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Proceedings of the 1997 5th Pacific conference on Computer Graphics and Applications

作者： Boier Martin, Ioana M. Marinescu, Dan C. Indiana Univ South Bend United States

In this paper we describe an environment for visualization and processing of low-dose, low-contrast electron micrographs of biological specimens. We focus on image selection, the first step in the process of reconstruction of the 3D structure of a specimen from its projections. Noise from a variety of sources makes automatic detection of particle positions a difficult task. New image acquisition devices and modern electron microscopy methods require processing and rendering of very large images (50-100 million pixels). We describe techniques for processing large images, algorithms for detecting particle positions on compressed images using the Crosspoint method, and methods for position refinement. EMMA, an interactive visualization environment for experimenting with particle identification methods is presented.

关键词： Three dimensional computer graphics

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Three-dimensional imaging through millimeter thick tissue specimens

Three-dimensional imaging through millimeter thick tissue sp...

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conference on Three-dimensional microscopy - image acquisition and processing IV

作者： Jones, MG Halliwell, M Bull, DR Davies, D Chinyama, C Wells, PNT United Bristol & NHS Trust & Bristol General Hospital (United Kingdom) Univ. of Bristol (United Kingdom) Univ. of Bristol and Southmead Hospital (United Kingdom) Univ. of Bristol and NHS Trust (United Kingdom)

ISBN: (纸本)0819423955

A 780 nm stage-scanned confocal transmission microscope using compact disk (CD) player optics has been constructed and used to study test objects (including scattering effects) and breast tissue specimens (25-1500 mu m thick). Confocal alignment in transmission is achieved using the CD optical mechanism moving coils to scan the objective lens until intensity peaks;the specimen is present but motionless, Intensity variation as a 3D function of mis-alignment of the two foci may allow estimation of optical deterioration caused by the specimen;appropriate confocal apertures and sample spacings can then be selected. Experimental measurements have been supplemented by 2D Monte-Carlo modeling of photon transport for a scattering-limited confocal transmission system. Modeling has characterized: transmission as a function of focal depth in a slab;contrast produced by a range of embedded spherical target radii;and optical mis-alignment. Poor dye perfusion within thick stained specimens results in little visible internal structure, This may be improved using partially phase dependent imaging (congruent to split-detector), sensitive to specimen refractive index variations.

关键词： confocal transmission imaging thick-tissue Monte-Carlo scattering phase-sensitive imaging

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Tomographic phase microscopy using optical tweezers 4

Tomographic phase microscopy using optical tweezers

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conference on Advanced microscopy Techniques IV and Neurophotonics II

作者： Habaza, Mor Gilboa, Barak Roichman, Yael Shaked, Natan T. Tel Aviv Univ Dept Biomed Engn IL-69978 Tel Aviv Israel Tel Aviv Univ Dept Exact Sci IL-69978 Tel Aviv Israel

ISBN: (纸本)9781628417012

We review our technique for tomographic phase microscopy with optical tweezers [1]. This tomographic phase microscopy approach enables full 3-D refractive-index reconstruction. Tomographic phase microscopy measures quantitatively the 3-D distribution of refractive-index in biological cells. We integrated our external interferometric module with holographic optical tweezers for obtaining quantitative phase maps of biological samples from a wide range of angles. The close-to-common-path, off-axis interferometric system enables a full-rotation tomographic acquisition of a single cell using holographic optical tweezers for trapping and manipulating with a desired array of traps, while acquiring phase information of a single cell from all different angles and maintaining the native surrounding medium. We experimentally demonstrated two reconstruction algorithms: the filtered back-projection method and the Fourier diffraction method for 3-D refractive index imaging of yeast cells.

关键词： Holography Interference microscopy Tomography Optical tweezers image reconstruction techniques Three dimensional image processing

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Three-dimensional microscopy using a diffraction grating primary objective

Three-dimensional microscopy using a diffraction grating pri...

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International conference on Applications of Photonics Technology

作者： Ditto, TD Aspex Inc New York NY 10013 USA

ISBN: (纸本)081945527X

Three-dimensional magnification of a diffusing surface can be achieved using profilometry based on holographic chirped frequency gratings and laser line projection. The recently patented method being investigated both supplants earlier 3-D microscopy methods using diffraction range finders and also competes favorably with extant confocal microscopy in coverage area, speed of acquisition and unit cost. The geometry of grazing incidence in a diffraction range finder shows an intrinsic anamorphic magnification. A narrow waist of input rays is expanded to the full width of the grating itself. The spatial magnification is simply the ratio of the length of the grating to the waist of the input column of rays. As the column of input rays approaches the grating plane, this magnification ratio approaches infinity. We develop a theory that predicts a limit to resolution as a function of illumination wave length and grating pitch of the primary objective. A simple microscope can achieve near micron resolution over several centimeters of depth in the visible light regime. An empirical demonstration is made using silver halide holograms.

