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检索条件"任意字段=Three-Dimensional and Multidimensional Microscopy: Image Acquisition and Processing IX"

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Hyperspectral fluorescence microscopy based on compressed sensing

Hyperspectral fluorescence microscopy based on compressed se...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Studer, Vincent Bobin, Jerome Chahid, Makhlad Moussavi, Hamed Candes, Emmanuel Dahan, Maxime Univ Bordeaux Interdisciplinary Inst Neurosci UMR 5297 F-33000 Bordeaux France Univ Bordeaux Interdisciplinary Inst Neurosci UMR 5297 F-33000 Bordeaux France CEA Saclay IRFU SEDI Sap Grenoble France Stanford Univ Dept Math Stanford CA 94305 USA Stanford Univ Dept Stat & Elect Engn Stanford CA 94305 USA Univ Paris 06 Ecole Normale Super CNRS Lab Kastler BrosselUMR 8552 Paris France

ISBN: (纸本)9780819488701

In fluorescence microscopy, one can distinguish two kinds of imaging approaches, wide field and raster scan microscopy, differing by their excitation and detection scheme. In both imaging modalities the acquisition is independent of the information content of the image. Rather, the number of acquisitions N, is imposed by the Nyquist-Shannon theorem. However, in practice, many biological images are compressible (or, equivalently here, sparse), meaning that they depend on a number of degrees of freedom K that is smaller that their size N. Recently, the mathematical theory of compressed sensing (CS) has shown how the sensing modality could take advantage of the image sparsity to reconstruct images with no loss of information while largely reducing the number M of acquisition. Here we present a novel fluorescence microscope designed along the principles of CS. It uses a spatial light modulator (DMD) to create structured wide field excitation patterns and a sensitive point detector to measure the emitted fluorescence. On sparse fluorescent samples, we could achieve compression ratio N/M of up to 64, meaning that an image can be reconstructed with a number of measurements of only 1.5 % of its pixel number. Furthemore, we extend our CS acquisition scheme to an hyperspectral imaging system.

关键词： Fluorescence microscopy compressive sensing hyperspectral imaging

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Digital holographic microscopy for the cytomorphological imaging of cells under zero gravity

Digital holographic microscopy for the cytomorphological ima...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Toy, M. Fatih Richard, Stephane Kuehn, Jonas Franco-Obregon, Alfredo Egli, Marcel Depeursinge, Christian Ecole Polytech Fed Lausanne Adv Photon Lab CH-1015 Lausanne Switzerland ETH Space Biol Grp CH-8005 Zurich Switzerland Ecole Polytech Fed Lausanne Biomol Screening Facil CH-1015 Lausanne Switzerland

ISBN: (纸本)9780819488701

Digital holographic microscopy (DHM) has been gaining interest from cell biology community because of its label free nature and quantitative phase signal output. Besides, fast shutter time, image reconstruction by numerical propagation of the wave fields, and numerical compensation of the aberrations are other intrinsic advantages of this technique that can be explored for harsh imaging conditions. In the frame of this work, a transmission type DHM is developed with a decoupled epifluorescence microscopy mode for cytomorphological monitoring under zero gravity and hyper gravity. With the implemented automatic post processing routines, real time observation of the cell morphology is proven to be feasible under the influence of mechanical disturbances of zero gravity platforms. Post processing of holograms is composed from dynamic numerical compensation of holograms, robust autofocusing and phase image registration. Experiments on live myoblast cells are carried out on two different platforms;random positioning machine (RPM), a ground base microgravity simulation platform, and parabolic flight campaign (PFC), a fixed wing plane flight providing short durations of alternating gravity conditions. Results show clear perinuclear phase increase. During seconds scale microgravity exposure, measurable scale morphological modifications are observed with the accumulated effect of repetitive exposures and short breaks.

