditions. The nominal resolution of subtomograms can be significantly increased when individual subtomograms of the same kind are aligned and averaged. A vital step for such a procedure are algorithms that speedup subtomogram alignment and improve accuracy for reference-free subtomogram classification, which will facilitate automation of tomography analysis and overall high throughput in the data processing. In this paper, we propose a fast rotational alignment method that uses the Fourier equivalent form of a popular constrained correlation measure that considers missing wedge corrections and density variances in the subtomograms. The fast rotational search is based on 3D volumetric matching, which significantly improves the rotational alignment accuracy in particular for highly distorted subtomograms with low SNR and tilt angle ranges in comparison to a fast rotational alignment based on matching of projected 2D spherical images. We further integrate our fast rotational alignment method in a reference free iterative subtomogram classification scheme, and propose a local feature enhancement strategy in the classification process. We can demonstrate that the automatic method can be used to successfully classify a large number of experimental subtomograms without the need of a reference structure. PMID:22420977

  11. Survey of Volumetric Grid Generators

    NASA Technical Reports Server (NTRS)

    Woo, Alex; Volakis, John; Hulbert, Greg; Case, Jeff; Presley, Leroy L. (Technical Monitor)

    1994-01-01

    This document is the result of an Internet Survey of Volumetric grid generators. As such we have included information from only the responses which were sent to us. After the initial publication and posting of this survey, we would encourage authors and users of grid generators to send further information. Here is the initial query posted to SIGGRID@nas and the USENET group sci.physics.computational.fluid-dynamics. Date: Sun, 30 Jan 94 11:37:52 -0800 From: woo (Alex Woo x6010 227-6 rm 315) Subject: Info Sought for Survey of Grid Generators I am collecting information and reviews of both government sponsored and commercial mesh generators for large scientific calculations, both block structured and unstructured. If you send me a review of a mesh generator, please indicate its availability and cost. If you are a commercial concern with information on a product, please also include references for possible reviewers. Please email to woo@ra-next.arc.nasa.gov. I will post a summary and probably write a short note for the IEEE Antennas and Propagation Magazine. Alex Woo, MS 227-6 woo@ames.arc.nasa.gov NASA Ames Research Center NASAMAIL ACWOO Moffett Field, CA 94035-1000 SPANET 24582::W00 (415) 604-6010 (FAX) 604-4357 fhplabs,decwrl,uunet)!ames!woo Disclaimer: These are not official statements of NASA or EMCC. We did not include all the submitted text here. Instead we have created a database entry in the freely available and widely used BIBTeX format which has an Uniform Resource Locator (URL) field pointing to more details. The BIBTeX database is modeled after those available from the BIBNET project at University of Utah.

  12. Whole-Organism Cellular Pathology: A Systems Approach to Phenomics.

    PubMed

    Cheng, K C; Katz, S R; Lin, A Y; Xin, X; Ding, Y

    2016-01-01

    Phenotype is defined as the state of an organism resulting from interactions between genes, environment, disease, molecular mechanisms, and chance. The purpose of the emerging field of phenomics is to systematically determine and measure phenotypes across biology for the sake of understanding. Phenotypes can affect more than one cell type and life stage, so ideal phenotyping would include the state of every cell type within the context of both tissue architecture and the whole organism at each life stage. In medicine, high-resolution anatomic assessment of phenotype is obtained from histology. Histology's interpretative power, codified by Virchow as cellular pathology, is derived from its ability to discern diagnostic and characteristic cellular changes in diseased tissues. Cellular pathology is observed in every major human disease and relies on the ability of histology to detect cellular change in any cell type due to unbiased pan-cellular staining, even in optically opaque tissues. Our laboratory has shown that histology is far more sensitive than stereomicroscopy for detecting phenotypes in zebrafish mutants. Those studies have also shown that more complete sampling, greater consistency in sample orientation, and the inclusion of phenotypes extending over longer length scales would provide greater coverage of common phenotypes. We are developing technical approaches to achieve an ideal detection of cellular pathology using an improved form of X-ray microtomography that retains the strengths and addresses the weaknesses of histology as a screening tool. We are using zebrafish as a vertebrate model based on the overlaps between zebrafish and mammalian tissue architecture, and a body size small enough to allow whole-organism, volumetric imaging at cellular resolution. Automation of whole-organism phenotyping would greatly increase the value of phenomics. Potential societal benefits would include reduction in the cost of drug development, a reduction in the

  13. Volumetric imaging of the auroral ionosphere: Initial results from PFISR

    NASA Astrophysics Data System (ADS)

    Semeter, Joshua; Butler, Thomas; Heinselman, Craig; Nicolls, Michael; Kelly, John; Hampton, Donald

    2009-05-01

    The Poker Flat Incoherent Scatter Radar (PFISR) is the first dedicated ISR built with an electronically steerable array. This paper demonstrates the capabilities of PFISR for producing three-dimensional volumetric images of E-region ionization patterns produced by the aurora. The phase table was configured to cycle through 121 beam positions arranged in an 11×11 grid. A 13-baud Barker coded pulse was used, which provided ~1.5-km range resolution out to a maximum range of 250 km. Backscattered power was converted to electron density by correcting for path loss and applying the Buneman approximation assuming equal electron and ion temperatures. The results were then interpolated onto a three-dimensional cartesian grid. Volumetric images are presented at 5-min, 1-min, and 14.6-s integration times (corresponding to 960, 192, and 48 pulses-per-position, respectively) to illustrate the tradeoff between spatio-temporal resolution and data quality. At 14.6 s cadence, variability in plasma density within the volume appears to be fully resolved in space and time, a result that is supported by both observational evidence and theoretical predictions of ionospheric response times. Some potential applications of this mode for studying magnetosphere-ionosphere interactions in the auroral zone are discussed.

  14. Performance-scalable volumetric data classification for online industrial inspection

    NASA Astrophysics Data System (ADS)

    Abraham, Aby J.; Sadki, Mustapha; Lea, R. M.

    2002-03-01

    Non-intrusive inspection and non-destructive testing of manufactured objects with complex internal structures typically requires the enhancement, analysis and visualization of high-resolution volumetric data. Given the increasing availability of fast 3D scanning technology (e.g. cone-beam CT), enabling on-line detection and accurate discrimination of components or sub-structures, the inherent complexity of classification algorithms inevitably leads to throughput bottlenecks. Indeed, whereas typical inspection throughput requirements range from 1 to 1000 volumes per hour, depending on density and resolution, current computational capability is one to two orders-of-magnitude less. Accordingly, speeding up classification algorithms requires both reduction of algorithm complexity and acceleration of computer performance. A shape-based classification algorithm, offering algorithm complexity reduction, by using ellipses as generic descriptors of solids-of-revolution, and supporting performance-scalability, by exploiting the inherent parallelism of volumetric data, is presented. A two-stage variant of the classical Hough transform is used for ellipse detection and correlation of the detected ellipses facilitates position-, scale- and orientation-invariant component classification. Performance-scalability is achieved cost-effectively by accelerating a PC host with one or more COTS (Commercial-Off-The-Shelf) PCI multiprocessor cards. Experimental results are reported to demonstrate the feasibility and cost-effectiveness of the data-parallel classification algorithm for on-line industrial inspection applications.

  15. Volumetric 3D Display System with Static Screen

    NASA Technical Reports Server (NTRS)

    Geng, Jason

    2011-01-01

    Current display technology has relied on flat, 2D screens that cannot truly convey the third dimension of visual information: depth. In contrast to conventional visualization that is primarily based on 2D flat screens, the volumetric 3D display possesses a true 3D display volume, and places physically each 3D voxel in displayed 3D images at the true 3D (x,y,z) spatial position. Each voxel, analogous to a pixel in a 2D image, emits light from that position to form a real 3D image in the eyes of the viewers. Such true volumetric 3D display technology provides both physiological (accommodation, convergence, binocular disparity, and motion parallax) and psychological (image size, linear perspective, shading, brightness, etc.) depth cues to human visual systems to help in the perception of 3D objects. In a volumetric 3D display, viewers can watch the displayed 3D images from a completely 360 view without using any special eyewear. The volumetric 3D display techniques may lead to a quantum leap in information display technology and can dramatically change the ways humans interact with computers, which can lead to significant improvements in the efficiency of learning and knowledge management processes. Within a block of glass, a large amount of tiny dots of voxels are created by using a recently available machining technique called laser subsurface engraving (LSE). The LSE is able to produce tiny physical crack points (as small as 0.05 mm in diameter) at any (x,y,z) location within the cube of transparent material. The crack dots, when illuminated by a light source, scatter the light around and form visible voxels within the 3D volume. The locations of these tiny voxels are strategically determined such that each can be illuminated by a light ray from a high-resolution digital mirror device (DMD) light engine. The distribution of these voxels occupies the full display volume within the static 3D glass screen. This design eliminates any moving screen seen in previous

  16. Temporal Coding of Volumetric Imagery

    NASA Astrophysics Data System (ADS)

    Llull, Patrick Ryan

    'Image volumes' refer to realizations of images in other dimensions such as time, spectrum, and focus. Recent advances in scientific, medical, and consumer applications demand improvements in image volume capture. Though image volume acquisition continues to advance, it maintains the same sampling mechanisms that have been used for decades; every voxel must be scanned and is presumed independent of its neighbors. Under these conditions, improving performance comes at the cost of increased system complexity, data rates, and power consumption. This dissertation explores systems and methods capable of efficiently improving sensitivity and performance for image volume cameras, and specifically proposes several sampling strategies that utilize temporal coding to improve imaging system performance and enhance our awareness for a variety of dynamic applications. Video cameras and camcorders sample the video volume (x,y,t) at fixed intervals to gain understanding of the volume's temporal evolution. Conventionally, one must reduce the spatial resolution to increase the framerate of such cameras. Using temporal coding via physical translation of an optical element known as a coded aperture, the compressive temporal imaging (CACTI) camera emonstrates a method which which to embed the temporal dimension of the video volume into spatial (x,y) measurements, thereby greatly improving temporal resolution with minimal loss of spatial resolution. This technique, which is among a family of compressive sampling strategies developed at Duke University, temporally codes the exposure readout functions at the pixel level. Since video cameras nominally integrate the remaining image volume dimensions (e.g. spectrum and focus) at capture time, spectral (x,y,t,lambda) and focal (x,y,t,z) image volumes are traditionally captured via sequential changes to the spectral and focal state of the system, respectively. The CACTI camera's ability to embed video volumes into images leads to exploration

  17. Volumetric imaging with an amplitude-steered array

    NASA Astrophysics Data System (ADS)

    Frazier, Catherine H.; Hughes, W. Jack; O'Brien, William D.

    2002-12-01

    Volumetric acoustic imaging is desirable for the visualization of underwater objects and structures; however, the implementation of a volumetric imaging system is difficult due to the high channel count of a fully populated two-dimensional array. Recently, a linear amplitude-steered array with a reduced electronics requirement was presented, which is capable of collecting a two-dimensional set of data with a single transmit pulse. In this study, we demonstrate the use of the linear amplitude-steered array and associated image formation algorithms for collecting and displaying volumetric data; that is, proof of principle of the amplitude-steering concept and the associated image formation algorithms is demonstrated. Range and vertical position are obtained by taking advantage of the frequency separation of a vertical linear amplitude-steered array. The third dimension of data is obtained by rotating the array such that the mainlobe is mechanically steered in azimuth. Data are collected in a water tank at the Pennsylvania State University Applied Research Laboratory for two targets: a ladder and three pipes. These data are the first experimental data collected with an amplitude-steered array for the purposes of imaging. The array is 10 cm in diameter and is operated in the frequency range of 80 to 304 kHz. Although the array is small for high-resolution imaging at these frequencies, the rungs of the ladder are recognizable in the images. The three pipes are difficult to discern in two of the projection images; however, the pipes separated in range are clear in the image showing vertical position versus range. The imaging concept is demonstrated on measured data, and the simulations agree well with the experimental results.

  18. Volumetric retinal fluorescence microscopic imaging with extended depth of field

    NASA Astrophysics Data System (ADS)

    Li, Zengzhuo; Fischer, Andrew; Li, Wei; Li, Guoqiang

    2016-03-01

    Wavefront-engineered microscope with greatly extended depth of field (EDoF) is designed and demonstrated for volumetric imaging with near-diffraction limited optical performance. A bright field infinity-corrected transmissive/reflective light microscope is built with Kohler illumination. A home-made phase mask is placed in between the objective lens and the tube lens for ease of use. General polynomial function is adopted in the design of the phase plate for robustness and custom merit function is used in Zemax for optimization. The resulting EDoF system achieves an engineered point spread function (PSF) that is much less sensitive to object depth variation than conventional systems and therefore 3D volumetric information can be acquired in a single frame with expanded tolerance of defocus. In Zemax simulation for a setup using 32X objective (NA = 0.6), the EDoF is 20μm whereas a conventional one has a DoF of 1.5μm, indicating a 13 times increase. In experiment, a 20X objective lens with NA = 0.4 was used and the corresponding phase plate was designed and fabricated. Retinal fluorescence images of the EDoF microscope using passive adaptive optical phase element illustrate a DoF around 100μm and it is able to recover the volumetric fluorescence images that are almost identical to in-focus images after post processing. The image obtained from the EDoF microscope is also better in resolution and contrast, and the retinal structure is better defined. Hence, due to its high tolerance of defocus and fine restored image quality, EDoF optical systems have promising potential in consumer portable medical imaging devices where user's ability to achieve focus is not optimal, and other medical imaging equipment where achieving best focus is not a necessary.

  19. Volumetric imaging with an amplitude-steered array.

    PubMed

    Frazier, Catherine H; Hughes, W Jack; O'Brien, William D

    2002-12-01

    Volumetric acoustic imaging is desirable for the visualization of underwater objects and structures; however, the implementation of a volumetric imaging system is difficult due to the high channel count of a fully populated two-dimensional array. Recently, a linear amplitude-steered array with a reduced electronics requirement was presented, which is capable of collecting a two-dimensional set of data with a single transmit pulse. In this study, we demonstrate the use of the linear amplitude-steered array and associated image formation algorithms for collecting and displaying volumetric data; that is, proof of principle of the amplitude-steering concept and the associated image formation algorithms is demonstrated. Range and vertical position are obtained by taking advantage of the frequency separation of a vertical linear amplitude-steered array. The third dimension of data is obtained by rotating the array such that the mainlobe is mechanically steered in azimuth. Data are collected in a water tank at the Pennsylvania State University Applied Research Laboratory for two targets: a ladder and three pipes. These data are the first experimental data collected with an amplitude-steered array for the purposes of imaging. The array is 10 cm in diameter and is operated in the frequency range of 80 to 304 kHz. Although the array is small for high-resolution imaging at these frequencies, the rungs of the ladder are recognizable in the images. The three pipes are difficult to discern in two of the projection images; however, the pipes separated in range are clear in the image showing vertical position versus range. The imaging concept is demonstrated on measured data, and the simulations agree well with the experimental results. PMID:12508995

  20. Volumetric display based on multiple mini-projectors and a rotating screen

    NASA Astrophysics Data System (ADS)

    Song, Weitao; Zhu, Qiudong; Huang, Tao; Liu, Yue; Wang, Yongtian

    2015-01-01

    A method has been proposed to realize a transparent volumetric display using multiple mini-projectors and a rotating screen. Correct two-dimensional cross-sectional images are projected on a bidirectional scattering projection screen, which rotates to form a three-dimensional (3-D) image due to human vision persistence. An illumination subsystem is designed to ensure the accurate synchronization between the projectors and the rotating screen. Therefore, low-speed and low-cost miniature display devices can be used in the mini-projectors to realize dynamic volumetric imaging, which can satisfy all criteria of real 3-D vision with full color and high resolution. Experimental results of volumetric imaging realized by this method are also presented.

  1. Nonequilibrium volumetric response of shocked polymers

    SciTech Connect

    Clements, B E

    2009-01-01

    Polymers are well known for their non-equilibrium deviatoric behavior. However, investigations involving both high rate shock experiments and equilibrium measured thermodynamic quantities remind us that the volumetric behavior also exhibits a non-equilibrium response. Experiments supporting the notion of a non-equilibrium volumetric behavior will be summarized. Following that discussion, a continuum-level theory is proposed that will account for both the equilibrium and non-equilibrium response. Upon finding agreement with experiment, the theory is used to study the relaxation of a shocked polymer back towards its shocked equilibrium state.

  2. A volumetric flask as a projector

    NASA Astrophysics Data System (ADS)

    Limsuwan, P.; Asanithi, P.; Thongpool, V.; Piriyawong, V.; Limsuwan, S.

    2012-03-01

    A lens based on liquid in the confined volume of a volumetric flask was presented as a potential projector to observe microscopic floating organisms or materials. In this experiment, a mosquito larva from a natural pond was selected as a demonstration sample. By shining a light beam from a laser pointer of any visible wavelength through the volumetric flask filled with liquid, the movements of floating objects were clearly observed on a screen. The magnification was simply controlled by changing either the volume of the flask or the distance of the screen from the flask.

  3. Bronchoalveolar lavage cellular analyses in conjunction with high-resolution computed tomography imaging as a diagnostic intervention for patients with suspected interstitial lung disease

    PubMed Central

    Chockalingam, Ammaiyappan; Duraiswamy, Ranganathan; Jagadeesan, Madhavan

    2016-01-01

    Background: Bronchoalveolar lavage (BAL) has gained acceptance for diagnosis of Interstitial lung disease (ILD). The advent of high-resolution computed tomography (HRCT) has reduced the clinical utility of BAL. This work has utilized the recommendations of the American Thoracic Society (ATS) to optimize BAL and the findings have been associated with clinical examination and HRCT to precisely narrow down the cause of ILD. Materials and Methods: BAL was performed on ILD suspects at the target site chosen based on HRCT. The procedure, transport, processing, and analysis of BAL fluid were performed as per the ATS guidelines. The clinical data, HRCT findings and BAL report were used to narrow down the diagnosis of ILD. The statistical analysis was performed to assess the significance. Results: The BAL procedure was optimized as per the recommendations of the ATS. In a cohort of 50 patients, Idiopathic pulmonary fibrosis, (8) hypersensitivity pneumonitis, (17) connective tissue disorder, (9) sarcoidosis, (3) pneumoconiosis, (5) acute respiratory distress syndrome, (2) eosinophilic lung disease (2) and lymphangitic carcinomatosa, (2) aspiration bronchiolitis (1) and pulmonary histiocytosis (1) were diagnosed. Statistically significant variation in differential counts was found in different ILDs. The different ILDs were classified based on the criteria described by the ATS. Clinical Significance: BAL along with clinical and HRCT findings improved the diagnostic accuracy by incorporating, the acute or chronic nature of the disease and the cause for acute exacerbation, which helped in the better management of ILDs. PMID:27185993

  4. Integrated adaptive optics optical coherence tomography and adaptive optics scanning laser ophthalmoscope system for simultaneous cellular resolution in vivo retinal imaging

    PubMed Central

    Zawadzki, Robert J.; Jones, Steven M.; Pilli, Suman; Balderas-Mata, Sandra; Kim, Dae Yu; Olivier, Scot S.; Werner, John S.

    2011-01-01

    We describe an ultrahigh-resolution (UHR) retinal imaging system that combines adaptive optics Fourier-domain optical coherence tomography (AO-OCT) with an adaptive optics scanning laser ophthalmoscope (AO-SLO) to allow simultaneous data acquisition by the two modalities. The AO-SLO subsystem was integrated into the previously described AO-UHR OCT instrument with minimal changes to the latter. This was done in order to ensure optimal performance and image quality of the AO- UHR OCT. In this design both imaging modalities share most of the optical components including a common AO-subsystem and vertical scanner. One of the benefits of combining Fd-OCT with SLO includes automatic co-registration between two acquisition channels for direct comparison between retinal structures imaged by both modalities (e.g., photoreceptor mosaics or microvasculature maps). Because of differences in the detection scheme of the two systems, this dual imaging modality instrument can provide insight into retinal morphology and potentially function, that could not be accessed easily by a single system. In this paper we describe details of the components and parameters of the combined instrument, including incorporation of a novel membrane magnetic deformable mirror with increased stroke and actuator count used as a single wavefront corrector. We also discuss laser safety calculations for this multimodal system. Finally, retinal images acquired in vivo with this system are presented. PMID:21698028

  5. Volumetric three-dimensional display system with rasterization hardware

    NASA Astrophysics Data System (ADS)

    Favalora, Gregg E.; Dorval, Rick K.; Hall, Deirdre M.; Giovinco, Michael; Napoli, Joshua

    2001-06-01

    An 8-color multiplanar volumetric display is being developed by Actuality Systems, Inc. It will be capable of utilizing an image volume greater than 90 million voxels, which we believe is the greatest utilizable voxel set of any volumetric display constructed to date. The display is designed to be used for molecular visualization, mechanical CAD, e-commerce, entertainment, and medical imaging. As such, it contains a new graphics processing architecture, novel high-performance line- drawing algorithms, and an API similar to a current standard. Three-dimensional imagery is created by projecting a series of 2-D bitmaps ('image slices') onto a diffuse screen that rotates at 600 rpm. Persistence of vision fuses the slices into a volume-filling 3-D image. A modified three-panel Texas Instruments projector provides slices at approximately 4 kHz, resulting in 8-color 3-D imagery comprised of roughly 200 radially-disposed slices which are updated at 20 Hz. Each slice has a resolution of 768 by 768 pixels, subtending 10 inches. An unusual off-axis projection scheme incorporating tilted rotating optics is used to maintain good focus across the projection screen. The display electronics includes a custom rasterization architecture which converts the user's 3- D geometry data into image slices, as well as 6 Gbits of DDR SDRAM graphics memory.