关键词： Diffraction gratings Diffraction Microscopes Grazing incidence Cameras 3D acquisition 3D image processing microscopy Spectral resolution 3D metrology

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Three dimensional simulations of SEM imaging and charging

Three dimensional simulations of SEM imaging and charging

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conference on Metrology, Inspection, and Process Control for Microlithography XV

作者： Grella, L Lorusso, G Niemi, T Chuang, TC Adler, DL KLA Tencor Corp San Jose CA 95134 USA

ISBN: (纸本)0819440302

SEM based CD control and wafer inspection has an increasingly active role in the semiconductor industry. Current design rules require a CD control with a precision in the nanometer range. In order to achieve this precision, a complete model of the image formation mechanism is desirable. For this reason we present a three-dimensional simulation of scanning electron microscope (SEM) images. The simulations include Monte Carlo electron scattering, charging in the substrate and electron ray-tracing in the column. We investigate some specific cases in CD-SEM metrology: We will describe the effect of scan orientation relative to the orientation of the imaged feature on the apparent beam width (ABW), the effect of magnification on contact imaging, and the effect of residue in resist trenches. Our results, regarding these examples, clearly indicate that a fully three-dimensional numerical simulation is needed to obtain an understanding of image formation and resolution limiting factors.

关键词： Monte Carlo methods Scanning electron microscopy 3D image processing 3D modeling image acquisition 3D metrology Computer simulations image resolution Metrology Scattering

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Three-dimensional localization microscopy by deep learning

Three-dimensional localization microscopy by deep learning

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3D image acquisition and Display: Technology, Perception and Applications, 3D 2021 - Part of Imaging and Applied Optics Congress 2021

作者： Nehme, Elias Ferdman, Boris Freedman, Daniel Weiss, Lucien E. Gordon-Soffer, Racheli Naor, Tal Kedem, Reut Orange Alalouf, Onit Michaeli, Tomer Shechtman, Yoav Department of Biomedical Engineering Technion – Israel Institute of Technology Haifa Israel Department of Electrical Engineering Technion – Israel Institute of Technology Haifa Israel Russell Berrie Nanotechnology Institute Technion – Israel Institute of Technology Haifa Israel Google research Haifa Israel

In this talk I will describe how joint optimization of the microscope’s point-spread-function alongside the image processing algorithm, both using neural nets, enables dense emitter fitting for super-resolution micro... 详细信息

ISBN: (纸本)9781557528209

关键词： Optical transfer function

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The study of muscle remodeling in Drosophila metamorphosis using in vivo microscopy and bioimage informatics

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BMC BIOINFORMATICS 2012年第17期13卷 1-13页

作者： Chinta, Rambabu Tan, Joo Huang Wasser, Martin ASTAR Bioinformat Inst BII Imaging Informat Div Live Cell Imaging & Automat Image Anal Grp Singapore Singapore Natl Univ Singapore Dept Biol Sci Singapore 117548 Singapore

Background: Metamorphosis in insects transforms the larval into an adult body plan and comprises the destruction and remodeling of larval and the generation of adult tissues. The remodeling of larval into adult muscles promises to be a genetic model for human atrophy since it is associated with dramatic alteration in cell size. Furthermore, muscle development is amenable to 3D in vivo microscopy at high cellular resolution. However, multi-dimensional image acquisition leads to sizeable amounts of data that demand novel approaches in image processing and analysis. Results: To handle, visualize and quantify time-lapse datasets recorded in multiple locations, we designed a workflow comprising three major modules. First, the previously introduced TLM-converter concatenates stacks of single time-points. The second module, TLM-2D-Explorer, creates maximum intensity projections for rapid inspection and allows the temporal alignment of multiple datasets. The transition between prepupal and pupal stage serves as reference point to compare datasets of different genotypes or treatments. We demonstrate how the temporal alignment can reveal novel insights into the east gene which is involved in muscle remodeling. The third module, TLM-3D-Segmenter, performs semi-automated segmentation of selected muscle fibers over multiple frames. 3D image segmentation consists of 3 stages. First, the user places a seed into a muscle of a key frame and performs surface detection based on level-set evolution. Second, the surface is propagated to subsequent frames. Third, automated segmentation detects nuclei inside the muscle fiber. The detected surfaces can be used to visualize and quantify the dynamics of cellular remodeling. To estimate the accuracy of our segmentation method, we performed a comparison with a manually created ground truth. Key and predicted frames achieved a performance of 84% and 80%, respectively. Conclusions: We describe an analysis pipeline for the efficient handling and

关键词： Maximum Intensity Projection Pupal Stage Surface Evolution Genetic Perturbation Prepupal Stage

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Detection, identification and tracking of biological micro/nano organisms by computational 3D optical imaging

Detection, identification and tracking of biological micro/n...

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conference on Biosensing III

作者： Javidi, Bahram Moon, Inkyu Daneshpanaha, Mehdi Univ Connecticut Dept Elect & Comp Engn U-2157 Storrs CT 06269 USA Chosun Univ Sch Comp Engn Gwangju 501759 South Korea

ISBN: (纸本)9780819482556

In this paper we present an overview of our work on a method to provide three-dimensional (3D) identification and tracking of biological micro/nano-organisms. This approach connects digital holographic microscopy and statistical methods for cell identification. For 3D data acquisition of living biological microorganisms, a filtered white light source, LED or laser diode beam propagates through a biological microorganism and the transversely and longitudinally magnified Gabor hologram pattern of the biological microorganism by microscope objective is optically recorded with a CCD camera interfaced with a computer. 3D imaging of the biological microorganism from the magnified Gabor hologram pattern is obtained by applying the computational Fresnel propagation algorithm. For identification and tracking of the biological microorganism, statistical approaches based on statistical estimation and inference algorithms are developed to the segmented holographic 3D image. Overviews of analytical frameworks are discussed and experimental results are presented.