关键词： microscopy holography digital holographic microscopy fluorescence microscopy microgravity cell morphology cytoskeleton

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Self-referenced quantitative phase microscopy

Self-referenced quantitative phase microscopy

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three-dimensional and multidimensional microscopy: image acquisition and processing Xix

作者： Hillman, Timothy R. Lue, Niyom Sung, Yongjin Dasari, Ramachandra R. So, Peter T. C. Yaqoob, Zahid MIT Laser Biomedical Research Center G.R. Harrison Spectroscopy Laboratory MIT Cambridge MA 02139 United States Mechanical Engineering and Biological Engineering Departments MIT 77 Massachusetts Ave. Cambridge MA 02139 United States

ISBN: (纸本)9780819488701

Self-referenced quantitative phase microscopy (SrQPM) is reported, wherein quantitative phase imaging is achieved through the interference of the sample wave with a reflected version of itself. The off-axis interference between the two beams generates a spatially modulated hologram that is analyzed to quantify the sample's amplitude and phase profile. SrQPM requires approximately one-half of the object field of view to be empty and optically flat, which serves as a reference for the other half of the field of view containing the sample. © 2012 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

关键词： Holograms

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Multi Angle View of Lung Using Optical Coherence Tomography (OCT)

Multi Angle View of Lung Using Optical Coherence Tomography ...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Golabchi, Ali Gouldstone, Andrew DiMarzio, Charles A. Northeastern Univ Dept Elect & Comp Engn Boston MA 02115 USA Northeastern Univ Dept Engn Mech Boston MA USA Bernard M Gordon Ctr Subsurface Sensing & Imaging Boston MA USA

ISBN: (纸本)9780819488701

Lung imaging, visualization and measurement of alveolar volume has great importance in determining lung health. However, the heterogeneity of lung tissue complicates this task. In this paper multi angle Optical Coherence Tomography (OCT) is used to overcome this problem. One of the limitations of utilizing OCT in lung is the speckle noise and artifacts that originate from the refraction at the tissue-air interface inside the lung. Multi angle view of lung using OCT is incoherent summation of multiple angle-diverse images. Utilizing image registration of multi angle OCT scans of the lung helps reduce the speckle noise and refraction artifacts. This technique helps extract more information from the images which improves visualization and the ability to measure the geometry of alveoli. The other difficulty of utilizing OCT is interpreting the images due to the low numerical aperture (NA) on the OCT. The multi angle view of the lung increases NA, which increase the imaging resolution through synthetic aperture imaging. In this paper inflated excised lung tissue and lung phantom are presented.

关键词： Lung imaging Alveoli Optical Coherence Tomography (OCT) 3D microscopy

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Real-time quantitative differential interference contrast (DIC) microscopy implemented via novel liquid crystal prisms

Real-time quantitative differential interference contrast (D...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Zahreddine, Ramzi N. Cormack, Robert H. Masterson, Hugh King, Sharon V. Cogswell, Carol J. Univ Colorado Dept Elect Engn 425 UCB Boulder CO 80309 USA Boulder Nonlinear Systems Lafayette CO 80026 USA

ISBN: (纸本)9780819488701

A phase shifting differential interference contrast (DIC) microscope, which provides quantitative phase information and is capable of imaging at video rates, has been constructed. Using a combination of phase shifting and bi-directional shear, the microscope captures a series of eight images which are then integrated in Fourier space. In the resultant image the intensity profile linearly maps to the phase differential across the object. The necessary operations are performed by various liquid crystal devices (LCDs) which can operate at high speeds. A set of four liquid crystal prisms shear the beam in both the x and y directions. A liquid crystal bias cell delays the phase between the e- and o-beams providing phase-shifted images. The liquid crystal devices are then synchronized with a CCD camera in order to provide real-time image acquisition. Previous implementation of this microscope utilized Nomarski prisms, a rotation stage and a manually operated Senarmont compensator to perform the necessary operations and was only capable of fixed sample imaging. In the present work, a series of images were taken using both the new LCD prism based microscope and the previously implemented Senarmont compensator based system. A comparison between these images shows that the new system achieves equal and in some cases superior results to that of the old system with the added benefit of real-time imaging.

关键词： Differential interference contrast (DIC) microscopy quantitative phase imaging liquid crystal devices live cell imaging

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Double helix PSF engineering for computational fluorescence microscopy imaging

Double helix PSF engineering for computational fluorescence ...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Ghosh, Sreya Quirin, Sean A. Grover, Ginni Piestun, Rafael Preza, Chrysanthe Univ Memphis Dept Elect & Comp Engn Memphis TN 38152 USA Univ Colorado Dept Elect Comp & Energy Eng Boulder CO 80309 USA

