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

作者： Ghosh, Sreya Schaefer, Lutz Schuster, Dietwald Preza, Chrysanthe Univ Memphis Dept Elect & Comp Engn Memphis TN 38152 USA Adv Imaging Methodol Consultat Kitchener ON Canada Regensburg Univ Appl Sci Regensburg Germany

ISBN: (纸本)9780819498625

three-dimensional (3D) imaging with optical sectioning microscopy uses computational methods to obtain the true fluorescence distribution by ameliorating the effect of defocus, spherical aberration and noise. Inverse algorithms improve image quality at a fraction of the cost of implementing an optical system by accurate modeling of the imaging system. Good inverse imaging algorithms need to be accurate as well as fast. Better understanding of the image formation model is vital to obtain improved restoration through model-based algorithms. Forward imaging models based on a depth-varying point-spread function (DV-PSF) leads to a substantial improvement in the resulting images because it accounts for depth-induced aberrations present in the imaging system. PSFs at every layer can be represented using their principal components. Computation of the forward imaging model using a principal component analysis (PCA) representation of the DV-PSF requires fewer convolutions than a strata based approach investigated in the past. In this paper we present a new algorithm for maximum likelihood image restoration developed based on a PCA representation of the DV-PSF and an accelerated conjugate gradient (CG) iteration scheme. Results obtained with this PCA-CG algorithm from both simulated and experimental fluorescence microscope data are discussed and compared with results obtained from a CG iteration method based on the strata model and linear interpolation of the DV-PSF. The performance of the PCA-CG algorithms is shown to be promising for practical applications.

关键词： Point spread functions Principal component analysis 3D image processing Expectation maximization algorithms 3D modeling image restoration Algorithm development Computer simulations Luminescence Reconstruction algorithms

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Snapshot Spectral Imaging System

Snapshot Spectral Imaging System

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

作者： Arnold, Thomas De Biasio, Martin McGunnigle, Gerald Leitner, Raimund Ctr Carinthian Tech Res Villach Austria

ISBN: (纸本)9780819479662

Spectral imaging is the combination of spectroscopy and imaging. These fields are well developed and are used intensively in many application fields including industry and the life sciences. The classical approach to acquire hyper-spectral data is to sequentially scan a sample in space or wavelength. These acquisition methods are time consuming because only two spatial dimensions, or one spatial and the spectral dimension, can be acquired simultaneously. With a computed tomography imaging spectrometer (CTIS) it is possible to acquire two spatial dimensions and a spectral dimension during a single integration time, without scanning either spatial or spectral dimensions. This makes it possible to acquire dynamic image scenes without spatial registration of the hyper-spectral data. This is advantageous compared to tunable filter based systems which need sophisticated image registration techniques. While tunable filters provide full spatial and spectral resolution, for CTIS systems there is always a tradeoff between spatial and spectral resolution as the spatial and spectral information corresponding to an image cube is squeezed onto a 2D image. The presented CTIS system uses a spectral-dispersion element to project the spectral and spatial image information onto a 2D CCD camera array. The system presented in this paper is designed for a microscopy application for the analysis of fixed specimens in pathology and cytogenetics, cell imaging and material analysis. However, the CTIS approach is not limited to microscopy applications, thus it would be possible to implement it in a hand-held device for e. g. real-time, intra-surgery tissue classification.

关键词： spectral imaging CTIS computed tomography microscopy snapshot

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Analysis of the Effects of Different Resampling Techniques for Optical Coherence Tomography

Analysis of the Effects of Different Resampling Techniques f...

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

作者： Copeland, Christopher N. Ellerbee, Audrey K. Stanford Univ EL Ginzton Lab Stanford CA 94305 USA Stanford Univ Dept Elect Engn Stanford CA 94305 USA

ISBN: (纸本)9780819488701

Fourier domain optical coherence tomography (FD-OCT) uses interferometry and spatially coherent, polychromatic light to acquire cross-sectional images of scattering media such as biological tissue. Phase-sensitive derivatives of FD-OCT, such as spectral domain phase microscopy (SDPM), can perform quantitative phase imaging of cellular dynamics with sub-Angstrom sensitivity. FD-OCT and SDPM images are generated by taking the Fourier Transform of the raw spectral interferogram;the accuracy of the reconstruction depends on the choice of processing algorithms used, system noise, calibration and quantization errors. To decrease the processing time, the Fast Fourier transform (FFT) algorithm can be applied when the data are evenly sampled in wavenumber. Unfortunately, most OCT systems are designed for constant wavelength sampling, not constant wavenumber sampling. While there is general agreement on the qualitative superiority of some resampling methods over others, to the best of our knowledge there has been no study that compares these methods for OCT phase data. We examine the effects of various resampling techniques on simulated phase and amplitude OCT data. Given the trend towards high-speed imaging with OCT, the choice of resampling methods is critical, as one need balance processing time and image accuracy - not merely quality - when analyzing medical image data.