  6. Clinical Applications of Volumetric Modulated Arc Therapy

    SciTech Connect

    Matuszak, Martha M.; Yan Di; Grills, Inga; Martinez, Alvaro

    2010-06-01

    Purpose: To present treatment planning case studies for several treatment sites for which volumetric modulated arc therapy (VMAT) could have a positive impact; and to share an initial clinical experience with VMAT for stereotactic body radiotherapy (SBRT). Methods and Materials: Four case studies are presented to show the potential benefit of VMAT compared with conformal and intensity-modulated radiotherapy (IMRT) techniques in pediatric cancer, bone marrow-sparing whole-abdominopelvic irradiation (WAPI), and SBRT of the lung and spine. Details of clinical implementation of VMAT for SBRT are presented. The VMAT plans are compared with conventional techniques in terms of dosimetric quality and delivery efficiency. Results: Volumetric modulated arc therapy reduced the treatment time of spine SBRT by 37% and improved isodose conformality. Conformal and VMAT techniques for lung SBRT had similar dosimetric quality, but VMAT had improved target coverage and took 59% less time to deliver, although monitor units were increased by 5%. In a complex pediatric pelvic example, VMAT reduced treatment time by 78% and monitor units by 25% compared with IMRT. A double-isocenter VMAT technique for WAPI can spare bone marrow while maintaining good delivery efficiency. Conclusions: Volumetric modulated arc therapy is a new technology that may benefit different patient populations, including pediatric cancer patients and those undergoing concurrent chemotherapy and WAPI. Volumetric modulated arc therapy has been used and shown to be beneficial for significantly improving delivery efficiency of lung and spine SBRT.

  7. A Volumetric Flask as a Projector

    ERIC Educational Resources Information Center

    Limsuwan, P.; Asanithi, P.; Thongpool, V.; Piriyawong, V.; Limsuwan, S.

    2012-01-01

    A lens based on liquid in the confined volume of a volumetric flask was presented as a potential projector to observe microscopic floating organisms or materials. In this experiment, a mosquito larva from a natural pond was selected as a demonstration sample. By shining a light beam from a laser pointer of any visible wavelength through the…

  8. Skeletal muscle tissue engineering: strategies for volumetric constructs

    PubMed Central

    Cittadella Vigodarzere, Giorgio; Mantero, Sara

    2014-01-01

    Skeletal muscle tissue is characterized by high metabolic requirements, defined structure and high regenerative potential. As such, it constitutes an appealing platform for tissue engineering to address volumetric defects, as proven by recent works in this field. Several issues common to all engineered constructs constrain the variety of tissues that can be realized in vitro, principal among them the lack of a vascular system and the absence of reliable cell sources; as it is, the only successful tissue engineering constructs are not characterized by active function, present limited cellular survival at implantation and possess low metabolic requirements. Recently, functionally competent constructs have been engineered, with vascular structures supporting their metabolic requirements. In addition to the use of biochemical cues, physical means, mechanical stimulation and the application of electric tension have proven effective in stimulating the differentiation of cells and the maturation of the constructs; while the use of co-cultures provided fine control of cellular developments through paracrine activity. This review will provide a brief analysis of some of the most promising improvements in the field, with particular attention to the techniques that could prove easily transferable to other branches of tissue engineering. PMID:25295011

  9. Volumetric HiLo microscopy employing an electrically tunable lens.

    PubMed

    Philipp, Katrin; Smolarski, André; Koukourakis, Nektarios; Fischer, Andreas; Stürmer, Moritz; Wallrabe, Ulrike; Czarske, Jürgen W

    2016-06-27

    Electrically tunable lenses exhibit strong potential for fast motion-free axial scanning in a variety of microscopes. However, they also lead to a degradation of the achievable resolution because of aberrations and misalignment between illumination and detection optics that are induced by the scan itself. Additionally, the typically nonlinear relation between actuation voltage and axial displacement leads to over- or under-sampled frame acquisition in most microscopic techniques because of their static depth-of-field. To overcome these limitations, we present an Adaptive-Lens-High-and-Low-frequency (AL-HiLo) microscope that enables volumetric measurements employing an electrically tunable lens. By using speckle-patterned illumination, we ensure stability against aberrations of the electrically tunable lens. Its depth-of-field can be adjusted a-posteriori and hence enables to create flexible scans, which compensates for irregular axial measurement positions. The adaptive HiLo microscope provides an axial scanning range of 1 mm with an axial resolution of about 4 μm and sub-micron lateral resolution over the full scanning range. Proof of concept measurements at home-built specimens as well as zebrafish embryos with reporter gene-driven fluorescence in the thyroid gland are shown. PMID:27410654

  10. Volumetric PIV with a Plenoptic Camera

    NASA Astrophysics Data System (ADS)

    Thurow, Brian; Fahringer, Tim

    2012-11-01

    Plenoptic cameras have received attention recently due to their ability to computationally refocus an image after it has been acquired. We describe the development of a robust, economical and easy-to-use volumetric PIV technique using a unique plenoptic camera built in our laboratory. The tomographic MART algorithm is used to reconstruct pairs of 3D particle volumes with velocity determined using conventional cross-correlation techniques. 3D/3C velocity measurements (volumetric dimensions of 2 . 8 ' ' × 1 . 9 ' ' × 1 . 6 ' ') of a turbulent boundary layer produced on the wall of a conventional wind tunnel are presented. This work has been supported by the Air Force Office of Scientific Research,(Grant #FA9550-100100576).

  11. Cellular resilience.

    PubMed

    Smirnova, Lena; Harris, Georgina; Leist, Marcel; Hartung, Thomas

    2015-01-01

    Cellular resilience describes the ability of a cell to cope with environmental changes such as toxicant exposure. If cellular metabolism does not collapse directly after the hit or end in programmed cell death, the ensuing stress responses promote a new homeostasis under stress. The processes of reverting "back to normal" and reversal of apoptosis ("anastasis") have been studied little at the cellular level. Cell types show astonishingly similar vulnerability to most toxicants, except for those that require a very specific target, metabolism or mechanism present only in specific cell types. The majority of chemicals triggers "general cytotoxicity" in any cell at similar concentrations. We hypothesize that cells differ less in their vulnerability to a given toxicant than in their resilience (coping with the "hit"). In many cases, cells do not return to the naive state after a toxic insult. The phenomena of "pre-conditioning", "tolerance" and "hormesis" describe this for low-dose exposures to toxicants that render the cell more resistant to subsequent hits. The defense and resilience programs include epigenetic changes that leave a "memory/scar" - an alteration as a consequence of the stress the cell has experienced. These memories might have long-term consequences, both positive (resistance) and negative, that contribute to chronic and delayed manifestations of hazard and, ultimately, disease. This article calls for more systematic analyses of how cells cope with toxic perturbations in the long-term after stressor withdrawal. A technical prerequisite for these are stable (organotypic) cultures and a characterization of stress response molecular networks. PMID:26536287

  12. Low-Pass Filtered Volumetric Shadows.

    PubMed

    Ament, Marco; Sadlo, Filip; Dachsbacher, Carsten; Weiskopf, Daniel

    2014-12-01

    We present a novel and efficient method to compute volumetric soft shadows for interactive direct volume visualization to improve the perception of spatial depth. By direct control of the softness of volumetric shadows, disturbing visual patterns due to hard shadows can be avoided and users can adapt the illumination to their personal and application-specific requirements. We compute the shadowing of a point in the data set by employing spatial filtering of the optical depth over a finite area patch pointing toward each light source. Conceptually, the area patch spans a volumetric region that is sampled with shadow rays; afterward, the resulting optical depth values are convolved with a low-pass filter on the patch. In the numerical computation, however, to avoid expensive shadow ray marching, we show how to align and set up summed area tables for both directional and point light sources. Once computed, the summed area tables enable efficient evaluation of soft shadows for each point in constant time without shadow ray marching and the softness of the shadows can be controlled interactively. We integrated our method in a GPU-based volume renderer with ray casting from the camera, which offers interactive control of the transfer function, light source positions, and viewpoint, for both static and time-dependent data sets. Our results demonstrate the benefit of soft shadows for visualization to achieve user-controlled illumination with many-point lighting setups for improved perception combined with high rendering speed. PMID:26356957

  13. Thousand-fold volumetric concentration of live cells with a recirculating acoustofluidic device.

    PubMed

    Jakobsson, Ola; Oh, Seung Soo; Antfolk, Maria; Eisenstein, Michael; Laurell, Thomas; Soh, H Tom

    2015-08-18

    The ability to concentrate cells from dilute samples into smaller volumes is an essential process step for most biological assays. Volumetric concentration is typically achieved via centrifugation, but this technique is not well suited for handling small number of cells, especially outside of the laboratory setting. In this work, we describe a novel device that combines acoustofluidics with a recirculating architecture to achieve >1000-fold enrichment of cells in a label-free manner, at high volumetric throughput (>500 μL min(-1)) and with high recovery (>98.7%). We demonstrate that our device can be used with a wide variety of different cell types and show that this concentration strategy does not affect cell viability. Importantly, our device could be readily adopted to serve as a "sample preparation" module that can be integrated with other microfluidic devices to allow analysis of dilute cellular samples in large volumes. PMID:26226316

  14. Quenching correction for volumetric scintillation dosimetry of proton beams

    PubMed Central

    Robertson, Daniel; Mirkovic, Dragan; Sahoo, Narayan; Beddar, Sam

    2013-01-01

    Purpose Volumetric scintillation dosimetry has the potential to provide fast, high-resolution, three-dimensional radiation dosimetry. However, scintillators exhibit a nonlinear response at the high linear energy transfer (LET) values characteristic of proton Bragg peaks. The purpose of this study was to develop a quenching correction method for volumetric scintillation dosimetry of proton beams. Methods Scintillation light from a miniature liquid scintillator detector was measured along the central axis of a 161.6-MeV proton pencil beam. Three-dimensional dose and LET distributions were calculated for 85.6-, 100.9-, 144.9-, and 161.6-MeV beams using a validated Monte Carlo model. LET values were also calculated using an analytical formula. A least-squares fit to the data established the empirical parameters of a quenching correction model. The light distribution in a tank of liquid scintillator was measured with a CCD camera at all four beam energies. The quenching model and LET data were used to correct the measured light distribution. Results The calculated and measured Bragg peak heights agreed within ±3% for all energies except 85.6 MeV, where the agreement was within ±10%. The quality of the quenching correction was poorer for sharp low-energy Bragg peaks because of blurring and detector size effects. The corrections performed using analytical LET values resulted in doses within 1% of those obtained using Monte Carlo LET values. Conclusion The proposed method can correct for quenching with sufficient accuracy for dosimetric purposes. The required LET values may be computed effectively using Monte Carlo or analytical methods. Future detectors should improve blurring correction methods and optimize the pixel size to improve accuracy for low-energy Bragg peaks. PMID:23257200

  15. Efficient volumetric estimation from plenoptic data

    NASA Astrophysics Data System (ADS)

    Anglin, Paul; Reeves, Stanley J.; Thurow, Brian S.

    2013-03-01

    The commercial release of the Lytro camera, and greater availability of plenoptic imaging systems in general, have given the image processing community cost-effective tools for light-field imaging. While this data is most commonly used to generate planar images at arbitrary focal depths, reconstruction of volumetric fields is also possible. Similarly, deconvolution is a technique that is conventionally used in planar image reconstruction, or deblurring, algorithms. However, when leveraged with the ability of a light-field camera to quickly reproduce multiple focal planes within an imaged volume, deconvolution offers a computationally efficient method of volumetric reconstruction. Related research has shown than light-field imaging systems in conjunction with tomographic reconstruction techniques are also capable of estimating the imaged volume and have been successfully applied to particle image velocimetry (PIV). However, while tomographic volumetric estimation through algorithms such as multiplicative algebraic reconstruction techniques (MART) have proven to be highly accurate, they are computationally intensive. In this paper, the reconstruction problem is shown to be solvable by deconvolution. Deconvolution offers significant improvement in computational efficiency through the use of fast Fourier transforms (FFTs) when compared to other tomographic methods. This work describes a deconvolution algorithm designed to reconstruct a 3-D particle field from simulated plenoptic data. A 3-D extension of existing 2-D FFT-based refocusing techniques is presented to further improve efficiency when computing object focal stacks and system point spread functions (PSF). Reconstruction artifacts are identified; their underlying source and methods of mitigation are explored where possible, and reconstructions of simulated particle fields are provided.

  16. Volumetric Near-Field Microwave Plasma Generation

    NASA Technical Reports Server (NTRS)

    Exton, R. J.; Balla, R. Jeffrey; Herring, G. C.; Popovic, S.; Vuskovic, L.

    2003-01-01

    A periodic series of microwave-induced plasmoids is generated using the outgoing wave from a microwave horn and the reflected wave from a nearby on-axis concave reflector. The plasmoids are spaced at half-wavelength separations according to a standing-wave pattern. The plasmoids are enhanced by an effective focusing in the near field of the horn (Fresnel region) as a result of a diffractive narrowing. Optical imaging, electron density, and rotational temperature measurements characterize the near field plasma region. Volumetric microwave discharges may have application to combustion ignition in scramjet engines.

  17. Volumetric Measurements of Amnioserosa Cells in Developing Drosophila

    NASA Astrophysics Data System (ADS)

    Mashburn, David; Jayasinghe, Aroshan; Hutson, Shane

    2013-03-01

    The behavior of cells in tissue in developing Drosophila melanogaster has become increasingly clearer over the past few decades, in large part due to advances in imaging techniques, genetic markers, predictive modeling, and micromanipulation (notably laser microsurgery). We now know apical contractions in amnioserosa cells are a significant factor in large scale processes like germ band retraction and dorsal closure. Also, laser microsurgery induces cellular recoil that strongly mimics a 2D elastic sheet. Still, what we know about these processes comes entirely from the apical surface where the standard fluorescent markers like cadherin are located, but many open questions exist concerning the remaining ``dark'' portion of cells. Does cell volume remain constant during contraction or do cells leak? Also, what shape changes do cells undergo? Do they bulge, wedge, contract prismatically, or something else? By using a marker that labels the entire membrane of amnioserosa cells (Resille, 117) and adapting our watershed segmentation routines for 4D datasets, we have been able to quantify the entire volumetric region of cells in tissue through time and compare changes in apical area and volume. Preliminary results suggest a fairly constant volume over the course of a contraction cycle.

  18. FELIX: a volumetric 3D laser display

    NASA Astrophysics Data System (ADS)

    Bahr, Detlef; Langhans, Knut; Gerken, Martin; Vogt, Carsten; Bezecny, Daniel; Homann, Dennis

    1996-03-01

    In this paper, an innovative approach of a true 3D image presentation in a space filling, volumetric laser display will be described. The introduced prototype system is based on a moving target screen that sweeps the display volume. Net result is the optical equivalent of a 3D array of image points illuminated to form a model of the object which occupies a physical space. Wireframe graphics are presented within the display volume which a group of people can walk around and examine simultaneously from nearly any orientation and without any visual aids. Further to the detailed vector scanning mode, a raster scanned system and a combination of both techniques are under development. The volumetric 3D laser display technology for true reproduction of spatial images can tremendously improve the viewers ability to interpret data and to reliably determine distance, shape and orientation. Possible applications for this development range from air traffic control, where moving blips of light represent individual aircrafts in a true to scale projected airspace of an airport, to various medical applications (e.g. electrocardiography, computer-tomography), to entertainment and education visualization as well as imaging in the field of engineering and Computer Aided Design.

  19. BOREAS HYD-1 Volumetric Soil Moisture Data

    NASA Technical Reports Server (NTRS)

    Cuenca, Richard H.; Kelly, Shaun F.; Stangel, David E.; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Hydrology (HYD)-1 team made measurements of volumetric soil moisture at the Southern Study Area (SSA) and Northern Study Area (NSA) tower flux sites in 1994 and at selected tower flux sites in 1995-97. Different methods were used to collect these measurements, including neutron probe and manual and automated Time Domain Reflectometry (TDR). In 1994, the measurements were made every other day at the NSA-OJP (Old Jack Pine), NSA-YJP (Young Jack Pine), NSA-OBS (Old Black Spruce), NSA-Fen, SSA-OJP, SSA-YJP, SSA-Fen, SSA-YA (Young Aspen), and SSA-OBS sites. In 1995-97, when automated equipment was deployed at NSA-OJP, NSA-YJP, NSA-OBS, SSA-OBS, and SSA-OA (Old Aspen), the measurements were made as often as every hour. The data are stored in tabular ASCII files. The volumetric soil moisture data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  20. Volumetric capnography in the mechanically ventilated patient.

    PubMed

    Blanch, L; Romero, P V; Lucangelo, U

    2006-06-01

    Expiratory capnogram provides qualitative information on the waveform patterns associated with mechanical ventilation and quantitative estimation of expired CO2. Volumetric capnography simultaneously measures expired CO2 and tidal volume and allows identification of CO2 from 3 sequential lung compartments: apparatus and anatomic dead space, from progressive emptying of alveoli and alveolar gas. Lung heterogeneity creates regional differences in CO2 concentration and sequential emptying contributes to the rise of the alveolar plateau and to the steeper the expired CO2 slope. The concept of dead space accounts for those lung areas that are ventilated but not perfused. In patients with sudden pulmonary vascular occlusion due to pulmonary embolism, the resultant high V/Q mismatch produces an increase in alveolar dead space. Calculations derived from volumetric capnography are useful to suspect pulmonary embolism at the bedside. Alveolar dead space is large in acute lung injury and when the effect of positive end-expiratory pressure (PEEP) is to recruit collapsed lung units resulting in an improvement of oxygenation, alveolar dead space may decrease, whereas PEEP-induced overdistension tends to increase alveolar dead space. Finally, measurement of physiologic dead space and alveolar ejection volume at admission or the trend during the first 48 hours of mechanical ventilation might provide useful information on outcome of critically ill patients with acute lung injury or acute respiratory distress syndrome. PMID:16682932

  1. Adaptive controller for volumetric display of neuroimaging studies

    NASA Astrophysics Data System (ADS)

    Bleiberg, Ben; Senseney, Justin; Caban, Jesus

    2014-03-01

    Volumetric display of medical images is an increasingly relevant method for examining an imaging acquisition as the prevalence of thin-slice imaging increases in clinical studies. Current mouse and keyboard implementations for volumetric control provide neither the sensitivity nor specificity required to manipulate a volumetric display for efficient reading in a clinical setting. Solutions to efficient volumetric manipulation provide more sensitivity by removing the binary nature of actions controlled by keyboard clicks, but specificity is lost because a single action may change display in several directions. When specificity is then further addressed by re-implementing hardware binary functions through the introduction of mode control, the result is a cumbersome interface that fails to achieve the revolutionary benefit required for adoption of a new technology. We address the specificity versus sensitivity problem of volumetric interfaces by providing adaptive positional awareness to the volumetric control device by manipulating communication between hardware driver and existing software methods for volumetric display of medical images. This creates a tethered effect for volumetric display, providing a smooth interface that improves on existing hardware approaches to volumetric scene manipulation.