ISBN: (纸本)9780819488701

Point spread function engineering with a double helix (DH) phase mask has been recently used in a joint computational-optical approach for the determination of depth and intensity information from fluorescence images. In this study, theoretically determined DH-PSFs computed from a model that incorporates different amounts of depth-induced spherical aberration (SA) due to refractive-index mismatch in the three-dimensional imaging layers, are evaluated through a comparison to empirically determined DH-PSFs measured from quantum dots. The theoretically-determined DH-PSFs show a trend that captures the main effects observed in the empirically-determined DH-PSFs. Calibration curves computed from these DH-PSFs show that SA slows down the rate of rotation observed in a DH-PSF which results in: 1) an extended range of rotation;and 2) asymmetric rotation ranges as the focus is moved in opposite directions. Thus, for accurate particle localization different calibration curves need to be known for different amounts of SA. Results also show that the DH-PSF is less sensitive to SA than the conventional PSF. Based on this result, it is expected that fewer depth-variant (DV) DH-PSFs will be required for 3D computational microscopy imaging in the presence of SA compared to the required number of conventional DV PSFs.

关键词： Point-Spread Function Engineering Double-Helix Point-Spread Function Spherical Aberration Computational Imaging 3D Fluorescence microscopy

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Dynamic quantitative microscopy and nanoscopy of red blood cells in sickle cell disease

Dynamic quantitative microscopy and nanoscopy of red blood c...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Shaked, Natan T. Satterwhite, Lisa L. Telen, Marilyn J. Truskey, George A. Wax, Adam Tel Aviv Univ Dept Biomed Engn Fac Engn IL-69978 Tel Aviv Israel Duke Univ Fitzpatrick Inst Photon Dept Biomed Engn Durham NC 27708 USA Duke Univ Med Ctr Dept Med Div Hematol Durham NC 27708 USA

ISBN: (纸本)9780819488701

We have applied wide-field digital interferometric techniques to quantitatively image sickle red blood cells (RBCs) [1] in a noncontact label-free manner, and measure the nanometer-scale fluctuations in their thickness as an indication of their stiffness. The technique can simultaneously measure the fluctuations for multiple spatial points on the RBC and thus yields a map describing the stiffness of each RBC in the field of view. Using this map, the local rigidity regions of the RBC are evaluated quantitatively. Since wide-field digital interferometry is a quantitative holographic imaging technique rather than one-point measurement, it can be used to simultaneously evaluate cell transverse morphology plus thickness in addition to its stiffness profile. Using this technique, we examine the morphology and dynamics of RBCs from individuals who suffer from sickle cell disease, and find that the sickle RBCs are significantly stiffer than healthy RBCs. Furthermore, we show that the technique is sensitive enough to distinguish various classes of sickle RBCs, including sickle RBCs with visibly-normal morphology, compared to the stiffer crescent-shaped sickle RBCs.

关键词： Interferometric phase microscopy holographic microscopy red blood cells sickle cell disease

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Localization accuracy in single molecule microscopy using electron-multiplying charge-coupled device cameras

Localization accuracy in single molecule microscopy using el...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Chao, Jerry Ward, E. Sally Ober, Raimund J. Univ Texas Dallas Dept Elect Engn Richardson TX 75083 USA Univ Texas Southwestern Med Ctr Dallas Dept Immunol Dallas TX USA

ISBN: (纸本)9780819488701

The electron-multiplying charge-coupled device (EMCCD) is a popular technology for imaging under extremely low light conditions. It has become widely used, for example, in single molecule microscopy experiments where few photons can be detected from the individual molecules of interest. Despite its important role in low light microscopy, however, little has been done in the way of determining how accurately parameters of interest (e. g., location of a single molecule) can be estimated from an image that it produces. Here, we develop the theory for calculating the Fisher information matrix, and hence the Cramer-Rao lower bound-based limit of the accuracy, for estimating parameters from an EMCCD image. An EMCCD operates by amplifying a weak signal that would otherwise be drowned out by the detector's readout noise as in the case of a conventional charge-coupled device (CCD). The signal amplification is a stochastic electron multiplication process, and is modeled here as a geometrically multiplied branching process. In developing our theory, we also introduce a "noise coefficient" which enables the comparison of the Fisher information of different data models via a scalar quantity. This coefficient importantly allows the selection of the best detector (e.g., EMCCD or CCD), based on factors such as the signal level, and regardless of the specific estimation problem at hand. We apply our theory to the problem of localizing a single molecule, and compare the calculated limits of the localization accuracy with the standard deviations of maximum likelihood location estimates obtained from simulated images of a single molecule.