关键词： optical coherence tomography low coherence interferometry phase retrieval microscopy

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Intensity-based segmentation and visualization of cells in 3D microscopic images using the GPU

Intensity-based segmentation and visualization of cells in 3...

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

作者： Kang, Mi-Sun Lee, Jeong-Eom Jeon, Woong-Ki Choi, Heung-Kook Kim, Myoung-Hee Ewha Womans Univ Dept Comp Sci & Engn Seoul 120750 South Korea Inje Univ UHRC Sch Comp Engn Gyeong 621749 South Korea

ISBN: (纸本)9780819493583

3D microscopy images contain abundant astronomical data, rendering 3D microscopy image processing time-consuming and laborious on a central processing unit (CPU). To solve these problems, many people crop a region of interest (ROI) of the input image to a small size. Although this reduces cost and time, there are drawbacks at the image processing level, e. g., the selected ROI strongly depends on the user and there is a loss in original image information. To mitigate these problems, we developed a 3D microscopy image processing tool on a graphics processing unit (GPU). Our tool provides efficient and various automatic thresholding methods to achieve intensity-based segmentation of 3D microscopy images. Users can select the algorithm to be applied. Further, the image processing tool provides visualization of segmented volume data and can set the scale, transportation, etc. using a keyboard and mouse. However, the 3D objects visualized fast still need to be analyzed to obtain information for biologists. To analyze 3D microscopic images, we need quantitative data of the images. Therefore, we label the segmented 3D objects within all 3D microscopic images and obtain quantitative information on each labeled object. This information can use the classification feature. A user can select the object to be analyzed. Our tool allows the selected object to be displayed on a new window, and hence, more details of the object can be observed. Finally, we validate the effectiveness of our tool by comparing the CPU and GPU processing times by matching the specification and configuration.

关键词： GPU CUDA 3D microscopic image processing visualization

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Dynamic photothermal interferometric phase microscopy 13

Dynamic photothermal interferometric phase microscopy

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

作者： Turko, Nir A. Blum, Omry Shaked, Natan T. Tel Aviv Univ Fac Engn Dept Biomed Engn IL-69978 Ramat Aviv Israel

ISBN: (纸本)9781628419474

We present our latest advances in highly dynamic photothermal interferometric phase microscopy for quantitative, selective contrast imaging. Gold nanoparticles can be bio-functionalized to bind specific cells. When stimulating gold nanoparticles at their plasmon-peak wavelength, local increase of temperature occurs due to plasmon resonance. This causes a rapid change of optical phase of the light beam interacting with the sample. These phase changes can be recorded by interferometric phase microscopy and analyzed to form a photothermal image of the binding sites of the nanoparticles in the cells. Furthermore, by increasing the excitation laser light, one can deplete certain cells at will. Usually, the analysis of the photothermal signals utilizes a Fourier transform, which is computational time consuming. This makes photothermal imaging not suitable for applications requiring dynamic imaging or real-time quantitative analysis, such as for analyzing and sorting cells during their fast flow. For this goal, we have developed new algorithms, based on discrete Fourier transform variants, enabling fast analysis of photothermal signals from nanoparticles in live and highly dynamic cells. For the first time, video-rate photothermal signals are obtained, which forms the basis for real-time interferometric phase microscopy with molecular specificity. This technique holds great potential for using photothermal imaging in flow cytometry.

关键词： Photothermal imaging gold nanoparticles interferometric phase microscopy digital holographic microscopy

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Wave-optical calibration of a light-field fluorescence microscopy 26

Wave-optical calibration of a light-field fluorescence micro...

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

作者： Pribosek, J. Steinbrener, J. Baumgart, M. Bereczki, T. Harms, K. Tortschanoff, A. Kenda, A. Carinthian Tech Res Europastr 12 A-9524 Villach Austria Mol Devicess Lagerhausstr 45 A-5071 Wals Austria

ISBN: (纸本)9781510624092

In light-field microscopy, a single point emitter gives rise to a complex diffraction pattern, which varies with the position of the emitter in object space. In order to use deconvolution-based wave-optical reconstruction schemes for light-field imaging systems, established methods rely on theoretical estimation of such diffraction patterns. In this paper we propose a novel method for direct experimental estimation of the light-field point spread function. Our approach relies on a modified reversed micro-Hartmann test to acquire a composite light-field point spread function of several thousand point emitters in the object plane simultaneously. By using fiducial markers and a custom image processing algorithm we separate the contributions of individual point emitters directly in raw light-field images and allow the construction of the forward imaging process without any prior assumption about the optical system required. The constructed forward imaging model can finally be applied in the 3D-deconvolution based wave-optical reconstruction scheme.