  2. A method for generating volumetric fault zone grids for pillar gridded reservoir models

    NASA Astrophysics Data System (ADS)

    Qu, Dongfang; Røe, Per; Tveranger, Jan

    2015-08-01

    The internal structure and petrophysical property distribution of fault zones are commonly exceedingly complex compared to the surrounding host rock from which they are derived. This in turn produces highly complex fluid flow patterns which affect petroleum migration and trapping as well as reservoir behavior during production and injection. Detailed rendering and forecasting of fluid flow inside fault zones require high-resolution, explicit models of fault zone structure and properties. A fundamental requirement for achieving this is the ability to create volumetric grids in which modeling of fault zone structures and properties can be performed. Answering this need, a method for generating volumetric fault zone grids which can be seamlessly integrated into existing standard reservoir modeling tools is presented. The algorithm has been tested on a wide range of fault configurations of varying complexity, providing flexible modeling grids which in turn can be populated with fault zone structures and properties.

  3. Selective-plane illumination microscopy for high-content volumetric biological imaging

    NASA Astrophysics Data System (ADS)

    McGorty, Ryan; Huang, Bo

    2016-03-01

    Light-sheet microscopy, also named selective-plane illumination microscopy, enables optical sectioning with minimal light delivered to the sample. Therefore, it allows one to gather volumetric datasets of developing embryos and other light-sensitive samples over extended times. We have configured a light-sheet microscope that, unlike most previous designs, can image samples in formats compatible with high-content imaging. Our microscope can be used with multi-well plates or with microfluidic devices. In designing our optical system to accommodate these types of sample holders we encounter large optical aberrations. We counter these aberrations with both static optical components in the imaging path and with adaptive optics. Potential applications of this microscope include studying the development of a large number of embryos in parallel and over long times with subcellular resolution and doing high-throughput screens on organisms or cells where volumetric data is necessary.

  4. GPU-based Scalable Volumetric Reconstruction for Multi-view Stereo

    SciTech Connect

    Kim, H; Duchaineau, M; Max, N

    2011-09-21

    We present a new scalable volumetric reconstruction algorithm for multi-view stereo using a graphics processing unit (GPU). It is an effectively parallelized GPU algorithm that simultaneously uses a large number of GPU threads, each of which performs voxel carving, in order to integrate depth maps with images from multiple views. Each depth map, triangulated from pair-wise semi-dense correspondences, represents a view-dependent surface of the scene. This algorithm also provides scalability for large-scale scene reconstruction in a high resolution voxel grid by utilizing streaming and parallel computation. The output is a photo-realistic 3D scene model in a volumetric or point-based representation. We demonstrate the effectiveness and the speed of our algorithm with a synthetic scene and real urban/outdoor scenes. Our method can also be integrated with existing multi-view stereo algorithms such as PMVS2 to fill holes or gaps in textureless regions.

  5. Live volumetric imaging (LVI) intracardiac ultrasound catheter.

    PubMed

    Dausch, David E; Castellucci, John B; Gilchrist, Kristin H; Carlson, James B; Hall, Stephen D; von Ramm, Olaf T

    2013-01-01

    The Live Volumetric Imaging (LVI) catheter is capable of real-time 3D intracardiac echo (ICE) imaging, uniquely providing full volume sectors with deep penetration depth and high volume frame rate. The key enabling technology in this catheter is an integrated piezoelectric micromachined ultrasound transducer (pMUT), a novel matrix phased array transducer fabricated using semiconductor microelectromechanical systems (MEMS) manufacturing techniques. This technology innovation may enable better image guidance to improve accuracy, reduce risk, and reduce procedure time for transcatheter intracardiac therapies which are currently done with limited direct visualization of the endocardial tissue. Envisioned applications for LVI include intraprocedural image guidance of cardiac ablation therapies as well as transcatheter mitral and aortic valve repair. PMID:23773496

  6. Volumetric techniques: three-dimensional midface modeling

    PubMed Central

    Pierzchała, Ewa; Placek, Waldemar

    2014-01-01

    Aging is a complex process caused by many factors. The most important factors include exposure to UV radiation, smoking, facial muscle movement, gravity, loss and displacement of fat and bone resorption. As a symptom of aging, face loses elasticity, volume and cheerful look. While changing face proportions, the dominant part of a face is its bottom instead of the mid part. The use of three-dimensional face modelling techniques, particularly the mid-face – tear through and cheeks, restores the skin firmness, volume and healthy look. For this purpose the hyaluronic acid is used, calcium hydroxyapatite, and L-polylactic acid fillers. Volumetric techniques require precision and proper selection of the filling agent to give a sense of satisfaction to both the patient and the doctor. PMID:25610354

  7. Progressive Compression of Volumetric Subdivision Meshes

    SciTech Connect

    Laney, D; Pascucci, V

    2004-04-16

    We present a progressive compression technique for volumetric subdivision meshes based on the slow growing refinement algorithm. The system is comprised of a wavelet transform followed by a progressive encoding of the resulting wavelet coefficients. We compare the efficiency of two wavelet transforms. The first transform is based on the smoothing rules used in the slow growing subdivision technique. The second transform is a generalization of lifted linear B-spline wavelets to the same multi-tier refinement structure. Direct coupling with a hierarchical coder produces progressive bit streams. Rate distortion metrics are evaluated for both wavelet transforms. We tested the practical performance of the scheme on synthetic data as well as data from laser indirect-drive fusion simulations with multiple fields per vertex. Both wavelet transforms result in high quality trade off curves and produce qualitatively good coarse representations.

  8. Interactive stereoscopic rendering of volumetric environments.

    PubMed

    Wan, Ming; Zhang, Nan; Qu, Huamin; Kaufman, Arie E

    2004-01-01

    We present an efficient stereoscopic rendering algorithm supporting interactive navigation through large-scale 3D voxel-based environments. In this algorithm, most of the pixel values of the right image are derived from the left image by a fast 3D warping based on a specific stereoscopic projection geometry. An accelerated volumetric ray casting then fills the remaining gaps in the warped right image. Our algorithm has been parallelized on a multiprocessor by employing effective task partitioning schemes and achieved a high cache coherency and load balancing. We also extend our stereoscopic rendering to include view-dependent shading and transparency effects. We have applied our algorithm in two virtual navigation systems, flythrough over terrain and virtual colonoscopy, and reached interactive stereoscopic rendering rates of more than 10 frames per second on a 16-processor SGI Challenge. PMID:15382695

  9. Functional transcranial brain imaging by optical-resolution photoacoustic microscopy

    NASA Astrophysics Data System (ADS)

    Hu, Song; Maslov, Konstantin; Tsytsarev, Vassiliy; Wang, Lihong V.

    2009-07-01

    Optical-resolution photoacoustic microscopy (OR-PAM) is applied to functional brain imaging in living mice. A near-diffraction-limited bright-field optical illumination is employed to achieve micrometer lateral resolution, and a dual-wavelength measurement is utilized to extract the blood oxygenation information. The variation in hemoglobin oxygen saturation (sO2) along vascular branching has been imaged in a precapillary arteriolar tree and a postcapillary venular tree, respectively. To the best of our knowledge, this is the first report on in vivo volumetric imaging of brain microvascular morphology and oxygenation down to single capillaries through intact mouse skulls. It is anticipated that: (i) chronic imaging enabled by this minimally invasive procedure will advance the study of cortical plasticity and neurological diseases; (ii) revealing the neuroactivity-dependent changes in hemoglobin concentration and oxygenation will facilitate the understanding of neurovascular coupling at the capillary level; and (iii) combining functional OR-PAM and high-resolution blood flowmetry will have the potential to explore cellular pathways of brain energy metabolism.

  10. Normative biometrics for fetal ocular growth using volumetric MRI reconstruction

    PubMed Central

    Velasco-Annis, Clemente; Gholipour, Ali; Afacan, Onur; Prabhu, Sanjay P.; Estroff, Judy A.; Warfield, Simon K.

    2015-01-01

    Objective To determine normative ranges for fetal ocular biometrics between 19 and 38 weeks gestational age (GA) using volumetric MRI reconstruction. Method 3D images of 114 healthy fetuses between 19 and 38 weeks GA were created using super-resolution volume reconstructions from MRI slice acquisitions. These 3D images were semi-automatically segmented to measure fetal orbit volume, binocular distance (BOD), interocular distance (IOD), and ocular diameter (OD). Results All biometry correlated with GA (Volume, CC = 0.9680; BOD, CC = 0.9552; OD, CC = 0.9445; and IOD, CC = 0.8429), and growth curves were plotted against linear and quadratic growth models. Regression analysis showed quadratic models to best fit BOD, IOD and OD, and a linear model to best fit volume. Conclusion Orbital volume had the greatest correlation with GA, though BOD and OD also showed strong correlation. The normative data found in this study may be helpful for the detection of congenital fetal anomalies with more consistent measurements than are currently available. PMID:25601041

  11. A volumetric flow sensor for automotive injection systems

    NASA Astrophysics Data System (ADS)

    Schmid, U.; Krötz, G.; Schmitt-Landsiedel, D.

    2008-04-01

    For further optimization of the automotive power train of diesel engines, advanced combustion processes require a highly flexible injection system, provided e.g. by the common rail (CR) injection technique. In the past, the feasibility to implement injection nozzle volumetric flow sensors based on the thermo-resistive measurement principle has been demonstrated up to injection pressures of 135 MPa (1350 bar). To evaluate the transient behaviour of the system-integrated flow sensors as well as an injection amount indicator used as a reference method, hydraulic simulations on the system level are performed for a CR injection system. Experimentally determined injection timings were found to be in good agreement with calculated values, especially for the novel sensing element which is directly implemented into the hydraulic system. For the first time pressure oscillations occurring after termination of the injection pulse, predicted theoretically, could be verified directly in the nozzle. In addition, the injected amount of fuel is monitored with the highest resolution ever reported in the literature.

  12. Cortical thickness and brain volumetric analysis in body dysmorphic disorder

    PubMed Central

    Madsen, Sarah K.; Zai, Alex; Pirnia, Tara; Arienzo, Donatello; Zhan, Liang; Moody, Teena D.; Thompson, Paul M.; Feusner, Jamie D.

    2015-01-01

    Individuals with body dysmorphic disorder (BDD) suffer from preoccupations with perceived defects in physical appearance, causing severe distress and disability. Although BDD affects 1-2% of the population, the neurobiology is not understood. Discrepant results in previous volumetric studies may be due to small sample sizes, and no study has investigated cortical thickness in BDD. The current study is the largest neuroimaging analysis of BDD. Participants included 49 medication-free, right-handed individuals with DSM-IV BDD and 44 healthy controls matched by age, sex, and education. Using high-resolution T1-weighted magnetic resonance imaging, we computed vertex-wise gray matter (GM) thickness on the cortical surface and GM volume using voxel-based morphometry. We also computed volumes in cortical and subcortical regions of interest. In addition to group comparisons, we investigated associations with symptom severity, insight, and anxiety within the BDD group. In BDD, greater anxiety was significantly associated with thinner GM in the left superior temporal cortex and greater GM volume in the right caudate nucleus. There were no significant differences in cortical thickness, GM volume, or volumes in regions of interest between BDD and control subjects. Subtle associations with clinical symptoms may characterize brain morphometric patterns in BDD, rather than large group differences in brain structure. PMID:25797401

  13. Volumetric Rendering of Geophysical Data on Adaptive Wavelet Grid

    NASA Astrophysics Data System (ADS)

    Vezolainen, A.; Erlebacher, G.; Vasilyev, O.; Yuen, D. A.

    2005-12-01

    Numerical modeling of geological phenomena frequently involves processes across a wide range of spatial and temporal scales. In the last several years, transport phenomena governed by the Navier-Stokes equations have been simulated in wavelet space using second generation wavelets [1], and most recently on fully adaptive meshes. Our objective is to visualize this time-dependent data using volume rendering while capitalizing on the available sparse data representation. We present a technique for volumetric ray casting of multi-scale datasets in wavelet space. Rather of working with the wavelets at the finest possible resolution, we perform a partial inverse wavelet transform as a preprocessing step to obtain scaling functions on a uniform grid at a user-prescribed resolution. As a result, a function in physical space is represented by a superposition of scaling functions on a coarse regular grid and wavelets on an adaptive mesh. An efficient and accurate ray casting algorithm is based just on these scaling functions. Additional detail is added during the ray tracing by taking an appropriate number of wavelets into account based on support overlap with the interpolation point, wavelet amplitude, and other characteristics, such as opacity accumulation (front to back ordering) and deviation from frontal viewing direction. Strategies for hardware implementation will be presented if available, inspired by the work in [2]. We will pressent error measures as a function of the number of scaling and wavelet functions used for interpolation. Data from mantle convection will be used to illustrate the method. [1] Vasilyev, O.V. and Bowman, C., Second Generation Wavelet Collocation Method for the Solution of Partial Differential Equations. J. Comp. Phys., 165, pp. 660-693, 2000. [2] Guthe, S., Wand, M., Gonser, J., and Straßer, W. Interactive rendering of large volume data sets. In Proceedings of the Conference on Visualization '02 (Boston, Massachusetts, October 27 - November

  14. Volumetric breast density evaluation from ultrasound tomography images

    SciTech Connect

    Glide-Hurst, Carri K.; Duric, Neb; Littrup, Peter

    2008-09-15

    Previous ultrasound tomography work conducted by our group showed a direct correlation between measured sound speed and physical density in vitro, and increased in vivo sound speed with increasing mammographic density, a known risk factor for breast cancer. Building on these empirical results, the purpose of this work was to explore a metric to quantify breast density using our ultrasound tomography sound speed images in a manner analogous to computer-assisted mammogram segmentation for breast density analysis. Therefore, volumetric ultrasound percent density (USPD) is determined by segmenting high sound speed areas from each tomogram using a k-means clustering routine, integrating these results over the entire volume of the breast, and dividing by whole-breast volume. First, a breast phantom comprised of fat inclusions embedded in fibroglandular tissue was scanned four times with both our ultrasound tomography clinical prototype (with 4 mm spatial resolution) and CT. The coronal transmission tomograms and CT images were analyzed using semiautomatic segmentation routines, and the integrated areas of the phantom's fat inclusions were compared between the four repeated scans. The average variability for inclusion segmentation was {approx}7% and {approx}2%, respectively, and a close correlation was observed in the integrated areas between the two modalities. Next, a cohort of 93 patients was imaged, yielding volumetric coverage of the breast (45-75 sound speed tomograms/patient). The association of USPD with mammographic percent density (MPD) was evaluated using two measures: (1) qualitative, as determined by a radiologist's visual assessment using BI-RADS Criteria and (2) quantitative, via digitization and semiautomatic segmentation of craniocaudal and mediolateral oblique mammograms. A strong positive association between BI-RADS category and USPD was demonstrated [Spearman {rho}=0.69 (p<0.001)], with significant differences between all BI-RADS categories as assessed

  15. Quantification of volumetric cerebral blood flow using hybrid laser speckle contract and optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Valim, Niksa; Dunn, Andrew K.

    2016-03-01

    Studying neurovascular blood flow function in cerebrovascular activities requires accurate visualization and characterization of blood flow volume as well as the dynamics of blood cells in microcirculation. In this study, we present a novel integration of laser speckle contrast imaging (LSCI) and spectral domain optical coherence tomography (SD-OCT) for rapid volumetric imaging of blood flow in cortical capillaries. LSCI uses the illumination of wide-field near infrared light (NIR) and monitors back scattered light to characterize the relative dynamics of blood flow in microcirculation. Absolute measurement of blood cells and blood volume requires high-resolution volumetric structural information. SD-OCT system uses coherence gating to measure scattered light from a small volume within high structural resolution. The structural imaging system rapidly assesses large number of capillaries for spatio-temporal tracking of red blood cells (RBC). A very fast-ultra resolution SD-OCT system was developed for imaging high-resolution volumetric samples. The system employed an ultra wideband light source (1310 ± 200 nm in wavelength) corresponding to an axial resolution of 3 micrometers in tissue. The spectrometer of the SD-OCT was customized for a maximum scanning rate of 147,000 line/s. We demonstrated a fast volumetric OCT angiography algorithm to visualize large numbers of vessels in a 2-mm deep sample volume. A LSCI system that has been developed previously in our group was integrated to the imaging system for the characterization of dynamic blood cells. The conjunction data from LSCI and SD-OCT systems imply the feasibility of accurate quantification of absolute cortical blood flow.

  16. Volumetric measurement of residual stress using high energy x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Whitesell, R.; McKenna, A.; Wendt, S.; Gray, J.

    2016-02-01

    We present results and recent developments from our laboratory, bench-top high energy x-ray diffraction system (HEXRD), between diffraction energies 50 and 150 KeV, to measure internal strain of moderately sized objects. Traditional x-ray strain measurements are limited to a few microns depth due to the use of Cu Kα1 Mo Kα1 radiation. The use of high energy x-rays for volumetric measurements of strain is typically the domain of synchrotron sources. We discuss the use of industrial 320kVp tube sources to generate a brighter x-ray beam along with a method using the intrinsic 43 eV width of the Kα1 characteristic peak of tungsten to measure volumetric strains in a number of industrially relevant materials. We will present volumetric strain measurements from two examples, first, additive manufacturing (AM) parts with various build configurations and, secondly, residual strain depth profiles from shot peened surface treatments. The spatial resolution of these depth profiles is ˜75 microns. The development of a faster method as compared to energy dispersive or θ-2θ scans is based on the intensity variation measurement of the strain using the aforementioned 43 eV characteristic tungsten kα line. We will present recent results on the development of this new tool and on x-ray diffraction measurements at high energy.

  17. Bulk volumetric liquid water content in a seasonal snowpack: modeling its dynamics in different climatic conditions

    NASA Astrophysics Data System (ADS)

    Avanzi, Francesco; Yamaguchi, Satoru; Hirashima, Hiroyuki; De Michele, Carlo

    2015-12-01

    We focus on the dynamics of volumetric liquid water content in seasonal snow covers. This is a key variable describing the fate of snowpacks during the melting season. However, its measurement and/or prediction by means of models at high spatial and temporal resolutions is still difficult due to both practical and theoretical reasons. To overcome these limitations in operational applications, we test the capability of a one-dimensional model to predict the dynamics of bulk volumetric liquid water content during a snow season. Multi-year data collected in three experimental sites in Japan are used as an evaluation. These sites are subjected to different climatic conditions. The model requires the calibration of one or two parameters, according to the degree of detail used. Either a simple temperature-index or a coupled melt-freeze temperature-index approach are considered to predict melting and/or melt-freeze dynamics of liquid water. Results show that, if melt-freeze dynamics are modeled, median absolute differences between data and predictions are consistently lower than 1 vol% at the sites where data of liquid water content are available. In addition, we find also that the model predicts correctly a dry condition in 80% of the observed cases at a site where calibration data are scarce. At the same site, observed isothermal conditions of the snow cover at 0 °C correspond to predictions of bulk volumetric liquid water content that are greater than 0.

  18. A new contrast-assisted method in microcirculation volumetric flow assessment

    NASA Astrophysics Data System (ADS)

    Lu, Sheng-Yi; Chen, Yung-Sheng; Yeh, Chih-Kuang

    2007-03-01

    Microcirculation volumetric flow rate is a significant index in diseases diagnosis and treatment such as diabetes and cancer. In this study, we propose an integrated algorithm to assess microcirculation volumetric flow rate including estimation of blood perfused area and corresponding flow velocity maps based on high frequency destruction/contrast replenishment imaging technique. The perfused area indicates the blood flow regions including capillaries, arterioles and venules. Due to the echo variance changes between ultrasonic contrast agents (UCAs) pre- and post-destruction two images, the perfused area can be estimated by the correlation-based approach. The flow velocity distribution within the perfused area can be estimated by refilling time-intensity curves (TICs) after UCAs destruction. Most studies introduced the rising exponential model proposed by Wei (1998) to fit the TICs. Nevertheless, we found the TICs profile has a great resemblance to sigmoid function in simulations and in vitro experiments results. Good fitting correlation reveals that sigmoid model was more close to actual fact in describing destruction/contrast replenishment phenomenon. We derived that the saddle point of sigmoid model is proportional to blood flow velocity. A strong linear relationship (R = 0.97) between the actual flow velocities (0.4-2.1 mm/s) and the estimated saddle constants was found in M-mode and B-mode flow phantom experiments. Potential applications of this technique include high-resolution volumetric flow rate assessment in small animal tumor and the evaluation of superficial vasculature in clinical studies.