关键词： Branching process Cramer-Rao lower bound electron multiplication Fisher information matrix single molecule microscopy

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Depth aberrations characterization in linear and nonlinear microscopy schemes using a shack-Hartmann wavefront sensor

Depth aberrations characterization in linear and nonlinear m...

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Conference on three-dimensional and multidimensional microscopy - image acquisition and processing Xix

作者： Aviles-Espinosa, Rodrigo Andilla, Jordi Porcar-Guezenec, Rafael Levecq, Xavier Artigas, David Loza-Alvarez, Pablo ICFO Inst Photon Sci Parc Mediterrani TecnolAv Carl Friedrich Gauss 3 Castelldefels 08860 Barcelona Spain Imagine Opt F-91400 Orsay France Univ Politecn Cataluna Dept Signal Theory & Commun Barcelona 08034 Spain

ISBN: (纸本)9780819488701

The performance of imaging devices such as linear and nonlinear microscopes (NLM) can be limited by the optical properties of the imaged sample. Such an important aspect has already been described using theoretical models due to the difficulties of implementing a direct wavefront sensing scheme. However, these only stand for simple interfaces and cannot be generalized to biological samples given its structural complexity. This has leaded to the development of sensor-less adaptive optics (AO) implementations. In this approach, aberrations are iteratively corrected trough an image related parameter (aberrations are not measured), being prone of causing sample damage. In this work, we perform a practical implementation of a Shack-Hartman wavefront sensor to compensate for sample induced aberrations, demonstrating its applicability in linear and NLM. We perform an extensive analysis of wavefront distortion effects through different depths employing phantom samples. Aberration effects originated by the refractive index mismatch and depth are quantified using the linear and nonlinear guide-star concept. More over we analyze off-axis aberrations in NLM, an important aspect that is commonly overlooked. In this case spherical aberration behaves similarly to the wavefront error compared with the on-axis case. Finally we give examples of aberration compensation using epi-fluorescence and nonlinear microscopy.

关键词： Biological imaging Fluorescence microscopy Nonlinear microscopy Aberration compensation Adaptive optics

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Optimisation of the diffractive optical element for snapshot spectral imaging used in fluorescence microscopy

Optimisation of the diffractive optical element for snapshot...

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three-dimensional and multidimensional microscopy: image acquisition and processing Xix

作者： Leitner, R. Arnold, T. De Biasio, M. McGunnigle, G. Rogojanu, R. Steiner, G.E. Hermerschmidt, A. CTR AG Europastrasse 4/1 9500 Villach Austria TissueGnostics GmbH Taborstraße 10/2/8 1020 Vienna Austria Holoeye Photonics AG Albert-Einstein-Straße 14 12489 Berlin Germany

ISBN: (纸本)9780819488701

Snapshot approaches address various possibilities to acquire the spectral and spatial information of a scene within a single camera frame. One advantage over the classical push broom or staring imager approaches is that the temporal inconsistency between consecutive scan lines in first case or between the acquired monochromatic images in the second case is avoided. However, this has to be paid by some effort to rearrange or reconstruct the explicit spectral cube from the entangled raw data in the single camera frame. Besides others, the utilization of a diffractive optical element (DOE) is one such snapshot approach (CTIS - computed tomography imaging spectrometer). The DOE is used to create an optical transfer function that projects both the spectral and spatial information of a scene onto a sensor array and a reconstruction algorithm is used that recovers the spectral cube from the dispersed image pattern. The design of the DOE is crucial for the overall system performance as the absolute transmission efficiency of the zeroth and first order versus the relative efficiency between the two over the required wavelength range are difficult to optimize if the limited dynamic range of a real camera is considered. We describe the optimization of such a DOE for the wavelength range from 400 to 780nm and the required reconstruction algorithm to recover the spectral cube from the entangled snapshot image. The described snapshot approach has been evaluated using experiments to assess the spatial and spectral resolution using diffuse reflectance standards. Additionally the results achieved using the described setup for multi-color in-situ fluorescence hybridized preparations (M-FISH) are discussed. © 2012 Copyright Society of Photo-Optical Instrumentation Engineers (SPIE).

关键词： Diffractive optical elements

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