关键词： light-field microscopy light-field point spread function wave-optical calibration fluorescence imaging

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Testing for nonrandom shape similarity between sister cells using automated shape comparison

Testing for nonrandom shape similarity between sister cells ...

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

作者： Guo, Monica Marshall, Wallace F. Univ Calif San Francisco Dept Biochem & Biophys Integrat Program Quantitat Biol San Francisco CA 94143 USA

ISBN: (纸本)9780819474308

Several reports in the biological literature have indicated that when a living cell divides, the two daughter cells have a tendency to be mirror images of each other in terms of their overall cell shape. This phenomenon would be consistent with inheritance of spatial organization from mother cell to daughters. However the published data rely on a small number of examples that were visually chosen, raising potential concerns about inadvertent selection bias. We propose to revisit this issue using automated quantitative shape comparison methods which would have no contribution from the observer and which would allow statistical testing of similarity in large numbers of cells. In this report we describe a first order approach to the problem using rigid curve matching. Using test images, we compare a pointwise correspondence based distance metric with a chamfer matching strategy and find that the latter provides better correspondence and smaller distances between aligned curves, especially when we allow nonrigid deformation of the outlines in addition to rotation.

关键词： Morphological image processing curve matching microscopy cytoskeleton actin cytokinesis cell shape

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Study of the spatial point spread function with depth in two-photon microscopy

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Proceedings of SPIE - The International Society for Optical Engineering 1999年 3605卷 112-119页

作者： Dunn, Andrew Wallace, Vincent Coleno, Maria So, Peter Tromberg, Bruce Univ of California at Irvine Irvine United States

ISBN: (纸本)0819430757;9780819430755

The spatial point spread function is studied for two-photon fluorescence imaging in turbid media. Using a Monte Carlo based model the effects of tissue optical properties on the point spread function, fluorescence generation, and fluorescence collection are studied. The simulated results are compared to measured point spread functions at different depths within a scattering sample. Results indicate that the limiting factor in two-photon imaging is a loss of signal caused by scattering rather than a loss of resolution.

关键词： Microscopic examination

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A multiplexed confocal FLIM microscope with 4-taps time-gated imager 27

A multiplexed confocal FLIM microscope with 4-taps time-gate...

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

作者： Richards, Morgan Shirakawa, Yuya Badr, Fares Kagawa, Keiichiro Kawahito, Shoji Fang, Qiyin McMaster Univ Dept Engn Phys 1280 Main St West Hamilton ON L8S 4L7 Canada Shizuoka Univ Res Inst Elect 3-5-1 Johoku Hamamatsu Shizuoka 4328011 Japan McMaster Univ Sch Biomed Engn 1280 Main St West Hamilton ON L8S 4L7 Canada

ISBN: (纸本)9781510632547

Combined with confocal imaging, Fluorescence lifetime imaging microscopy (FLIM) can achieve 3-dimensional optical sectional capability with sub-nanosecond lifetime information. As confocal FLIM acquires multi-dimensional data 4D (3D space + time), it is inherently slow. Recent developments in lock-in pixel imagers with time gated pixels show such detectors are capable of collecting as many as 8-time gates in a single pixel cycle. We present a multiplexed confocal FLIM microscope, equipped with a 4-taps time-gated lock-in pixel imager. The multiplexing setup allows the use of the sparse array with sub-nanosecond time-gating to achieve high throughput FLIM acquisition.

关键词： Multipoint Confocal Fluorescence FLIM Time-resolved CMOS image sensor lock-in pixel biomedical imaging

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Benefits and applications of programmable spectral devices in confocal Microscopes

Benefits and applications of programmable spectral devices i...

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Conference on 3-dimensional and multidimensional microscopy - image acquisition and processing X

作者： Borlinghaus, R Leica Microsyst Heidelberg GmbH Mannheim Germany

ISBN: (纸本)0819447641

Recent developement in confocal microscope systems allow to tune the spectral characteristics of those elements which separate excitation and emission. The new devices replace the classical filter-devices, which have been used in fluorescence microscopy for many yeas. Excitation filters have been replaced by acousto optical filters, which work as multichannel dimmer devices and allow fine tuning of excitation energy as well as tunig the excitation ratio of multiple excitations. Emission filters have been replaced by tunable multiband detectors, which allow tuning of emission band width for higher efficiency and better band separation. The multiband detector also allows spectral scanning modes. Dichroitic beam splitters have been replaced by acousto optical beam splitters (AOBS((R))) giving significantly increased signal efficiency and allow fast switching of excitation modes without moving mechanical parts. All three devices touether lead to much better primary images, either giving highly improved signal to noise ratio or much less photobleaching (which is identically with viability of life samples).

关键词： confocal microscopy spectral confocal imaging multiband detector acousto optical tunable filter acousto optical beam splitter

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