  19. An improved tamper detection and localization scheme for volumetric DICOM images.

    PubMed

    Dou, Wenbo; Poh, Chueh Loo; Guan, Yong Liang

    2012-12-01

    The development of teleradiology brings the convenience of global medical record access along with the concerns over the security of medical images transmitted over the open network. With the prevailing adoption of three-dimensional (3-D) imaging modalities, it is vital to develop a security mechanism to provide large volumes of medical images with privacy and reliability. This paper presents the development of a new and improved method of implementing tamper detection and localization based on a fully reversible digital watermarking scheme for the protection of volumetric DICOM images. This tamper detection and localization method utilizes the 3-D property of volumetric data to achieve much faster processing time at both sender and receiver sides without compromising tamper localization accuracy. The performance of the proposed scheme was evaluated by using sample volumetric DICOM images. Results show that the scheme achieved on average about 65 % and 72 % reduction in watermarking and dewatermarking processing time, respectively. For cases where the images had been tampered, it is possible to detect and localize the tampered areas with improved localization resolution in the images using the scheme. PMID:22832896

  20. Random Volumetric MRI Trajectories via Genetic Algorithms

    PubMed Central

    Curtis, Andrew Thomas; Anand, Christopher Kumar

    2008-01-01

    A pseudorandom, velocity-insensitive, volumetric k-space sampling trajectory is designed for use with balanced steady-state magnetic resonance imaging. Individual arcs are designed independently and do not fit together in the way that multishot spiral, radial or echo-planar trajectories do. Previously, it was shown that second-order cone optimization problems can be defined for each arc independent of the others, that nulling of zeroth and higher moments can be encoded as constraints, and that individual arcs can be optimized in seconds. For use in steady-state imaging, sampling duty cycles are predicted to exceed 95 percent. Using such pseudorandom trajectories, aliasing caused by under-sampling manifests itself as incoherent noise. In this paper, a genetic algorithm (GA) is formulated and numerically evaluated. A large set of arcs is designed using previous methods, and the GA choses particular fit subsets of a given size, corresponding to a desired acquisition time. Numerical simulations of 1 second acquisitions show good detail and acceptable noise for large-volume imaging with 32 coils. PMID:18604305

  1. Iterative reconstruction of volumetric particle distribution

    NASA Astrophysics Data System (ADS)

    Wieneke, Bernhard

    2013-02-01

    For tracking the motion of illuminated particles in space and time several volumetric flow measurement techniques are available like 3D-particle tracking velocimetry (3D-PTV) recording images from typically three to four viewing directions. For higher seeding densities and the same experimental setup, tomographic PIV (Tomo-PIV) reconstructs voxel intensities using an iterative tomographic reconstruction algorithm (e.g. multiplicative algebraic reconstruction technique, MART) followed by cross-correlation of sub-volumes computing instantaneous 3D flow fields on a regular grid. A novel hybrid algorithm is proposed here that similar to MART iteratively reconstructs 3D-particle locations by comparing the recorded images with the projections calculated from the particle distribution in the volume. But like 3D-PTV, particles are represented by 3D-positions instead of voxel-based intensity blobs as in MART. Detailed knowledge of the optical transfer function and the particle image shape is mandatory, which may differ for different positions in the volume and for each camera. Using synthetic data it is shown that this method is capable of reconstructing densely seeded flows up to about 0.05 ppp with similar accuracy as Tomo-PIV. Finally the method is validated with experimental data.

  2. Volumetric depth peeling for medical image display

    NASA Astrophysics Data System (ADS)

    Borland, David; Clarke, John P.; Fielding, Julia R.; TaylorII, Russell M.

    2006-01-01

    Volumetric depth peeling (VDP) is an extension to volume rendering that enables display of otherwise occluded features in volume data sets. VDP decouples occlusion calculation from the volume rendering transfer function, enabling independent optimization of settings for rendering and occlusion. The algorithm is flexible enough to handle multiple regions occluding the object of interest, as well as object self-occlusion, and requires no pre-segmentation of the data set. VDP was developed as an improvement for virtual arthroscopy for the diagnosis of shoulder-joint trauma, and has been generalized for use in other simple and complex joints, and to enable non-invasive urology studies. In virtual arthroscopy, the surfaces in the joints often occlude each other, allowing limited viewpoints from which to evaluate these surfaces. In urology studies, the physician would like to position the virtual camera outside the kidney collecting system and see inside it. By rendering invisible all voxels between the observer's point of view and objects of interest, VDP enables viewing from unconstrained positions. In essence, VDP can be viewed as a technique for automatically defining an optimal data- and task-dependent clipping surface. Radiologists using VDP display have been able to perform evaluations of pathologies more easily and more rapidly than with clinical arthroscopy, standard volume rendering, or standard MRI/CT slice viewing.

  3. Autologous Fat Grafting in Facial Volumetric Restoration

    PubMed Central

    Pasquale, Piombino; Gaetano, Marenzi; Giovanni, Dell’Aversana Orabona; Luigi, Califano; Gilberto, Sammartino

    2015-01-01

    Abstract The authors reported their surgical experience about structural fat grafting in the management of facial volumetric deficit. The purpose of this study was to assess the real indications, cosmetic results, complications, and global patient satisfaction of the Coleman technique in redefining facial contours in congenital and postoperative deformities. A retrospective analysis of 32 patients grafted according to Coleman's technique was performed, and the long-term outcomes and patient satisfaction were evaluated. The mean postoperative clinical follow-up was 14 months. The morphological changes were analyzed by comparing the photographic presurgical facial contour and the postoperative correction of soft tissue defects. All consecutive cases reported showed a progressive fat resorption for 3 months after surgery and its stable integration only after this period. Best results were performed in the treatment of genetically determined syndromes, such as the Franceschetti and Romberg syndromes. The authors suggest this surgical technique also for the treatment of unaesthetic cutaneous abscess cavity after incision and drainage. Unsatisfactory outcomes were obtained in the treatment of the posttraumatic facial scar, which needed more surgical procedures. PMID:25974786

  4. A hand-held immaterial volumetric display

    NASA Astrophysics Data System (ADS)

    Sand, Antti; Rakkolainen, Ismo

    2014-03-01

    We have created an ultralight, movable, "immaterial" fogscreen. It is based on the fogscreen mid-air imaging technology. The hand-held unit is roughly the size and weight of an ordinary toaster. If the screen is tracked, it can be swept in the air to create mid-air slices of volumetric objects, or to show augmented reality (AR) content on top of real objects. Interfacing devices and methodologies, such as hand and gesture trackers, camera-based trackers and object recognition, can make the screen interactive. The user can easily interact with any physical object or virtual information, as the screen is permeable. Any real objects can be seen through the screen, instead of e.g., through a video-based augmented reality screen. It creates a mixed reality setup where both the real world object and the augmented reality content can be viewed and interacted with simultaneously. The hand-held mid-air screen can be used e.g., as a novel collaborating or classroom tool for individual students or small groups.

  5. Volumetric imaging system for the ionosphere (VISION)

    NASA Astrophysics Data System (ADS)

    Dymond, Kenneth F.; Budzien, Scott A.; Nicholas, Andrew C.; Thonnard, Stefan E.; Fortna, Clyde B.

    2002-01-01

    The Volumetric Imaging System for the Ionosphere (VISION) is designed to use limb and nadir images to reconstruct the three-dimensional distribution of electrons over a 1000 km wide by 500 km high slab beneath the satellite with 10 km x 10 km x 10 km voxels. The primary goal of the VISION is to map and monitor global and mesoscale (> 10 km) electron density structures, such as the Appleton anomalies and field-aligned irregularity structures. The VISION consists of three UV limb imagers, two UV nadir imagers, a dual frequency Global Positioning System (GPS) receiver, and a coherently emitting three frequency radio beacon. The limb imagers will observe the O II 83.4 nm line (daytime electron density), O I 135.6 nm line (nighttime electron density and daytime O density), and the N2 Lyman-Birge-Hopfield (LBH) bands near 143.0 nm (daytime N2 density). The nadir imagers will observe the O I 135.6 nm line (nighttime electron density and daytime O density) and the N2 LBH bands near 143.0 nm (daytime N2 density). The GPS receiver will monitor the total electron content between the satellite containing the VISION and the GPS constellation. The three frequency radio beacon will be used with ground-based receiver chains to perform computerized radio tomography below the satellite containing the VISION. The measurements made using the two radio frequency instruments will be used to validate the VISION UV measurements.

  6. Morphological and Volumetric Assessment of Cerebral Ventricular System with 3D Slicer Software.

    PubMed

    Gonzalo Domínguez, Miguel; Hernández, Cristina; Ruisoto, Pablo; Juanes, Juan A; Prats, Alberto; Hernández, Tomás

    2016-06-01

    We present a technological process based on the 3D Slicer software for the three-dimensional study of the brain's ventricular system with teaching purposes. It values the morphology of this complex brain structure, as a whole and in any spatial position, being able to compare it with pathological studies, where its anatomy visibly changes. 3D Slicer was also used to obtain volumetric measurements in order to provide a more comprehensive and detail representation of the ventricular system. We assess the potential this software has for processing high resolution images, taken from Magnetic Resonance and generate the three-dimensional reconstruction of ventricular system. PMID:27147517

  7. Dual Frequency Band Annular Probe for Volumetric Pulse-echo Optoacoustic Imaging

    NASA Astrophysics Data System (ADS)

    Kalkhoran, Mohammad Azizian; Varray, François; Vray, Didier

    Optoacoustic (OA) pulse echo (PE) imaging is a hybridized modality that is capable of providing physiological information on the basis of anatomical structure. In this work, we propose a dual frequency band annular probe for backward mode volumetric PE/OA imaging. The performance of this design is evaluated based on the spatio-temporal impulse response, three dimensional steerability of the transducer and point spread function. Optimum settings for number of elements in each ring and maximum steering are suggested. The transducer design and synthetic array beamforming simulation are presented. The resolution performance and reconstruction capabilities are shown with the in-silico measurements.

  8. Volumetric structured illumination microscopy enabled by a tunable-focus lens

    PubMed Central

    Hinsdale, Taylor; Malik, Bilal H.; Olsovsky, Cory; Jo, Javier A.; Maitland, Kristen C.

    2016-01-01

    We present a mechanical-scan-free method for volumetric imaging of biological tissue. The optical sectioning is provided by structured illumination, and the depth of the imaging plane is varied using an electrically tunable-focus lens. We characterize and evaluate the ability of this axial-scanning mechanism in structured illumination microscopy and demonstrate its ability to perform subcellular resolution imaging in oral mucosa ex vivo. The proposed mechanism can potentially convert any wide-field microscope to a 3D-imaging platform without the need for mechanical scanning of imaging optics and/or sample. PMID:26512489

  9. Rapidly-steered single-element ultrasound for real-time volumetric imaging and guidance

    NASA Astrophysics Data System (ADS)

    Stauber, Mark; Western, Craig; Solek, Roman; Salisbury, Kenneth; Hristov, Dmitre; Schlosser, Jeffrey

    2016-03-01

    Volumetric ultrasound (US) imaging has the potential to provide real-time anatomical imaging with high soft-tissue contrast in a variety of diagnostic and therapeutic guidance applications. However, existing volumetric US machines utilize "wobbling" linear phased array or matrix phased array transducers which are costly to manufacture and necessitate bulky external processing units. To drastically reduce cost, improve portability, and reduce footprint, we propose a rapidly-steered single-element volumetric US imaging system. In this paper we explore the feasibility of this system with a proof-of-concept single-element volumetric US imaging device. The device uses a multi-directional raster-scan technique to generate a series of two-dimensional (2D) slices that were reconstructed into three-dimensional (3D) volumes. At 15 cm depth, 90° lateral field of view (FOV), and 20° elevation FOV, the device produced 20-slice volumes at a rate of 0.8 Hz. Imaging performance was evaluated using an US phantom. Spatial resolution was 2.0 mm, 4.7 mm, and 5.0 mm in the axial, lateral, and elevational directions at 7.5 cm. Relative motion of phantom targets were automatically tracked within US volumes with a mean error of -0.3+/-0.3 mm, -0.3+/-0.3 mm, and -0.1+/-0.5 mm in the axial, lateral, and elevational directions, respectively. The device exhibited a mean spatial distortion error of 0.3+/-0.9 mm, 0.4+/-0.7 mm, and -0.3+/-1.9 in the axial, lateral, and elevational directions. With a production cost near $1000, the performance characteristics of the proposed system make it an ideal candidate for diagnostic and image-guided therapy applications where form factor and low cost are paramount.

  10. Fast volumetric imaging of ethanol metabolism in rat liver with hyperpolarized [1-13C]-pyruvate

    PubMed Central

    Josan, Sonal; Spielman, Daniel; Yen, Yi-Fen; Hurd, Ralph; Pfefferbaum, Adolf; Mayer, Dirk

    2012-01-01

    Rapid, volumetric imaging of hyperpolarized 13C compounds allows the real time measurement of metabolic activity and can be useful in distinguishing between normal and diseased tissues. This work extends a fast 2D under-sampled spiral magnetic resonance spectroscopic imaging (MRSI) sequence to provide volumetric coverage, acquiring a 16×16×12 matrix with a nominal 5 mm isotropic resolution in 4.5 s. The rapid acquisition enables a high temporal resolution for dynamic imaging. This dynamic 3D MRSI method was used to investigate hyperpolarized [1-13C]-pyruvate metabolism modulated by the administration of ethanol in rat liver. A significant increase in the pyruvate to lactate conversion was observed in the liver due to the greater availability of NADH from ethanol metabolism. PMID:22331837

  11. Treatment planning for volumetric modulated arc therapy

    SciTech Connect

    Bedford, James L.

    2009-11-15

    Purpose: Volumetric modulated arc therapy (VMAT) is a specific type of intensity-modulated radiation therapy (IMRT) in which the gantry speed, multileaf collimator (MLC) leaf position, and dose rate vary continuously during delivery. A treatment planning system for VMAT is presented. Methods: Arc control points are created uniformly throughout one or more arcs. An iterative least-squares algorithm is used to generate a fluence profile at every control point. The control points are then grouped and all of the control points in a given group are used to approximate the fluence profiles. A direct-aperture optimization is then used to improve the solution, taking into account the allowed range of leaf motion of the MLC. Dose is calculated using a fast convolution algorithm and the motion between control points is approximated by 100 interpolated dose calculation points. The method has been applied to five cases, consisting of lung, rectum, prostate and seminal vesicles, prostate and pelvic lymph nodes, and head and neck. The resulting plans have been compared with segmental (step-and-shoot) IMRT and delivered and verified on an Elekta Synergy to ensure practicality. Results: For the lung, prostate and seminal vesicles, and rectum cases, VMAT provides a plan of similar quality to segmental IMRT but with faster delivery by up to a factor of 4. For the prostate and pelvic nodes and head-and-neck cases, the critical structure doses are reduced with VMAT, both of these cases having a longer delivery time than IMRT. The plans in general verify successfully, although the agreement between planned and measured doses is not very close for the more complex cases, particularly the head-and-neck case. Conclusions: Depending upon the emphasis in the treatment planning, VMAT provides treatment plans which are higher in quality and/or faster to deliver than IMRT. The scheme described has been successfully introduced into clinical use.

  12. Commissioning of Volumetric Modulated Arc Therapy (VMAT)

    SciTech Connect

    Bedford, James L. Warrington, Alan P.

    2009-02-01

    Purpose: Volumetric modulated arc therapy (VMAT) involves the simultaneous use of dynamic multileaf collimator (DMLC) techniques and gantry arcing; appropriate quality assurance is therefore required. This article describes the development and implementation of procedures for commissioning VMAT on a commercial linear accelerator (Elekta PreciseBeam VMAT with MLCi and Beam Modulator heads). Materials and Methods: Tests for beam flatness and symmetry at the variable dose rates required for VMAT were performed. Multileaf collimator (MLC) calibration was investigated using dynamic prescriptions. The cumulative dose delivered by a sliding window aperture was measured and compared with calculated values. Rotational accuracy was evaluated using dynamic prescriptions which required accurate correlated motion of both gantry and MLC leaves. Finally, measured and calculated dose distributions for complete VMAT treatment plans were compared and evaluated. Results: Beam symmetry was found to be better than 3% down to dose rates of 75 MU/min. MLC calibration provided continuity of dose at match planes of better than 4%, which was comparable to interleaf leakage effects. Integrated sliding window doses were within 3% of those calculated. Tests for rotational accuracy showed uniformity of peripheral dose mostly within {+-}4% of local control point dose, or approximately {+-}0.2% of total central dose. A two-arc prostate case showed an absolute dose difference between calculations and measurements of less than 3%, with gamma (3% and 3 mm) of better than 95%. Conclusions: VMAT has been successfully commissioned and has been introduced into clinical use. The Elekta DMLC has also been shown to be suitable for sliding window delivery.

  13. Volumetric interpretation of protein adsorption kinetics

    NASA Astrophysics Data System (ADS)

    Barnthip, Naris

    Protein adsorption is believed to be a very important factor ultimately leading to a predictive basis for biomaterials design and improving biocompatibility. Standard adsorption theories are modified to accommodate experimental observations. Adsorption from single-protein solutions and competitive adsorption from binary solutions are mainly considered. The standard solution-depletion method of measuring protein adsorption is implemented with SDS-gel electrophoresis as a multiplexing, separation-and-quantification tool to measure protein adsorption to hydrophobic octyl sepharose (OS) adsorbent particles. Standard radiometric methods have also been used as a further check on the electrophoresis method mentioned above for purified-protein cases. Experimental results are interpreted in terms of an alternative kinetic model called volumetric interpretation of protein adsorption. A partitioning process between bulk solution and a three-dimensional interphase region that separates bulk solution from the physical adsorbent surface is the concept of the model. Protein molecules rapidly diffuse into an inflating interphase that is spontaneously formed by bringing a protein solution into contact with a physical surface, then follows by rearrangement of proteins within this interphase to achieve the maximum interphase concentration (dictated by energetics of interphase dehydration) within the thinnest (lowest volume) interphase possible. An important role of water in protein adsorption is emphasized and supported by this model. The fundamental aspects including the reversibility/irreversibility of protein adsorption, the multilayer adsorption, the applicability of thermodynamic/computational models, the capacity of protein adsorption, and the mechanism of so called Vroman effect are discussed and compared to the conventional theories. Superhydrophobic effect on the adsorption of human serum albumin is also examined.

  14. Comprehensive volumetric confocal microscopy with adaptive focusing

    PubMed Central

    Kang, DongKyun; Yoo, Hongki; Jillella, Priyanka; Bouma, Brett E.; Tearney, Guillermo J.

    2011-01-01

    Comprehensive microscopy of distal esophagus could greatly improve the screening and surveillance of esophageal diseases such as Barrett’s esophagus by providing histomorphologic information over the entire region at risk. Spectrally encoded confocal microscopy (SECM) is a high-speed reflectance confocal microscopy technology that can be configured to image the entire distal esophagus by helically scanning the beam using optics within a balloon-centering probe. It is challenging to image the human esophagus in vivo with balloon-based SECM, however, because patient motion and anatomic tissue surface irregularities decenter the optics, making it difficult to keep the focus at a predetermined location within the tissue as the beam is scanned. In this paper, we present a SECM probe equipped with an adaptive focusing mechanism that can compensate for tissue surface irregularity and dynamic focal variation. A tilted arrangement of the objective lens is employed in the SECM probe to provide feedback signals to an adaptive focusing mechanism. The tilted configuration also allows the probe to obtain reflectance confocal data from multiple depth levels, enabling the acquisition of three-dimensional volumetric data during a single scan of the probe. A tissue phantom with a surface area of 12.6 cm2 was imaged using the new SECM probe, and 8 large-area reflectance confocal microscopy images were acquired over the depth range of 56 μm in 20 minutes. Large-area SECM images of excised swine small intestine tissue were also acquired, enabling the visualization of villous architecture, epithelium, and lamina propria. The adaptive focusing mechanism was demonstrated to enable acquisition of in-focus images even when the probe was not centered and the tissue surface was irregular. PMID:21698005

  15. Increasing the volumetric efficiency of Diesel engines by intake pipes

    NASA Technical Reports Server (NTRS)

    List, Hans

    1933-01-01

    Development of a method for calculating the volumetric efficiency of piston engines with intake pipes. Application of this method to the scavenging pumps of two-stroke-cycle engines with crankcase scavenging and to four-stroke-cycle engines. The utility of the method is demonstrated by volumetric-efficiency tests of the two-stroke-cycle engines with crankcase scavenging. Its practical application to the calculation of intake pipes is illustrated by example.