关键词： Three-dimensional image processing Three-dimensional image recognition Medical and biological imaging

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4D optical coherence tomography of the embryonic heart using gated imaging

4D optical coherence tomography of the embryonic heart using...

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conference on Coherence Domain Optical Methods and Optical Coherence Tomography in Biomedicine ix

作者： Jenkins, MW Rothenberg, F Roy, D Nikolski, VP Wilson, DL Efimov, IR Rollins, AM Case Western Reserve Univ Dept Biomed Engn Cleveland OH 44106 USA

ISBN: (纸本)0819456640

Computed tomography (CT), ultrasound, and magnetic resonance imaging have been used to image and diagnose diseases of the human heart. By gating the acquisition of the images to the heart cycle (gated imaging), these modalities enable one to produce 3D images of the heart without significant motion artifact and to more accurately calculate various parameters such as ejection fractions [1-3]. Unfortunately, these imaging modalities give inadequate resolution when investigating embryonic development in animal models. Defects in developmental mechanisms during embryogenesis have long been thought to result in congenital cardiac anomalies. Our understanding of normal mechanisms of heart development and how abnormalities can lead to defects has been hampered by our inability to detect anatomic and physiologic changes in these small (<2mm) organs. Optical coherence tomography (OCT) has made it possible to visualize internal structures of the living embryonic heart with high-resolution in two- and threedimensions. OCT offers higher resolution than ultrasound (30 um axial, 90 um lateral) and magnetic resonance microscopy (25 um axial, 31 um lateral) [4, 5], with greater depth penetration over confocal microscopy (200 um). Optical coherence tomography (OCT) uses back reflected light from a sample to create an image with axial resolutions ranging from 2-15 um, while penetrating 1-2 mm in depth [6]. In the past, OCT groups estimated ejection fractions using 2D images in a Xenopus laevis [7], created 3D renderings of chick embryo hearts [8], and used a gated reconstruction technique to produce 2D Doppler OCT image of an in vivo Xenopus laevis heart [9]. In this paper we present a gated imaging system that allowed us to produce a 16-frame 3D movie of a beating chick embryo heart. The heart was excised from a day two (stage 13) chicken embryo and electrically paced at 1 Hz. We acquired 2D images (B-scans) in 62.5 ms, which provides enough temporal resolution to distinguish end-c

关键词： Heart Optical coherence tomography 3D image processing Gated imaging 3D acquisition 3D image reconstruction 3D metrology Visualization Computed tomography Ultrasonography

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Space Imaging Measurement System based on fixed lens and moving detector

Space Imaging Measurement System based on fixed lens and mov...

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conference on Novel Optical Systems Design and Optimization ix

作者： Akiyama, Akira Doshida, Minoru Mutoh, Eiichiro Kumagai, Hideo Yamada, Hirofumi Ishii, Hiromitsu Kanazawa Tech Coll 2-270 Hisayasu Kanazawa Ishikawa 9218601 Japan Japan Def Agcy Tech Res & Dev Inst Tachikawa Tokyo 1908533 Japan Kawasaki Heavy Ind Co Ltd Aerosp Co Minato Ku Tokyo 1056116 Japan Tamagawa Seiki Co Guidance & Nav Sect Nagano 3958515 Japan Kanazawa Tech Coll Kanazawa Ishikawa 9218601 Japan Nihon Univ Dept Elect Engn Coll Sci & Technol Chiyoda Ku Tokyo 1018308 Japan

ISBN: (纸本)081946368X

We have developed the Space Imaging Measurement System based on the fixed lens and fast moving detector to the control of the autonomous ground vehicle. The space measurement is the most important task in the development of the autonomous ground vehicle. In this study we move the detector back and forth along the optical axis at the fast rate to measure the three-dimensional image data. This system is just appropriate to the autonomous ground vehicle because this system does not send out any optical energy to measure the distance and keep the safety. And we use the digital camera of the visible ray range. Therefore it gives us the cost reduction of the three-dimensional image data acquisition with respect to the imaging laser system. We can combine many pieces of the narrow space imaging measurement data to construct the wide range three-dimensional data. This gives us the improvement of the image recognition with respect to the object space. To develop the fast movement of the detector, we build the counter mass balance in the mechanical crank system of the Space Imaging Measurement System. And then we set up the duct to prevent the optical noise due to the ray not coming through lens. The object distance is derived from the focus distance which related to the best focused image data is selected from the image of the maximum standard deviation in the standard deviations of series images.

关键词： Sensors Imaging systems Modulation transfer functions CCD cameras Geometrical optics 3D image processing CCD image sensors Distance measurement image sensors Ranging

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