  16. Multi-scale Heat Kernel based Volumetric Morphology Signature

    PubMed Central

    Wang, Gang; Wang, Yalin

    2015-01-01

    Here we introduce a novel multi-scale heat kernel based regional shape statistical approach that may improve statistical power on the structural analysis. The mechanism of this analysis is driven by the graph spectrum and the heat kernel theory, to capture the volumetric geometry information in the constructed tetrahedral mesh. In order to capture profound volumetric changes, we first use the volumetric Laplace-Beltrami operator to determine the point pair correspondence between two boundary surfaces by computing the streamline in the tetrahedral mesh. Secondly, we propose a multi-scale volumetric morphology signature to describe the transition probability by random walk between the point pairs, which reflects the inherent geometric characteristics. Thirdly, a point distribution model is applied to reduce the dimensionality of the volumetric morphology signatures and generate the internal structure features. The multi-scale and physics based internal structure features may bring stronger statistical power than other traditional methods for volumetric morphology analysis. To validate our method, we apply support vector machine to classify synthetic data and brain MR images. In our experiments, the proposed work outperformed FreeSurfer thickness features in Alzheimer's disease patient and normal control subject classification analysis. PMID:26550613

  17. Visualization and volumetric structures from MR images of the brain

    SciTech Connect

    Parvin, B.; Johnston, W.; Robertson, D.

    1994-03-01

    Pinta is a system for segmentation and visualization of anatomical structures obtained from serial sections reconstructed from magnetic resonance imaging. The system approaches the segmentation problem by assigning each volumetric region to an anatomical structure. This is accomplished by satisfying constraints at the pixel level, slice level, and volumetric level. Each slice is represented by an attributed graph, where nodes correspond to regions and links correspond to the relations between regions. These regions are obtained by grouping pixels based on similarity and proximity. The slice level attributed graphs are then coerced to form a volumetric attributed graph, where volumetric consistency can be verified. The main novelty of our approach is in the use of the volumetric graph to ensure consistency from symbolic representations obtained from individual slices. In this fashion, the system allows errors to be made at the slice level, yet removes them when the volumetric consistency cannot be verified. Once the segmentation is complete, the 3D surfaces of the brain can be constructed and visualized.

  18. Quantification of ultrasonic texture intra-heterogeneity via volumetric stochastic modeling for tissue characterization

    PubMed Central

    Al-Kadi, Omar S.; Chung, Daniel Y.F.; Carlisle, Robert C.; Coussios, Constantin C.; Noble, J. Alison

    2015-01-01

    Intensity variations in image texture can provide powerful quantitative information about physical properties of biological tissue. However, tissue patterns can vary according to the utilized imaging system and are intrinsically correlated to the scale of analysis. In the case of ultrasound, the Nakagami distribution is a general model of the ultrasonic backscattering envelope under various scattering conditions and densities where it can be employed for characterizing image texture, but the subtle intra-heterogeneities within a given mass are difficult to capture via this model as it works at a single spatial scale. This paper proposes a locally adaptive 3D multi-resolution Nakagami-based fractal feature descriptor that extends Nakagami-based texture analysis to accommodate subtle speckle spatial frequency tissue intensity variability in volumetric scans. Local textural fractal descriptors – which are invariant to affine intensity changes – are extracted from volumetric patches at different spatial resolutions from voxel lattice-based generated shape and scale Nakagami parameters. Using ultrasound radio-frequency datasets we found that after applying an adaptive fractal decomposition label transfer approach on top of the generated Nakagami voxels, tissue characterization results were superior to the state of art. Experimental results on real 3D ultrasonic pre-clinical and clinical datasets suggest that describing tumor intra-heterogeneity via this descriptor may facilitate improved prediction of therapy response and disease characterization. PMID:25595523

  19. In vivo volumetric imaging of the human corneo-scleral limbus with spectral domain OCT

    PubMed Central

    Bizheva, Kostadinka; Hutchings, Natalie; Sorbara, Luigina; Moayed, Alireza A.; Simpson, Trefford

    2011-01-01

    The limbus is the structurally rich transitional region of tissue between the cornea on one side, and the sclera and conjunctiva on the other. This zone, among other things, contains nerves passing to the cornea, blood and lymph vasculature for oxygen and nutrient delivery and for waste, CO2 removal and drainage of the aqueous humour. In addition, the limbus contains stem cells responsible for the existence and healing of the corneal epithelium. Here we present 3D images of the healthy human limbus, acquired in vivo with a spectral domain optical coherence tomography system operating at 1060nm. Cross-sectional and volumetric images were acquired from temporal and nasal locations in the human limbus with ~3µm x 18µm (axial x lateral) resolution in biological tissue at the rate of 92,000 A-scans/s. The imaging enabled detailed mapping of the corneo-scleral tissue morphology, and visualization of structural details such as the Vogt palisades, the blood and lymph vasculature including the Schlemm’s canal and the trabecular meshwork, as well as corneal nerve fiber bundles. Non-invasive, volumetric, high resolution imaging reveals fine details of the normal human limbal structure, and promises to provide invaluable information about its changes in health and disease as well as during and after corneal surgery. PMID:21750758

  20. Volumetric Forest Change Detection Through Vhr Satellite Imagery

    NASA Astrophysics Data System (ADS)

    Akca, Devrim; Stylianidis, Efstratios; Smagas, Konstantinos; Hofer, Martin; Poli, Daniela; Gruen, Armin; Sanchez Martin, Victor; Altan, Orhan; Walli, Andreas; Jimeno, Elisa; Garcia, Alejandro

    2016-06-01

    Quick and economical ways of detecting of planimetric and volumetric changes of forest areas are in high demand. A research platform, called FORSAT (A satellite processing platform for high resolution forest assessment), was developed for the extraction of 3D geometric information from VHR (very-high resolution) imagery from satellite optical sensors and automatic change detection. This 3D forest information solution was developed during a Eurostars project. FORSAT includes two main units. The first one is dedicated to the geometric and radiometric processing of satellite optical imagery and 2D/3D information extraction. This includes: image radiometric pre-processing, image and ground point measurement, improvement of geometric sensor orientation, quasiepipolar image generation for stereo measurements, digital surface model (DSM) extraction by using a precise and robust image matching approach specially designed for VHR satellite imagery, generation of orthoimages, and 3D measurements in single images using mono-plotting and in stereo images as well as triplets. FORSAT supports most of the VHR optically imagery commonly used for civil applications: IKONOS, OrbView - 3, SPOT - 5 HRS, SPOT - 5 HRG, QuickBird, GeoEye-1, WorldView-1/2, Pléiades 1A/1B, SPOT 6/7, and sensors of similar type to be expected in the future. The second unit of FORSAT is dedicated to 3D surface comparison for change detection. It allows users to import digital elevation models (DEMs), align them using an advanced 3D surface matching approach and calculate the 3D differences and volume changes between epochs. To this end our 3D surface matching method LS3D is being used. FORSAT is a single source and flexible forest information solution with a very competitive price/quality ratio, allowing expert and non-expert remote sensing users to monitor forests in three and four dimensions from VHR optical imagery for many forest information needs. The capacity and benefits of FORSAT have been tested in

  1. Volumetric modulated arc radiotherapy for esophageal cancer

    SciTech Connect

    Vivekanandan, Nagarajan; Sriram, Padmanaban; Syam Kumar, S.A.; Bhuvaneswari, Narayanan; Saranya, Kamalakannan

    2012-04-01

    A treatment planning study was performed to evaluate the performance of volumetric arc modulation with RapidArc (RA) against 3D conformal radiation therapy (3D-CRT) and conventional intensity-modulated radiation therapy (IMRT) techniques for esophageal cancer. Computed tomgraphy scans of 10 patients were included in the study. 3D-CRT, 4-field IMRT, and single-arc and double-arc RA plans were generated with the aim to spare organs at risk (OAR) and healthy tissue while enforcing highly conformal target coverage. The planning objective was to deliver 54 Gy to the planning target volume (PTV) in 30 fractions. Plans were evaluated based on target conformity and dose-volume histograms of organs at risk (lung, spinal cord, and heart). The monitor unit (MU) and treatment delivery time were also evaluated to measure the treatment efficiency. The IMRT plan improves target conformity and spares OAR when compared with 3D-CRT. Target conformity improved with RA plans compared with IMRT. The mean lung dose was similar in all techniques. However, RA plans showed a reduction in the volume of the lung irradiated at V{sub 20Gy} and V{sub 30Gy} dose levels (range, 4.62-17.98%) compared with IMRT plans. The mean dose and D{sub 35%} of heart for the RA plans were better than the IMRT by 0.5-5.8%. Mean V{sub 10Gy} and integral dose to healthy tissue were almost similar in all techniques. But RA plans resulted in a reduced low-level dose bath (15-20 Gy) in the range of 14-16% compared with IMRT plans. The average MU needed to deliver the prescribed dose by RA technique was reduced by 20-25% compared with IMRT technique. The preliminary study on RA for esophageal cancers showed improvements in sparing OAR and healthy tissue with reduced beam-on time, whereas only double-arc RA offered improved target coverage compared with IMRT and 3D-CRT plans.

  2. Cellular Stress Responses and Monitored Cellular Activities.

    PubMed

    Sawa, Teiji; Naito, Yoshifumi; Kato, Hideya; Amaya, Fumimasa

    2016-08-01

    To survive, organisms require mechanisms that enable them to sense changes in the outside environment, introduce necessary responses, and resist unfavorable distortion. Consequently, through evolutionary adaptation, cells have become equipped with the apparatus required to monitor their fundamental intracellular processes and the mechanisms needed to try to offset malfunction without receiving any direct signals from the outside environment. It has been shown recently that eukaryotic cells are equipped with a special mechanism that monitors their fundamental cellular functions and that some pathogenic proteobacteria can override this monitoring mechanism to cause harm. The monitored cellular activities involved in the stressed intracellular response have been researched extensively in Caenorhabditis elegans, where discovery of an association between key mitochondrial activities and innate immune responses was named "cellular associated detoxification and defenses (cSADD)." This cellular surveillance pathway (cSADD) oversees core cellular activities such as mitochondrial respiration and protein transport into mitochondria, detects xenobiotics and invading pathogens, and activates the endocrine pathways controlling behavior, detoxification, and immunity. The cSADD pathway is probably associated with cellular responses to stress in human inflammatory diseases. In the critical care field, the pathogenesis of lethal inflammatory syndromes (e.g., respiratory distress syndromes and sepsis) involves the disturbance of mitochondrial respiration leading to cell death. Up-to-date knowledge about monitored cellular activities and cSADD, especially focusing on mitochondrial involvement, can probably help fill a knowledge gap regarding the pathogenesis of lethal inflammatory syndromes in the critical care field. PMID:26954943

  3. Ultra-high resolution polarization-sensitive optical coherence microscopy for brain imaging at 6 um, 3.4 um and 1.3 um resolution (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Akkin, Taner; Magnain, Caroline V.; Yaseen, Mohammad A.; Cramer, Avilash; Wang, Ruopeng; Sakadžic, Sava; Boas, David A.

    2016-03-01

    Neuroanatomical pathways form the basis for functional activity of brain circuits. In the past, we developed a polarization-sensitive optical coherence tomography with serial scanning to achieve large-scale brain imaging. The system was able to visualize 3D fiber tracts of ~20 um in diameter. To investigate the neuroanatomical pathways at finer scales, we have now built a polarization-maintaining fiber based ultra-high resolution polarization-sensitive optical coherence microscope (PS-OCM) at 1300 nm. The PS-OCM has an axial resolution of 3.5 um in tissue. The detection setup consists of two spectrometers, acquiring spectral interference on orthogonal polarization channels. With a single measurement, the setup generates four contrasts: reflectivity, cross-polarization, retardance and optic axis orientation. To investigate the capability of PS-OCM at different resolutions, we used three microscope objectives that yield lateral resolutions of 6.0 um, 3.4 um and 1.3 um. Blocks of formalin fixed mouse brain and human brain were scanned. The cross-polarization and retardance images clearly depict the neuronal fiber structures, which are comparable with that generated by the maximum projection of volumetric reflectivity data. The optic axis orientation quantifies the in-plane fiber orientation. With the lateral resolution of 1.3 um, the retardance contrast is weak in white matter due to the shallow depth of focus. Overall, the ultra-high resolution PS-OCM provides a new tool to reveal neuroanatomical maps in the brain at cellular resolution.

  4. Cellular Phone Towers

    MedlinePlus

    ... the call. How are people exposed to the energy from cellular phone towers? As people use cell ... where people can be exposed to them. The energy from a cellular phone tower antenna, like that ...

  5. Cellular and molecular mechanisms in kidney fibrosis

    PubMed Central

    Duffield, Jeremy S.

    2014-01-01

    Fibrosis is a characteristic feature of all forms of chronic kidney disease. Deposition of pathological matrix in the interstitial space and within the walls of glomerular capillaries as well as the cellular processes resulting in this deposition are increasingly recognized as important factors amplifying kidney injury and accelerating nephron demise. Recent insights into the cellular and molecular mechanisms of fibrogenesis herald the promise of new therapies to slow kidney disease progression. This review focuses on new findings that enhance understanding of cellular and molecular mechanisms of fibrosis, the characteristics of myofibroblasts, their progenitors, and molecular pathways regulating both fibrogenesis and its resolution. PMID:24892703

  6. Cellular energy metabolism

    SciTech Connect

    Glaser, M.

    1991-06-01

    Studies have been carried out on adenylate kinase which is an important enzyme in determining the concentrations of the adenine nucleotides. An efficient method has been developed to clone mutant adenylate kinase genes in E. coli. Site-specific mutagenesis of the wild type gene also has been used to obtain forms of adenylate kinase with altered amino acids. The wild type and mutant forms of adenylate kinase have been overexpressed and large quantities were readily isolated. The kinetic and fluorescence properties of the different forms of adenylate kinase were characterized. This has led to a new model for the location of the AMP and ATP bindings sites on the enzyme and a proposal for the mechanism of substrate inhibition. Crystals of the wild type enzyme were obtained that diffract to at least 2.3 {angstrom} resolution. Experiments were also initiated to determine the function of adenylate kinase in vivo. In one set of experiments, E. coli strains with mutations in adenylate kinase showed large changes in cellular nucleotides after reaching the stationary phase in a low phosphate medium. This was caused by selective proteolytic degradation of the mutant adenylate kinase caused by phosphate starvation.

  7. Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks

    NASA Astrophysics Data System (ADS)

    Dana, Hod; Marom, Anat; Paluch, Shir; Dvorkin, Roman; Brosh, Inbar; Shoham, Shy

    2014-06-01

    Planar neural networks and interfaces serve as versatile in vitro models of central nervous system physiology, but adaptations of related methods to three dimensions (3D) have met with limited success. Here, we demonstrate for the first time volumetric functional imaging in a bioengineered neural tissue growing in a transparent hydrogel with cortical cellular and synaptic densities, by introducing complementary new developments in nonlinear microscopy and neural tissue engineering. Our system uses a novel hybrid multiphoton microscope design combining a 3D scanning-line temporal-focusing subsystem and a conventional laser-scanning multiphoton microscope to provide functional and structural volumetric imaging capabilities: dense microscopic 3D sampling at tens of volumes per second of structures with mm-scale dimensions containing a network of over 1,000 developing cells with complex spontaneous activity patterns. These developments open new opportunities for large-scale neuronal interfacing and for applications of 3D engineered networks ranging from basic neuroscience to the screening of neuroactive substances.

  8. Hierarchical cellular materials

    SciTech Connect

    Gibson, L.J.

    1991-01-01

    In this paper a method for estimating the contributions of both the composite and the cellular microstructures to the overall material properties and the mechanical efficiency of natural cellular solids will be described. The method will be demonstrated by focusing on the Young's modulus; similar techniques can be used for other material properties. The results suggest efficient microstructures for engineered cellular materials.

  9. Hierarchical cellular materials

    SciTech Connect

    Gibson, L.J.

    1991-12-31

    In this paper a method for estimating the contributions of both the composite and the cellular microstructures to the overall material properties and the mechanical efficiency of natural cellular solids will be described. The method will be demonstrated by focusing on the Young`s modulus; similar techniques can be used for other material properties. The results suggest efficient microstructures for engineered cellular materials.

  10. Improved volumetric imaging in tomosynthesis using combined multiaxial sweeps.

    PubMed

    Gersh, Jacob A; Wiant, David B; Best, Ryan C M; Bennett, Marcus C; Munley, Michael T; King, June D; McKee, Mahta M; Baydush, Alan H

    2010-01-01

    This study explores the volumetric reconstruction fidelity attainable using tomosynthesis with a kV imaging system which has a unique ability to rotate isocentrically and with multiple degrees of mechanical freedom. More specifically, we seek to investigate volumetric reconstructions by combining multiple limited-angle rotational image acquisition sweeps. By comparing these reconstructed images with those of a CBCT reconstruction, we can gauge the volumetric fidelity of the reconstructions. In surgical situations, the described tomosynthesis-based system could provide high-quality volumetric imaging without requiring patient motion, even with rotational limitations present. Projections were acquired using the Digital Integrated Brachytherapy Unit, or IBU-D. A phantom was used which contained several spherical objects of varying contrast. Using image projections acquired during isocentric sweeps around the phantom, reconstructions were performed by filtered backprojection. For each image acquisition sweep configuration, a contrasting sphere is analyzed using two metrics and compared to a gold standard CBCT reconstruction. Since the intersection of a reconstructed sphere and an imaging plane is ideally a circle with an eccentricity of zero, the first metric presented compares the effective eccentricity of intersections of reconstructed volumes and imaging planes. As another metric of volumetric reconstruction fidelity, the volume of one of the contrasting spheres was determined using manual contouring. By comparing these manually delineated volumes with a CBCT reconstruction, we can gauge the volumetric fidelity of reconstructions. The configuration which yielded the highest overall volumetric reconstruction fidelity, as determined by effective eccentricities and volumetric contouring, consisted of two orthogonally-offset 60° L-arm sweeps and a single C-arm sweep which shared a pivot point with one the L-arm sweeps. When compared to a similar configuration that

  11. Volumetric loss quantification using ultrasonic inductively coupled transducers

    NASA Astrophysics Data System (ADS)

    Gong, Peng; Hay, Thomas R.; Greve, David W.; Oppenheim, Irving J.

    2015-03-01

    The pulse-echo method is widely used for plate and pipe thickness measurement. However, the pulse echo method does not work well for detecting localized volumetric loss in thick-wall tubes, as created by erosion damage, when the morphology of volumetric loss is irregular and can reflect ultrasonic pulses away from the transducer, making it difficult to detect an echo. In this paper, we propose a novel method using an inductively coupled transducer to generate longitudinal waves propagating in a thick-wall aluminum tube for the volumetric loss quantification. In the experiment, longitudinal waves exhibit diffraction effects during the propagation which can be explained by the Huygens-Fresnel principle. The diffractive waves are also shown to be significantly delayed by the machined volumetric loss on the inside surface of the thick-wall aluminum tube. It is also shown that the inductively coupled transducers can generate and receive similar ultrasonic waves to those from wired transducers, and the inductively coupled transducers perform as well as the wired transducers in the volumetric loss quantification when other conditions are the same.

  12. Volumetric image display for complex 3D data visualization

    NASA Astrophysics Data System (ADS)

    Tsao, Che-Chih; Chen, Jyh Shing

    2000-05-01

    A volumetric image display is a new display technology capable of displaying computer generated 3D images in a volumetric space. Many viewers can walk around the display and see the image from omni-directions simultaneously without wearing any glasses. The image is real and possesses all major elements in both physiological and psychological depth cues. Due to the volumetric nature of its image, the VID can provide the most natural human-machine interface in operations involving 3D data manipulation and 3D targets monitoring. The technology creates volumetric 3D images by projecting a series of profiling images distributed in the space form a volumetric image because of the after-image effect of human eyes. Exemplary applications in biomedical image visualization were tested on a prototype display, using different methods to display a data set from Ct-scans. The features of this display technology make it most suitable for applications that require quick understanding of the 3D relations, need frequent spatial interactions with the 3D images, or involve time-varying 3D data. It can also be useful for group discussion and decision making.

  13. A prototype table-top inverse-geometry volumetric CT system.

    PubMed

    Schmidt, Taly Gilat; Star-Lack, Josh; Bennett, N Robert; Mazin, Samuel R; Solomon, Edward G; Fahrig, Rebecca; Pelc, Norbert J

    2006-06-01

    A table-top volumetric CT system has been implemented that is able to image a 5-cm-thick volume in one circular scan with no cone-beam artifacts. The prototype inverse-geometry CT (IGCT) scanner consists of a large-area, scanned x-ray source and a detector array that is smaller in the transverse direction. The IGCT geometry provides sufficient volumetric sampling because the source and detector have the same axial, or slice direction, extent. This paper describes the implementation of the table-top IGCT scanner, which is based on the NexRay Scanning-Beam Digital X-ray system (NexRay, Inc., Los Gatos, CA) and an investigation of the system performance. The alignment and flat-field calibration procedures are described, along with a summary of the reconstruction algorithm. The resolution and noise performance of the prototype IGCT system are studied through experiments and further supported by analytical predictions and simulations. To study the presence of cone-beam artifacts, a "Defrise" phantom was scanned on both the prototype IGCT scanner and a micro CT system with a +/-5 cone angle for a 4.5-cm volume thickness. Images of inner ear specimens are presented and compared to those from clinical CT systems. Results showed that the prototype IGCT system has a 0.25-mm isotropic resolution and that noise comparable to that from a clinical scanner with equivalent spatial resolution is achievable. The measured MTF and noise values agreed reasonably well with theoretical predictions and computer simulations. The IGCT system was able to faithfully reconstruct the laminated pattern of the Defrise phantom while the micro CT system suffered severe cone-beam artifacts for the same object. The inner ear acquisition verified that the IGCT system can image a complex anatomical object, and the resulting images exhibited more high-resolution details than the clinical CT acquisition. Overall, the successful implementation of the prototype system supports the IGCT concept for single

  14. A prototype table-top inverse-geometry volumetric CT system

    SciTech Connect

    Schmidt, Taly Gilat; Star-Lack, Josh; Bennett, N. Robert; Mazin, Samuel R.; Solomon, Edward G.; Fahrig, Rebecca; Pelc, Norbert J.

    2006-06-15

    A table-top volumetric CT system has been implemented that is able to image a 5-cm-thick volume in one circular scan with no cone-beam artifacts. The prototype inverse-geometry CT (IGCT) scanner consists of a large-area, scanned x-ray source and a detector array that is smaller in the transverse direction. The IGCT geometry provides sufficient volumetric sampling because the source and detector have the same axial, or slice direction, extent. This paper describes the implementation of the table-top IGCT scanner, which is based on the NexRay Scanning-Beam Digital X-ray system (NexRay, Inc., Los Gatos, CA) and an investigation of the system performance. The alignment and flat-field calibration procedures are described, along with a summary of the reconstruction algorithm. The resolution and noise performance of the prototype IGCT system are studied through experiments and further supported by analytical predictions and simulations. To study the presence of cone-beam artifacts, a ''Defrise'' phantom was scanned on both the prototype IGCT scanner and a micro CT system with a {+-}5 deg.cone angle for a 4.5-cm volume thickness. Images of inner ear specimens are presented and compared to those from clinical CT systems. Results showed that the prototype IGCT system has a 0.25-mm isotropic resolution and that noise comparable to that from a clinical scanner with equivalent spatial resolution is achievable. The measured MTF and noise values agreed reasonably well with theoretical predictions and computer simulations. The IGCT system was able to faithfully reconstruct the laminated pattern of the Defrise phantom while the micro CT system suffered severe cone-beam artifacts for the same object. The inner ear acquisition verified that the IGCT system can image a complex anatomical object, and the resulting images exhibited more high-resolution details than the clinical CT acquisition. Overall, the successful implementation of the prototype system supports the IGCT concept for

  15. Determination of volumetric concentration of solids in vertical pipeline hydrotransport

    NASA Astrophysics Data System (ADS)

    Zych, Marcin; Hanus, Robert; Petryka, Leszek; Strzępowicz, Anna; Zych, Piotr

    2016-03-01

    This paper presents an application of radioisotopes with reference to the determination of the solid phase volumetric concentration in a hydromixture by calibration of the measuring set. It shows how the gamma absorption equipment consisting of radioactive isotopes 241Am and scintillation probe, may be applied to the measurement of solid particles volumetric concentration in a flow. It is based on fact that the intensity of a gamma beam decreases as it passes through matter. In the described experiments as solid phase the ceramic models representing natural polymetallic ocean nodules were used. The especially constructed calibration stand and obtained relation between the related intensity of radiation and mean volumetric concentration of the solid phase are presented.

  16. Automated segmentation and shape characterization of volumetric data.

    PubMed

    Galinsky, Vitaly L; Frank, Lawrence R

    2014-05-15

    Characterization of complex shapes embedded within volumetric data is an important step in a wide range of applications. Standard approaches to this problem employ surface-based methods that require inefficient, time consuming, and error prone steps of surface segmentation and inflation to satisfy the uniqueness or stability of subsequent surface fitting algorithms. Here we present a novel method based on a spherical wave decomposition (SWD) of the data that overcomes several of these limitations by directly analyzing the entire data volume, obviating the segmentation, inflation, and surface fitting steps, significantly reducing the computational time and eliminating topological errors while providing a more detailed quantitative description based upon a more complete theoretical framework of volumetric data. The method is demonstrated and compared to the current state-of-the-art neuroimaging methods for segmentation and characterization of volumetric magnetic resonance imaging data of the human brain. PMID:24521852

  17. Volumetric (3D) compressive sensing spectral domain optical coherence tomography

    PubMed Central

    Xu, Daguang; Huang, Yong; Kang, Jin U.

    2014-01-01

    In this work, we proposed a novel three-dimensional compressive sensing (CS) approach for spectral domain optical coherence tomography (SD OCT) volumetric image acquisition and reconstruction. Instead of taking a spectral volume whose size is the same as that of the volumetric image, our method uses a sub set of the original spectral volume that is under-sampled in all three dimensions, which reduces the amount of spectral measurements to less than 20% of that required by the Shan-non/Nyquist theory. The 3D image is recovered from the under-sampled spectral data dimension-by-dimension using the proposed three-step CS reconstruction strategy. Experimental results show that our method can significantly reduce the sampling rate required for a volumetric SD OCT image while preserving the image quality. PMID:25426320

  18. On the use of volumetric strain meters to infer additional characteristics of short-period seismic radiation

    USGS Publications Warehouse

    Borcherdt, R.D.; Johnston, M.J.S.; Glassmoyer, G.

    1989-01-01

    Volumetric strain meters (Sacks-Evertson design) are installed at 15 sites along the San Andreas fault system, to monitor long-term strain changes for earthquake prediction. Deployment of portable broadband, high-resolution digital recorders (GEOS) at several of the sites extends the detection band for volumetric strain to periods shorter than 5 ?? 10-2 sec and permits the simultaneous observation of seismic radiation fields using conventional short-period pendulum seismometers. Recordings of local and regional earthquakes indicate that dilatometers respond to P energy but not direct shear energy and that straingrams can be used to resolve superimposed reflect P and S waves for inference of wave characteristics not permitted by either sensor alone. Simultaneous measurements of incident P- and S-wave amplitudes are used to introduce a technique for single-station estimates of wave field inhomogeneity, free-surface reflection coefficients and local material P velocity. -from Authors

  19. Evaluation of feature-based 3-d registration of probabilistic volumetric scenes

    NASA Astrophysics Data System (ADS)

    Restrepo, Maria I.; Ulusoy, Ali O.; Mundy, Joseph L.

    2014-12-01

    Automatic estimation of the world surfaces from aerial images has seen much attention and progress in recent years. Among current modeling technologies, probabilistic volumetric models (PVMs) have evolved as an alternative representation that can learn geometry and appearance in a dense and probabilistic manner. Recent progress, in terms of storage and speed, achieved in the area of volumetric modeling, opens the opportunity to develop new frameworks that make use of the PVM to pursue the ultimate goal of creating an entire map of the earth, where one can reason about the semantics and dynamics of the 3-d world. Aligning 3-d models collected at different time-instances constitutes an important step for successful fusion of large spatio-temporal information. This paper evaluates how effectively probabilistic volumetric models can be aligned using robust feature-matching techniques, while considering different scenarios that reflect the kind of variability observed across aerial video collections from different time instances. More precisely, this work investigates variability in terms of discretization, resolution and sampling density, errors in the camera orientation, and changes in illumination and geographic characteristics. All results are given for large-scale, outdoor sites. In order to facilitate the comparison of the registration performance of PVMs to that of other 3-d reconstruction techniques, the registration pipeline is also carried out using Patch-based Multi-View Stereo (PMVS) algorithm. Registration performance is similar for scenes that have favorable geometry and the appearance characteristics necessary for high quality reconstruction. In scenes containing trees, such as a park, or many buildings, such as a city center, registration performance is significantly more accurate when using the PVM.

  20. Volumetric measurements of a spatially growing dust acoustic wave

    SciTech Connect

    Williams, Jeremiah D.

    2012-11-15

    In this study, tomographic particle image velocimetry (tomo-PIV) techniques are used to make volumetric measurements of the dust acoustic wave (DAW) in a weakly coupled dusty plasma system in an argon, dc glow discharge plasma. These tomo-PIV measurements provide the first instantaneous volumetric measurement of a naturally occurring propagating DAW. These measurements reveal over the measured volume that the measured wave mode propagates in all three spatial dimensional and exhibits the same spatial growth rate and wavelength in each spatial direction.

  1. Volumetric Hall Effect Tomography – A Feasibility Study

    PubMed Central

    Wen, Han

    2010-01-01

    Hall effect imaging is an ultrasound-based method of mapping spatial variations in the dielectric constants of an acoustically-uniform sample. This paper presents three-dimensional Hall effect images of phantoms obtained by scanning a single transducer across a two-dimensional grid, effectively simulating two-dimensional phased-array signal reception. The experiments demonstrate the feasibility of volumetric Hall effect tomography and show the advantage of volumetric scans over planar scans. The images reflect several limitations of the current scanning method and point to directions for further hardware development. The inherent limitations of Hall effect imaging are also discussed in light of these results. PMID:10604800

  2. Volumetric Pricing of Agricultural Water Supplies: A Case Study

    NASA Astrophysics Data System (ADS)

    Griffin, Ronald C.; Perry, Gregory M.

    1985-07-01

    Models of water consumption by rice producers are conceptualized and then estimated using cross-sectional time series data obtained from 16 Texas canal operators for the years 1977-1982. Two alternative econometric models demonstrate that both volumetric and flat rate water charges are strongly and inversely related to agricultural water consumption. Nonprice conservation incentives accompanying flat rates are hypothesized to explain the negative correlation of flat rate charges and water consumption. Application of these results suggests that water supply organizations in the sample population converting to volumetric pricing will generally reduce water consumption.

  3. Volumetric particle image velocimetry with a single plenoptic camera

    NASA Astrophysics Data System (ADS)

    Fahringer, Timothy W.; Lynch, Kyle P.; Thurow, Brian S.

    2015-11-01

    A novel three-dimensional (3D), three-component (3C) particle image velocimetry (PIV) technique based on volume illumination and light field imaging with a single plenoptic camera is described. A plenoptic camera uses a densely packed microlens array mounted near a high resolution image sensor to sample the spatial and angular distribution of light collected by the camera. The multiplicative algebraic reconstruction technique (MART) computed tomography algorithm is used to reconstruct a volumetric intensity field from individual snapshots and a cross-correlation algorithm is used to estimate the velocity field from a pair of reconstructed particle volumes. This work provides an introduction to the basic concepts of light field imaging with a plenoptic camera and describes the unique implementation of MART in the context of plenoptic image data for 3D/3C PIV measurements. Simulations of a plenoptic camera using geometric optics are used to generate synthetic plenoptic particle images, which are subsequently used to estimate the quality of particle volume reconstructions at various particle number densities. 3D reconstructions using this method produce reconstructed particles that are elongated by a factor of approximately 4 along the optical axis of the camera. A simulated 3D Gaussian vortex is used to test the capability of single camera plenoptic PIV to produce a 3D/3C vector field, where it was found that lateral displacements could be measured to approximately 0.2 voxel accuracy in the lateral direction and 1 voxel in the depth direction over a 300× 200× 200 voxel volume. The feasibility of the technique is demonstrated experimentally using a home-built plenoptic camera based on a 16-megapixel interline CCD camera and a 289× 193 array of microlenses and a pulsed Nd:YAG laser. 3D/3C measurements were performed in the wake of a low Reynolds number circular cylinder and compared with measurements made using a conventional 2D/2C PIV system. Overall, single camera

  4. CMUT-based Volumetric Ultrasonic Imaging Array Design for Forward Looking ICE and IVUS Applications

    PubMed Central

    Zahorian, Jaime; Xu, Toby; Rashid, Muhammad W.; Satir, Sarp; Gurun, Gokce; Karaman, Mustafa; Hasler, Jennifer; Degertekin, F. Levent

    2014-01-01

    Designing a mechanically flexible catheter based volumetric ultrasonic imaging device for intravascular and intracardiac imaging is challenging due to small transducer area and limited number of cables. With a few parallel channels, synthetic phased array processing is necessary to acquire data from a large number of transducer elements. This increases the data collection time and hence reduces frame rate and causes artifacts due to tissue-transducer motion. Some of these drawbacks can be resolved by different array designs offered by CMUT-on-CMOS approach. We recently implemented a 2.1-mm diameter single chip 10 MHz dual ring CMUT-on-CMOS array for forward looking ICE with 64-transmit and 56-receive elements along with associated electronics. These volumetric arrays have the small element size required by high operating frequencies and achieve sub mm resolution, but the system would be susceptible to motion artifacts. To enable real time imaging with high SNR, we designed novel arrays consisting of multiple defocused annular rings for transmit aperture and a single ring receive array. The annular transmit rings are utilized to act as a high power element by focusing to a virtual ring shaped line behind the aperture. In this case, image reconstruction is performed by only receive beamforming, reducing total required firing steps from 896 to 14 with a trade-off in image resolution. The SNR of system is improved more than 5 dB for the same frequency and frame rate as compared to the dual ring array, which can be utilized to achieve the same resolution by increasing the operating frequency. PMID:23366605

  5. Compton coincidence volumetric imaging: a new x-ray volumetric imaging modality based on Compton scattering

    NASA Astrophysics Data System (ADS)

    Xu, Xiaochao

    2014-03-01

    Compton scattering is a dominant interaction during radiography and computed tomography x-ray imaging. However, the scattered photons are not used for extracting imaging information, but seriously degrade image quality. Here we introduce a new scheme that overcomes most of the problems associated with existing Compton scattering imaging schemes and allows Compton scattered photons to be effectively used for imaging. In our scheme, referred as Compton coincidence volumetric imaging (CCVI), a collimated monoenergetic x-ray beam is directed onto a thin semiconductor detector. A small portion of the photons is Compton scattered by the detector and their energy loss is detected. Some of the scattered photons intersect the imaging object, where they are Compton scattered a second time. The finally scattered photons are recorded by an areal energy resolving detector panel around the object. The two detectors work in coincidence mode. CCVI images the spatial electron density distribution in the imaging object. Similar to PET imaging, the event location can be located within a curve; therefore the imaging reconstruction algorithms are also similar to those of PET. Two statistical iterative imaging reconstruction algorithms are tested. Our study verifies the feasibility of CCVI in imaging acquisition and reconstruction. Various aspects of CCVI are discussed. If successfully implemented, it will offer a great potential for imaging dose reduction compared with x-ray CT. Furthermore, a CCVI modality will have no moving parts, which potentially offers cost reduction and faster imaging speed.

  6. Volumetric synthetic aperture imaging with a piezoelectric 2D row-column probe

    NASA Astrophysics Data System (ADS)

    Bouzari, Hamed; Engholm, Mathias; Christiansen, Thomas Lehrmann; Beers, Christopher; Lei, Anders; Stuart, Matthias Bo; Nikolov, Svetoslav Ivanov; Thomsen, Erik Vilain; Jensen, Jørgen Arendt

    2016-04-01

    The synthetic aperture (SA) technique can be used for achieving real-time volumetric ultrasound imaging using 2-D row-column addressed transducers. This paper investigates SA volumetric imaging performance of an in-house prototyped 3 MHz λ/2-pitch 62+62 element piezoelectric 2-D row-column addressed transducer array. Utilizing single element transmit events, a volume rate of 90 Hz down to 14 cm deep is achieved. Data are obtained using the experimental ultrasound scanner SARUS with a 70 MHz sampling frequency and beamformed using a delay-and-sum (DAS) approach. A signal-to-noise ratio of up to 32 dB is measured on the beamformed images of a tissue mimicking phantom with attenuation of 0.5 dB cm-1 MHz-1, from the surface of the probe to the penetration depth of 300λ. Measured lateral resolution as Full-Width-at-Half-Maximum (FWHM) is between 4λ and 10λ for 18% to 65% of the penetration depth from the surface of the probe. The averaged contrast is 13 dB for the same range. The imaging performance assessment results may represent a reference guide for possible applications of such an array in different medical fields.

  7. Full-field pressure from snapshot and time-resolved volumetric PIV

    NASA Astrophysics Data System (ADS)

    Laskari, A.; de Kat, R.; Ganapathisubramani, B.

    2016-03-01

    This paper deals with pressure estimation from snapshot and time-resolved three-component (3C) volumetric PIV data using Taylor's hypothesis, an Eulerian and a pseudo-Lagrangian approach. The Taylor's hypothesis approach has been shown to provide accurate results for pressure in the case of 3C planar PIV data with an appropriate choice of convection velocity (de Kat and Ganapathisubramani 2013), and here we extend its use on 3C volumetric velocity snapshots. Application of the techniques to synthetic data shows that the Taylor's hypothesis approach performs best using the streamwise mean as the convection velocity and is affected the least by noise, while the Eulerian approach suffers the most. In terms of resolution, the pseudo-Lagrangian approach is the most sensitive. Its accuracy can be improved by increasing the frame time-separation when computing the material derivative, at the expense of volume loss from fluid parcels leaving the FOV. Comparison of the techniques on turbulent boundary layer data with DNS supports these observations and shows that the Taylor's hypothesis approach is the only way we can get pressure when time information is not present.

  8. Deep learning for automatic localization, identification, and segmentation of vertebral bodies in volumetric MR images

    NASA Astrophysics Data System (ADS)

    Suzani, Amin; Rasoulian, Abtin; Seitel, Alexander; Fels, Sidney; Rohling, Robert N.; Abolmaesumi, Purang

    2015-03-01

    This paper proposes an automatic method for vertebra localization, labeling, and segmentation in multi-slice Magnetic Resonance (MR) images. Prior work in this area on MR images mostly requires user interaction while our method is fully automatic. Cubic intensity-based features are extracted from image voxels. A deep learning approach is used for simultaneous localization and identification of vertebrae. The localized points are refined by local thresholding in the region of the detected vertebral column. Thereafter, a statistical multi-vertebrae model is initialized on the localized vertebrae. An iterative Expectation Maximization technique is used to register the vertebral body of the model to the image edges and obtain a segmentation of the lumbar vertebral bodies. The method is evaluated by applying to nine volumetric MR images of the spine. The results demonstrate 100% vertebra identification and a mean surface error of below 2.8 mm for 3D segmentation. Computation time is less than three minutes per high-resolution volumetric image.

  9. Controlling the light distribution through turbid media with wavefront shaping based on volumetric optoacoustic feedback

    NASA Astrophysics Data System (ADS)

    Deán-Ben, X. Luís.; Estrada, Héctor; Özbek, Ali; Razansky, Daniel

    2016-03-01

    Wavefront shaping based on optoacoustic (photoacoustic) feedback has recently emerged as a promising tool to control the light distribution in optically-scattering media. In this approach, the phase of a short-pulsed light beam is spatially-modulated to create constructive light interference (focusing) at specific locations in the speckle pattern of the scattered wavefield. The optoacoustic signals generated by light absorption provide a convenient feedback mechanism to optimize the phase mask of the spatial light modulator in order to achieve the desired light intensity distribution. The optimization procedure can be done by directly considering the acquired signals or the reconstructed images of the light absorption distribution. Recently, our group has introduced a volumetric (three-dimensional) optoacoustic wavefront shaping platform that enables monitoring the distribution of light absorption in an entire volume with frame rates of tens of Hz. With this approach, it is possible to simultaneously control the volumetric light distribution through turbid media. Experiments performed with absorbing microparticles distributed in a three-dimensional region showcase the feasibility of enhancing the light intensity at specific points, where the size of particles is also essential to maximize the signal enhancement. The advantages provided by optoacoustic imaging in terms of spatial and temporal resolution anticipate new capabilities of wavefront shaping techniques in biomedical optics.

  10. Obscuring Surface Anatomy in Volumetric Imaging Data

    PubMed Central

    Marcus, Daniel

    2012-01-01

    The identifying or sensitive anatomical features in MR and CT images used in research raise patient privacy concerns when such data are shared. In order to protect human subject privacy, we developed a method of anatomical surface modification and investigated the effects of such modification on image statistics and common neuroimaging processing tools. Common approaches to obscuring facial features typically remove large portions of the voxels. The approach described here focuses on blurring the anatomical surface instead, to avoid impinging on areas of interest and hard edges that can confuse processing tools. The algorithm proceeds by extracting a thin boundary layer containing surface anatomy from a region of interest. This layer is then “stretched” and “flattened” to fit into a thin “box” volume. After smoothing along a plane roughly parallel to anatomy surface, this volume is transformed back onto the boundary layer of the original data. The above method, named normalized anterior filtering, was coded in MATLAB and applied on a number of high resolution MR and CT scans. To test its effect on automated tools, we compared the output of selected common skull stripping and MR gain field correction methods used on unmodified and obscured data. With this paper, we hope to improve the understanding of the effect of surface deformation approaches on the quality of de-identified data and to provide a useful de-identification tool for MR and CT acquisitions. PMID:22968671

  11. Volumetric Video Motion Detection for Unobtrusive Human-Computer Interaction

    SciTech Connect

    SMALL, DANIEL E.; LUCK, JASON P.; CARLSON, JEFFREY J.

    2002-04-01

    The computer vision field has undergone a revolution of sorts in the past five years. Moore's law has driven real-time image processing from the domain of dedicated, expensive hardware, to the domain of commercial off-the-shelf computers. This thesis describes their work on the design, analysis and implementation of a Real-Time Shape from Silhouette Sensor (RT S{sup 3}). The system produces time-varying volumetric data at real-time rates (10-30Hz). The data is in the form of binary volumetric images. Until recently, using this technique in a real-time system was impractical due to the computational burden. In this thesis they review the previous work in the field, and derive the mathematics behind volumetric calibration, silhouette extraction, and shape-from-silhouette. For the sensor implementation, they use four color camera/framegrabber pairs and a single high-end Pentium III computer. The color cameras were configured to observe a common volume. This hardware uses the RT S{sup 3} software to track volumetric motion. Two types of shape-from-silhouette algorithms were implemented and their relative performance was compared. They have also explored an application of this sensor to markerless motion tracking. In his recent review of work done in motion tracking Gavrila states that results of markerless vision based 3D tracking are still limited. The method proposed in this paper not only expands upon the previous work but will also attempt to overcome these limitations.

  12. Video-rate volumetric optical coherence tomography-based microangiography

    NASA Astrophysics Data System (ADS)

    Baran, Utku; Wei, Wei; Xu, Jingjiang; Qi, Xiaoli; Davis, Wyatt O.; Wang, Ruikang K.

    2016-04-01

    Video-rate volumetric optical coherence tomography (vOCT) is relatively young in the field of OCT imaging but has great potential in biomedical applications. Due to the recent development of the MHz range swept laser sources, vOCT has started to gain attention in the community. Here, we report the first in vivo video-rate volumetric OCT-based microangiography (vOMAG) system by integrating an 18-kHz resonant microelectromechanical system (MEMS) mirror with a 1.6-MHz FDML swept source operating at ˜1.3 μm wavelength. Because the MEMS scanner can offer an effective B-frame rate of 36 kHz, we are able to engineer vOMAG with a video rate up to 25 Hz. This system was utilized for real-time volumetric in vivo visualization of cerebral microvasculature in mice. Moreover, we monitored the blood perfusion dynamics during stimulation within mouse ear in vivo. We also discussed this system's limitations. Prospective MEMS-enabled OCT probes with a real-time volumetric functional imaging capability can have a significant impact on endoscopic imaging and image-guided surgery applications.

  13. 100KE/KW fuel storage basin surface volumetric factors

    SciTech Connect

    Conn, K.R.

    1996-01-01

    This Supporting Document presents calculations of surface Volumetric factors for the 100KE and 100KW Fuel Storage Basins. These factors relate water level changes to basin loss or additions of water, or the equivalent water displacement volumes of objects added to or removed from the basin.

  14. Gas migration modeling improves volumetric method of well control

    SciTech Connect

    Leach, C.P.; Quentin, K.M. )

    1994-12-26

    In the volumetric method, gas expansion during gas migration is allowed for by bleeding small quantities of fluid through the choke. When gas first reaches the choke, the influx is distributed near the surface in the annulus. Rapid gas migration then occurs, and mud and gas may need to be bled to maintain constant bottom hole pressure. The volumetric method is a technique for controlling gas kicks when circulation is not possible. The industry-recognized method is based on simple calculations which assume a single bubble of gas, the classic kick. This technique can now be evaluated by using more realistic, deterministic kick models. The results from such models cast double on some of the conventional procedures taught and used in the industry. This article details the analysis of influx behavior following a typical volumetric method. Numerical modeling of fluid losses as the surface pressure rises, gas migration, and dispersion are included to correspond accurately with field observations of kicks. Revised procedures are suggested to deal with these events better, such that the goals of the volumetric method are still attained.

  15. Combination Gravimetric/Volumetric Sorption Instrument for Energy Applications

    NASA Astrophysics Data System (ADS)

    Bethea, Donald; Burress, Jacob

    The use of gaseous fuels such as hydrogen and methane (natural gas) will reduce emissions. Unfortunately, the storage of hydrogen and methane at room temperature is difficult because they are both supercritical gases, making the adoption of these fuels cumbersome. One means of overcoming the storage problem is to use physisorption-based systems which exploit the van der Waals interaction between the gas and a nanoporous material to compress the gases to near liquid densities. To measure the amount of gas in these materials, gravimetric or volumetric methods are employed. Gravimetric weighs the amount of gas and volumetric uses differences in gas pressures. Gravimetric systems typically have problems with buoyancy corrections. Volumetric systems normally have larger uncertainties that propagate through the isotherm. A modified system will be presented which allows for both gravimetric and volumetric gas sorption measurements. Additionally, the buoyancy corrections for the gravimetric measurements are significantly small and less than the uncertainties in the measurement. This apparatus can take measurements of most gases at room temperature and up to 200 bar.

  16. Modelling cellular behaviour

    NASA Astrophysics Data System (ADS)

    Endy, Drew; Brent, Roger

    2001-01-01

    Representations of cellular processes that can be used to compute their future behaviour would be of general scientific and practical value. But past attempts to construct such representations have been disappointing. This is now changing. Increases in biological understanding combined with advances in computational methods and in computer power make it possible to foresee construction of useful and predictive simulations of cellular processes.

  17. Cell biology of the future: Nanometer-scale cellular cartography

    PubMed Central

    2015-01-01

    Understanding cellular structure is key to understanding cellular regulation. New developments in super-resolution fluorescence imaging, electron microscopy, and quantitative image analysis methods are now providing some of the first three-dimensional dynamic maps of biomolecules at the nanometer scale. These new maps—comprehensive nanometer-scale cellular cartographies—will reveal how the molecular organization of cells influences their diverse and changeable activities. PMID:26483557

  18. Cell biology of the future: Nanometer-scale cellular cartography.

    PubMed

    Taraska, Justin W

    2015-10-26

    Understanding cellular structure is key to understanding cellular regulation. New developments in super-resolution fluorescence imaging, electron microscopy, and quantitative image analysis methods are now providing some of the first three-dimensional dynamic maps of biomolecules at the nanometer scale. These new maps--comprehensive nanometer-scale cellular cartographies--will reveal how the molecular organization of cells influences their diverse and changeable activities. PMID:26483557

  19. A Nanocrystal Sensor for Luminescence Detection of Cellular Forces

    SciTech Connect

    Choi, Charina; Chou, Jonathan; Lutker, Katie; Werb, Zena; Alivisatos, Paul

    2011-09-29

    Quantum dots have been used as bright fluorescent tags with high photostability to probe numerous biological systems. In this work we present the tetrapod quantum dot as a dynamic, next-generation nanocrystal probe that fluorescently reports cellular forces with spatial and temporal resolution. Its small size and colloidal state suggest that the tetrapod may be further developed as a tool to measure cellular forces in vivo and with macromolecular spatial resolution.

  20. 3D imaging in volumetric scattering media using phase-space measurements.

    PubMed

    Liu, Hsiou-Yuan; Jonas, Eric; Tian, Lei; Zhong, Jingshan; Recht, Benjamin; Waller, Laura

    2015-06-01

    We demonstrate the use of phase-space imaging for 3D localization of multiple point sources inside scattering material. The effect of scattering is to spread angular (spatial frequency) information, which can be measured by phase space imaging. We derive a multi-slice forward model for homogenous volumetric scattering, then develop a reconstruction algorithm that exploits sparsity in order to further constrain the problem. By using 4D measurements for 3D reconstruction, the dimensionality mismatch provides significant robustness to multiple scattering, with either static or dynamic diffusers. Experimentally, our high-resolution 4D phase-space data is collected by a spectrogram setup, with results successfully recovering the 3D positions of multiple LEDs embedded in turbid scattering media. PMID:26072807

  1. Two-dimensional reconstruction algorithm of an inverse-geometry volumetric CT system

    NASA Astrophysics Data System (ADS)

    Baek, Jongduk; Pelc, Norbert J.

    2007-03-01

    An inverse-geometry volumetric CT (IGCT) system uses a large source array opposite a smaller detector array. Conventional 2D IGCT reconstruction is performed by using gridding. We describe a 2D IGCT reconstruction algorithm without gridding. The IGCT raw data can be viewed as being composed of many fan beams, each with a detector at its focus. Each projection is undersampled but the missing samples are provided by other views. In order to get high spatial resolution, zeros are inserted between acquired projection samples in each fan beam, and reconstruction is performed using a direct fan beam reconstruction algorithm. Initial IGCT reconstruction results showed ringing artifacts caused by fact that the rho samples in the ensemble of views are not equally spaced. We present a new method for correcting the errors that reduces the artifacts to below one Hounsfield Unit

  2. Quantification of pulmonary arterial wall distensibility using parameters extracted from volumetric micro-CT images

    NASA Astrophysics Data System (ADS)

    Johnson, Roger H.; Karau, Kelly L.; Molthen, Robert C.; Dawson, Christopher A.

    1999-09-01

    Stiffening, or loss of distensibility, of arterial vessel walls is among the manifestations of a number of vascular diseases including pulmonary arterial hypertension. We are attempting to quantify the mechanical properties of vessel walls of the pulmonary arterial tree using parameters derived from high-resolution volumetric x-ray CT images of rat lungs. The pulmonary arterial trees of the excised lungs are filled with a contrast agent. The lungs are imaged with arterial pressures spanning the physiological range. Vessel segment diameters are measured from the inlet to the periphery, and distensibilities calculated from diameters as a function of pressure. The method shows promise as an adjunct to other morphometric techniques such as histology and corrosion casting. It possesses the advantages of being nondestructive, characterizing the vascular structures while the lungs are imaged rapidly and in a near-physiological state, and providing the ability to associate mechanical properties with vessel location in the intact tree hierarchy.

  3. Note: Scanned multi-light-emitting-diode illumination for volumetric particle image velocimetry.

    PubMed

    Patterson, M D; Wettlaufer, J S

    2010-09-01

    We describe the development of both multilevel two-dimensional and grid-based three-dimensional illumination systems for volumetric particle image velocimetry (PIV) that uses a single camera and an arbitrary number of low powered lasers. This flexible system is robust and capable of capturing results over a range of spatiotemporal scales determined by the choice of camera, the depth of field of the lens, and the laser power. The system is demonstrated on a rotating spin-up experiment where we extract high fidelity velocity fields at up to 62 frames/s at a spatial resolution of 2352×1728 pixels. The flexibility and economy offered by this system--approximately one-tenth that of a comparable commercial package--may make it attractive to many laboratory users. PMID:20887007

  4. Durga: A heuristically-optimized data collection strategy for volumetric magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Anand, Christopher Kumar; Curtis, Andrew Thomas; Kumar, Rakshit

    2008-02-01

    A heuristic design method for rapid volumetric magnetic resonance imaging data acquisition trajectories is presented, using a series of second-order cone optimization subproblems. Other researchers have considered non-raster data collection trajectories and under-sampled data patterns. This work demonstrates that much higher rates of under-sampling are possible with an asymmetric set of trajectories, with very little loss in resolution, but the addition of noise-like artefacts. The proposed data collection trajectory, Durga, further minimizes collection time by incorporating short un-refocused excitation pulses, resulting in above 98% collection efficiency for balanced steady state free precession imaging. The optimization subproblems are novel, in that they incorporate all requirements, including data collection (coverage), physicality (device limits), and signal generation (zeroth- and higher- moment properties) in a single convex problem, which allows the resulting trajectories to exhibit a higher collection efficiency than any existing trajectory design.

  5. Novel volumetric 3D display based on point light source optical reconstruction using multi focal lens array

    NASA Astrophysics Data System (ADS)

    Lee, Jin su; Lee, Mu young; Kim, Jun oh; Kim, Cheol joong; Won, Yong Hyub

    2015-03-01

    Generally, volumetric 3D display panel produce volume-filling three dimensional images. This paper discusses a volumetric 3D display based on periodical point light sources(PLSs) construction using a multi focal lens array(MFLA). The voxel of discrete 3D images is formed in the air via construction of point light source emitted by multi focal lens array. This system consists of a parallel beam, a spatial light modulator(SLM), a lens array, and a polarizing filter. The multi focal lens array is made with UV adhesive polymer droplet control using a dispersing machine. The MFLA consists of 20x20 circular lens array. Each lens aperture of the MFLA shows 300um on average. The polarizing filter is placed after the SLM and the MFLA to set in phase mostly mode. By the point spread function, the PLSs of the system are located by the focal length of each lens of the MFLA. It can also provide the moving parallax and relatively high resolution. However it has a limit of viewing angle and crosstalk by a property of each lens. In our experiment, we present the letter `C', `O', `DE' and ball's surface with the different depth location. It could be seen clearly that when CCD camera is moved to its position following as transverse axis of the display system. From our result, we expect that varifocal lens like EWOD and LC-lens can be applied for real time volumetric 3D display system.

  6. High-power, red-emitting DBR-TPL for possible 3d holographic or volumetric displays

    NASA Astrophysics Data System (ADS)

    Feise, D.; Fiebig, C.; Blume, G.; Pohl, J.; Eppich, B.; Paschke, K.

    2013-03-01

    To create holographic or volumetric displays, it is highly desirable to move from conventional imaging projection displays, where the light is filtered from a constant source towards flying spot, where the correct amount of light is generated for every pixel. The only light sources available for such an approach, which requires visible, high output power with a spatial resolution beyond conventional lamps, are lasers. When adding the market demands for high electro-optical conversion efficiency, direct electrical modulation capability, compactness, reliability and massproduction compliance, this leaves only semiconductor diode lasers. We present red-emitting tapered diode lasers (TPL) emitting a powerful, visible, nearly diffraction limited beam (M²1/e² < 1.5) and a single longitudinal mode, which are well suited for 3d holographic and volumetric imaging. The TPLs achieved an optical output power in excess of 500 mW in the wavelength range between 633 nm and 638 nm. The simultaneous inclusion of a distributed Bragg reflector (DBR) surface grating provides wavelength selectivity and hence a spectral purity with a width Δλ < 5 pm. These properties allow dense spectral multiplexing to achieve output powers of several watts, which would be required for 3d volumetric display applications.

  7. 3D real holographic image movies are projected into a volumetric display using dynamic digital micromirror device (DMD) holograms.

    NASA Astrophysics Data System (ADS)

    Huebschman, Michael L.; Hunt, Jeremy; Garner, Harold R.

    2006-04-01

    The Texas Instruments Digital Micromirror Device (DMD) is being used as the recording medium for display of pre-calculated digital holograms. The high intensity throughput of the reflected laser light from DMD holograms enables volumetric display of projected real images as well as virtual images. A single DMD and single laser projector system has been designed to reconstruct projected images in a 6''x 6''x 4.5'' volumetric display. The volumetric display is composed of twenty-four, 6''-square, PSCT liquid crystal plates which are each cycled on and off to reduce unnecessary scatter in the volume. The DMD is an XGA format array, 1024x768, with 13.6 micron pitch mirrors. This holographic projection system has been used in the assessment of hologram image resolution, maximum image size, optical focusing of the real image, image look-around, and physiological depth cues. Dynamic movement images are projected by transferring the appropriately sequenced holograms to the DMD at movie frame rates.

  8. In vivo label-free measurement of lymph flow velocity and volumetric flow rates using Doppler optical coherence tomography

    PubMed Central

    Blatter, Cedric; Meijer, Eelco F. J.; Nam, Ahhyun S.; Jones, Dennis; Bouma, Brett E.; Padera, Timothy P.; Vakoc, Benjamin J.

    2016-01-01

    Direct in vivo imaging of lymph flow is key to understanding lymphatic system function in normal and disease states. Optical microscopy techniques provide the resolution required for these measurements, but existing optical techniques for measuring lymph flow require complex protocols and provide limited temporal resolution. Here, we describe a Doppler optical coherence tomography platform that allows direct, label-free quantification of lymph velocity and volumetric flow rates. We overcome the challenge of very low scattering by employing a Doppler algorithm that operates on low signal-to-noise measurements. We show that this technique can measure lymph velocity at sufficiently high temporal resolution to resolve the dynamic pulsatile flow in collecting lymphatic vessels. PMID:27377852

  9. In vivo label-free measurement of lymph flow velocity and volumetric flow rates using Doppler optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Blatter, Cedric; Meijer, Eelco F. J.; Nam, Ahhyun S.; Jones, Dennis; Bouma, Brett E.; Padera, Timothy P.; Vakoc, Benjamin J.

    2016-07-01

    Direct in vivo imaging of lymph flow is key to understanding lymphatic system function in normal and disease states. Optical microscopy techniques provide the resolution required for these measurements, but existing optical techniques for measuring lymph flow require complex protocols and provide limited temporal resolution. Here, we describe a Doppler optical coherence tomography platform that allows direct, label-free quantification of lymph velocity and volumetric flow rates. We overcome the challenge of very low scattering by employing a Doppler algorithm that operates on low signal-to-noise measurements. We show that this technique can measure lymph velocity at sufficiently high temporal resolution to resolve the dynamic pulsatile flow in collecting lymphatic vessels.

  10. In vivo label-free measurement of lymph flow velocity and volumetric flow rates using Doppler optical coherence tomography.

    PubMed

    Blatter, Cedric; Meijer, Eelco F J; Nam, Ahhyun S; Jones, Dennis; Bouma, Brett E; Padera, Timothy P; Vakoc, Benjamin J

    2016-01-01

    Direct in vivo imaging of lymph flow is key to understanding lymphatic system function in normal and disease states. Optical microscopy techniques provide the resolution required for these measurements, but existing optical techniques for measuring lymph flow require complex protocols and provide limited temporal resolution. Here, we describe a Doppler optical coherence tomography platform that allows direct, label-free quantification of lymph velocity and volumetric flow rates. We overcome the challenge of very low scattering by employing a Doppler algorithm that operates on low signal-to-noise measurements. We show that this technique can measure lymph velocity at sufficiently high temporal resolution to resolve the dynamic pulsatile flow in collecting lymphatic vessels. PMID:27377852

  11. Cellular Reflectarray Antenna

    NASA Technical Reports Server (NTRS)

    Romanofsky, Robert R.

    2010-01-01

    The cellular reflectarray antenna is intended to replace conventional parabolic reflectors that must be physically aligned with a particular satellite in geostationary orbit. These arrays are designed for specified geographical locations, defined by latitude and longitude, each called a "cell." A particular cell occupies nominally 1,500 square miles (3,885 sq. km), but this varies according to latitude and longitude. The cellular reflectarray antenna designed for a particular cell is simply positioned to align with magnetic North, and the antenna surface is level (parallel to the ground). A given cellular reflectarray antenna will not operate in any other cell.

  12. Volumetric index of Tl-201 uptake in symptomatic patients after high - dose radiation treatment for high-grade gliomas

    SciTech Connect

    Carvalho, P.A.; Garada, B.M.; Loeffler, J.S. |

    1995-05-01

    To verify the utility of a volumetric estimation of Tl-201 uptake in the context of possible astrocytoma recurrence after surgery, radiotherapy plus stereotactic boost (radiosurgery/brachitherapy), we analyzed sequential Tl-201/Tc99m-HMPAO brain SPECT studies of 28 patients (18 m/10 f). These were categorized as having tumor mass recurrence (TM), infiltrating tumor cells but no definite tumor mass (IT), or radiation changes and necrosis (RCN) after stereotactic biopsy and/or craniotomy. SPECT studies were obtained with a high-resolution dedicated gamma camera (CERASPECT, Digital Scinitgraphics, Inc.) and image acquisition was performed after intravenous Tl-201 (18.5 MBq) and Tc-99m HMPAO (740 MBq). In order to include relevant information about tumor burden, a volumetric index of Tl-201 uptake was expressed in cm{sup 3} related to voxel size (4.6 x 10{sup -3} cc) within an elliptical ROI that included the tumor area. Only voxels with a threshold {ge} 2 in relation to the average scalp Tl-201 uptake were included and this total number of voxels expressed in cc was compared to previously established maximal tumor/scalp Tl-201 uptake ratios (T/S) and histopathology. Results are presented as the median (min-max) and differences were considered significant for p<0.05. Differences were significant between all groups for both ratios and volume indices and correlation between the two variables was 0.90. In conclusion, the volumetric index of Tl-201 is similar to the maximal Tl-201 T/S ratios in discriminating tumor recurrence and radiation necrosis, suggesting a future role for the volumetric index estimation in the evaluation of treatment efficacy and patient follow-up.

  13. In-situ volumetric topography of IC chips for defect detection using infrared confocal measurement with active structured light

    NASA Astrophysics Data System (ADS)

    Chen, Liang-Chia; Le, Manh-Trung; Cong Phuc, Dao; Lin, Shyh-Tsong

    2014-09-01

    The article presents the development of in-situ integrated circuit (IC) chip defect detection techniques for automated clipping detection by proposing infrared imaging and full-field volumetric topography. IC chip inspection, especially held during or post IC packaging, has become an extremely critical procedure in IC fabrication to assure manufacturing quality and reduce production costs. To address this, in the article, microscopic infrared imaging using an electromagnetic light spectrum that ranges from 0.9 to 1.7 µm is developed to perform volumetric inspection of IC chips, in order to identify important defects such as silicon clipping, cracking or peeling. The main difficulty of infrared (IR) volumetric imaging lies in its poor image contrast, which makes it incapable of achieving reliable inspection, as infrared imaging is sensitive to temperature difference but insensitive to geometric variance of materials, resulting in difficulty detecting and quantifying defects precisely. To overcome this, 3D volumetric topography based on 3D infrared confocal measurement with active structured light, as well as light refractive matching principles, is developed to detect defects the size, shape and position of defects in ICs. The experimental results show that the algorithm is effective and suitable for in-situ defect detection of IC semiconductor packaging. The quality of defect detection, such as measurement repeatability and accuracy, is addressed. Confirmed by the experimental results, the depth measurement resolution can reach up to 0.3 µm, and the depth measurement uncertainty with one standard deviation was verified to be less than 1.0% of the full-scale depth-measuring range.

  14. Design and image quality results from volumetric CT with a flat-panel imager

    NASA Astrophysics Data System (ADS)

    Ross, William; Basu, Samit; Edic, Peter M.; Johnson, Mark; Pfoh, Armin H.; Rao, Ramakrishna; Ren, Baorui

    2001-06-01

    Preliminary MTF and LCD results obtained on several volumetric computed tomography (VCT) systems, employing amorphous flat panel technology, are presented. Constructed around 20-cm x 20-cm, 200-mm pitch amorphous silicon x-ray detectors, the prototypes use standard vascular or CT x-ray sources. Data were obtained from closed-gantry, benchtop and C-arm-based topologies, over a full 360 degrees of rotation about the target object. The field of view of the devices is approximately 15 cm, with a magnification of 1.25-1.5, providing isotropic resolution at isocenter of 133-160 mm. Acquisitions have been reconstructed using the FDK algorithm, modified by motion corrections also developed by GE. Image quality data were obtained using both industry standard and custom resolution phantoms as targets. Scanner output is compared on a projection and reconstruction basis against analogous output from a dedicated simulation package, also developed at GE. Measured MTF performance is indicative of a significant advance in isotropic image resolution over commercially available systems. LCD results have been obtained, using industry standard phantoms, spanning a contrast range of 0.3-1%. Both MTF and LCD measurements agree with simulated data.

  15. Volumetric velocity measurements on flows through heart valves

    NASA Astrophysics Data System (ADS)

    Troolin, Daniel; Amatya, Devesh; Longmire, Ellen

    2009-11-01

    Volumetric velocity fields inside two types of artificial heart valves were obtained experimentally through the use of volumetric 3-component velocimetry (V3V). Index matching was used to mitigate the effects of optical distortions due to interfaces between the fluid and curved walls. The steady flow downstream of a mechanical valve was measured and the results matched well with previously obtained 2D PIV results, such as those of Shipkowitz et al. (2002). Measurements upstream and downstream of a deformable silicone valve in a pulsatile flow were obtained and reveal significant three-dimensional features of the flow. Plots and movies will be shown, and a detailed discussion of the flow and various experimental considerations will be included. Reference: Shipkowitz, T, Ambrus J, Kurk J, Wickramasinghe K (2002) Evaluation technique for bileaflet mechanical valves. J. Heart Valve Disease. 11(2) pp. 275-282.

  16. A feasibility study of digital tomosynthesis for volumetric dental imaging

    NASA Astrophysics Data System (ADS)

    Cho, M. K.; Kim, H. K.; Youn, H.; Kim, S. S.

    2012-03-01

    We present a volumetric dental tomography method that compensates for insufficient projection views obtained from limited-angle scans. The reconstruction algorithm is based on the backprojection filtering method which employs apodizing filters that reduce out-of-plane blur artifacts and suppress high-frequency noise. In order to accompolish this volumetric imaging two volume-reconstructed datasets are synthesized. These individual datasets provide two different limited-angle scans performed at orthogonal angles. The obtained reconstructed images, using less than 15% of the number of projection views needed for a full skull phantom scan, demonstrate the potential use of the proposed method in dental imaging applications. This method enables a much smaller radiation dose for the patient compared to conventional dental tomography.

  17. Automated volumetric segmentation of retinal fluid on optical coherence tomography

    PubMed Central

    Wang, Jie; Zhang, Miao; Pechauer, Alex D.; Liu, Liang; Hwang, Thomas S.; Wilson, David J.; Li, Dengwang; Jia, Yali

    2016-01-01

    We propose a novel automated volumetric segmentation method to detect and quantify retinal fluid on optical coherence tomography (OCT). The fuzzy level set method was introduced for identifying the boundaries of fluid filled regions on B-scans (x and y-axes) and C-scans (z-axis). The boundaries identified from three types of scans were combined to generate a comprehensive volumetric segmentation of retinal fluid. Then, artefactual fluid regions were removed using morphological characteristics and by identifying vascular shadowing with OCT angiography obtained from the same scan. The accuracy of retinal fluid detection and quantification was evaluated on 10 eyes with diabetic macular edema. Automated segmentation had good agreement with manual segmentation qualitatively and quantitatively. The fluid map can be integrated with OCT angiogram for intuitive clinical evaluation. PMID:27446676

  18. CELLULAR MAGNESIUM HOMEOSTASIS

    PubMed Central

    Romani, Andrea M.P.

    2011-01-01

    Magnesium, the second most abundant cellular cation after potassium, is essential to regulate numerous cellular functions and enzymes, including ion channels, metabolic cycles, and signaling pathways, as attested by more than 1000 entries in the literature. Despite significant recent progress, however, our understanding of how cells regulate Mg2+ homeostasis and transport still remains incomplete. For example, the occurrence of major fluxes of Mg2+ in either direction across the plasma membrane of mammalian cells following metabolic or hormonal stimuli has been extensively documented. Yet, the mechanisms ultimately responsible for magnesium extrusion across the cell membrane have not been cloned. Even less is known about the regulation in cellular organelles. The present review is aimed at providing the reader with a comprehensive and up-to-date understanding of the mechanisms enacted by eukaryotic cells to regulate cellular Mg2+ homeostasis and how these mechanisms are altered under specific pathological conditions. PMID:21640700

  19. Volumetric 3D display using a DLP projection engine

    NASA Astrophysics Data System (ADS)

    Geng, Jason

    2012-03-01

    In this article, we describe a volumetric 3D display system based on the high speed DLPTM (Digital Light Processing) projection engine. Existing two-dimensional (2D) flat screen displays often lead to ambiguity and confusion in high-dimensional data/graphics presentation due to lack of true depth cues. Even with the help of powerful 3D rendering software, three-dimensional (3D) objects displayed on a 2D flat screen may still fail to provide spatial relationship or depth information correctly and effectively. Essentially, 2D displays have to rely upon capability of human brain to piece together a 3D representation from 2D images. Despite the impressive mental capability of human visual system, its visual perception is not reliable if certain depth cues are missing. In contrast, volumetric 3D display technologies to be discussed in this article are capable of displaying 3D volumetric images in true 3D space. Each "voxel" on a 3D image (analogous to a pixel in 2D image) locates physically at the spatial position where it is supposed to be, and emits light from that position toward omni-directions to form a real 3D image in 3D space. Such a volumetric 3D display provides both physiological depth cues and psychological depth cues to human visual system to truthfully perceive 3D objects. It yields a realistic spatial representation of 3D objects and simplifies our understanding to the complexity of 3D objects and spatial relationship among them.

  20. Inorganic volumetric light source excited by ultraviolet light

    DOEpatents

    Reed, S.; Walko, R.J.; Ashley, C.S.; Brinker, C.J.

    1994-04-26

    The invention relates to a composition for the volumetric generation of radiation. The composition comprises a porous substrate loaded with a component capable of emitting radiation upon interaction with an exciting radiation. Preferably, the composition is an aerogel substrate loaded with a component, e.g., a phosphor, capable of interacting with exciting radiation of a first energy, e.g., ultraviolet light, to produce radiation of a second energy, e.g., visible light. 4 figures.

  1. Inorganic volumetric light source excited by ultraviolet light

    DOEpatents

    Reed, Scott; Walko, Robert J.; Ashley, Carol S.; Brinker, C. Jeffrey

    1994-01-01

    The invention relates to a composition for the volumetric generation of radiation. The composition comprises a porous substrate loaded with a component capable of emitting radiation upon interaction with an exciting radiation. Preferably, the composition is an aerogel substrate loaded with a component, e.g., a phosphor, capable of interacting with exciting radiation of a first energy, e.g., ultraviolet light, to produce radiation of a second energy, e.g., visible light.

  2. Determining the volumetric steam content in a BWR gravity leg

    SciTech Connect

    Fedulin, V.N.; Bartolomei, G.G.; Solodkii, V.A.; Shmelev, V.E.

    1987-09-01

    The structure of two-phase flow in a large-diameter limited-height gravity leg was investigated in the VK-50 reactor. Phase distribution properties and a physical model of the steam-water mixture flow in the gravity leg were described. On the basis of experimentally derived date a method was proposed for the calculation of volumetric steam content in the leg.

  3. Non-Equilibrium Volumetric Response of Shocked Polymers

    NASA Astrophysics Data System (ADS)

    Clements, Brad

    2009-06-01

    Polymers are well known for their non-equilibrium deviatoric behavior. However, recent investigations involving both high rate shock experiments and equilibrium measured thermodynamic quantities have reminded us that the volumetric behavior also exhibits a non-equilibrium response. An area where this work should be important is the impact of glassy polymers. At the time of impact and near the impact surface, the polymer's volumetric response will be described as being Hugoniot-like, i.e., standard shock Hugoniot jump conditions apply. However, at later times, release waves from neighboring free surfaces will cause the polymer's volumetric response to be far from Hugoniot. In this talk, experiments showing the non-equilibrium behavior will be described. Following that discussion, a continuum-level theory is proposed that will allow us to bridge the equilibrium and non-equilibrium behaviors with a single model that can go seamlessly from one regime to the other.[4pt] In collaboration with Philip Rae and Dana Dattelbaum, Los Alamos National Laboratory.

  4. Volumetric Echocardiographic Particle Image Velocimetry (V-Echo-PIV)

    NASA Astrophysics Data System (ADS)

    Falahatpisheh, Ahmad; Kheradvar, Arash

    2015-11-01

    Measurement of 3D flow field inside the cardiac chambers has proven to be a challenging task. Current laser-based 3D PIV methods estimate the third component of the velocity rather than directly measuring it and also cannot be used to image the opaque heart chambers. Modern echocardiography systems are equipped with 3D probes that enable imaging the entire 3D opaque field. However, this feature has not yet been employed for 3D vector characterization of blood flow. For the first time, we introduce a method that generates velocity vector field in 4D based on volumetric echocardiographic images. By assuming the conservation of brightness in 3D, blood speckles are tracked. A hierarchical 3D PIV method is used to account for large particle displacement. The discretized brightness transport equation is solved in a least square sense in interrogation windows of size 163 voxels. We successfully validate the method in analytical and experimental cases. Volumetric echo data of a left ventricle is then processed in the systolic phase. The expected velocity fields were successfully predicted by V-Echo-PIV. In this work, we showed a method to image blood flow in 3D based on volumetric images of human heart using no contrast agent.

  5. Accuracy of endodontic microleakage results: autoradiographic vs. volumetric measurements.

    PubMed

    Ximénez-Fyvie, L A; Ximénez-García, C; Carter-Bartlett, P M; Collado-Webber, F J

    1996-06-01

    The correlation between autoradiographic and volumetric leakage measurements was evaluated. Seventy-two anterior teeth with a single canal were selected and divided into three groups of 24. Group 1 served as control (no obturation), group 2 was obturated with gutta-percha only, and group 3 was obturated with gutta-percha and endodontic sealer. Samples were placed in a vertical position in 48-well cell culture plates and immersed in 1 ml of [14C]urea for 14 days. One-mm-thick horizontal serial sections were cut with a diamond disk cooled with liquid-nitrogen gas. Linear penetration was recorded by five independent evaluators from autoradiographs. Volumetric results were based on counts per minute registered in a liquid scintillation spectrometer. Pearson's correlation coefficient test was used to determine the lineal correlation between both methods of evaluation. No acceptable correlation values were found in any of the three groups (group 1, r = 0.34; group 2, r = 0.23; group 3, r = 0.20). Our results indicate that there is no correlation between linear and volumetric measurements of leakage. PMID:8934988

  6. Innovative system architecture for spatial volumetric acoustic seeing

    NASA Astrophysics Data System (ADS)

    Levin, Eugene; Sergeyev, Aleksandr V.

    2009-04-01

    Situational awareness is a critical issue for the modern battle and security systems improvement of which will increase human performance efficiency. There are multiple research project and development efforts based on omni-directional (fish-eye) electro-optical and other frequency sensor fusion systems implementing head-mounted visualization systems. However, the efficiency of these systems is limited by the human eye-brain system perception limitations. Humans are capable to naturally perceive the situations in front of them, but interpretation of omni-directional visual scenes increases the user's mental workload, increasing human fatigue and disorientation requiring more effort for object recognition. It is especially important to reduce this workload making rear scenes perception intuitive in battlefield situations where a combatant can be attacked from both directions. This paper describes an experimental model of the system fusion architecture of the Visual Acoustic Seeing (VAS) for representation spatial geometric 3D model in form of 3D volumetric sound. Current research in the area of auralization points to the possibility of identifying sound direction. However, for complete spatial perception it is necessary to identify the direction and the distance to an object by an expression of volumetric sound, we initially assume that the distance can be encoded by the sound frequency. The chain: object features -> sensor -> 3D geometric model-> auralization constitutes Volumetric Acoustic Seeing (VAS). Paper describes VAS experimental research for representing and perceiving spatial information by means of human hearing cues in more details.

  7. Volumetric lattice Boltzmann simulation for blood flow in aorta arteries

    NASA Astrophysics Data System (ADS)

    Deep, Debanjan; Yu, Huidan (Whitney); Teague, Shawn

    2012-11-01

    Complicated moving boundaries pose a major challenge in computational fluid dynamics for complex flows, especially in the biomechanics of both blood flow in the cardiovascular system and air flow in the respiratory system where the compliant nature of the vessels can have significant effects on the flow rate and wall shear stress. We develop a computation approach to treat arbitrarily moving boundaries using a volumetric representation of lattice Boltzmann method, which distributes fluid particles inside lattice cells. A volumetric bounce-back procedure is applied in the streaming step while momentum exchange between the fluid and moving solid boundary are accounted for in the collision sub-step. Additional boundary-induced migration is introduced to conserve fluid mass as the boundary moves across fluid cells. The volumetric LBM (VLBM) is used to simulate blood flow in both normal and dilated aorta arteries. We first compare flow structure and pressure distribution in steady state with results from Navier-Stokes based solver and good agreements are achieved. Then we focus on wall stress within the aorta for different heart pumping condition and present quantitative measurement of wall shear and normal stress.

  8. Volumetric full-range magnetomotive optical coherence tomography

    PubMed Central

    Ahmad, Adeel; Kim, Jongsik; Shemonski, Nathan D.; Marjanovic, Marina; Boppart, Stephen A.

    2014-01-01

    Abstract. Magnetomotive optical coherence tomography (MM-OCT) can be utilized to spatially localize the presence of magnetic particles within tissues or organs. These magnetic particle-containing regions are detected by using the capability of OCT to measure small-scale displacements induced by the activation of an external electromagnet coil typically driven by a harmonic excitation signal. The constraints imposed by the scanning schemes employed and tissue viscoelastic properties limit the speed at which conventional MM-OCT data can be acquired. Realizing that electromagnet coils can be designed to exert MM force on relatively large tissue volumes (comparable or larger than typical OCT imaging fields of view), we show that an order-of-magnitude improvement in three-dimensional (3-D) MM-OCT imaging speed can be achieved by rapid acquisition of a volumetric scan during the activation of the coil. Furthermore, we show volumetric (3-D) MM-OCT imaging over a large imaging depth range by combining this volumetric scan scheme with full-range OCT. Results with tissue equivalent phantoms and a biological tissue are shown to demonstrate this technique. PMID:25472770

  9. High Resolution Dsm and Classified Volumetric Generation: AN Operational Approach to the Improvement of Geospatial Intelligence

    NASA Astrophysics Data System (ADS)

    Boccardo, P.; Gentili, G.

    2011-09-01

    As mentioned by Bacastow and Bellafiore, Geospatial Intelligence (GEOINT) is a field of knowledge, a process, and a profession. As knowledge, it is information integrated in a coherent space-time context that supports descriptions, explanations, or forecasts of human activities with which decision makers take action. As a process, it is the means by which data and information are collected, manipulated, geospatially reasoned, and disseminated to decision-makers. The geospatial intelligence professional establishes the scope of activities, interdisciplinary associations, competencies, and standards in academe, government, and the private sectors. Taking into account the fact that GEOINT is crucial for broad organizations, BLOM Group, a leading International provider within acquisition, processing and modeling of geographic information and ITHACA, a non-profit organization devoted to products and services delivering to the UN System in the field of geomatics, set up and provided GEOINT data to the main Italian companies operating in the field of mobile phone networking. This data, extremely useful for telecom network planning, have derived and produced using a standardized and effective (from the production point of view) approach. In this paper, all the procedures used for the production are described and tested with the aim to investigate the suitability of the data and the procedures themselves to any others possible fields of application.

  10. The role of cellular environment in dynamic light scattering

    NASA Astrophysics Data System (ADS)

    An, Ran; Jeong, Kwan; Turek, John; Nolte, David

    2011-03-01

    We have developed motility contrast imaging (MCI) as a coherence-domain volumetric imaging approach that uses subcellular dynamics as an endogenous imaging contrast agent of living tissue. Fluctuation spectroscopy analysis of dynamic light scattering (DLS) from 3-D tissue has identified functional frequency bands related to organelle transport, membrane undulations and cell shape change. In this paper, we track the behavior of dynamic light scattering as we bridge the gap between the two extremes of 2-D cell culture on the one hand, and 3-D tissue spheroids on the other. In a light backscattering geometry, we capture speckle from 2-D cell culture consisting of isolated cells or planar rafts of cells on cell-culture surfaces. DLS from that cell culture shows differences and lower sensitivity to intra-cellular dynamics compared with the 3-D tissue. The motility contrast is weak in this limit. As the cellular density increases to cover the surface, the motility contrast increases. As environmental perturbations or pharmaceuticals are applied, the fluctuation spectral response becomes more dramatic as the dimensionality of the cellular aggregations increases. We show that changing optical thickness of the cellular-to-tissue targets usually causes characteristic frequency shifts in the spectrograms, while changing cellular dimensionality causes characteristic frequencies to be enhanced or suppressed.