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Simulation of light attenuation within fluorescent microspheres used for liquid fraction separation recorded by a CSLM

Simulation of light attenuation within fluorescent microsphe...

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

作者： Liljeborg, A ROYAL INST TECHNOL S-10044 STOCKHOLMSWEDEN

ISBN: (纸本)0819420298

In order to separate different proteins, liquid chromatography is often used. The sample is pumped through a column filled with microspheres. The velocity of the proteins are depending on their interaction with the microspheres. The proteins could be labelled with a fluorescent marker and the distribution of the protein within the sphere can be recorded using a CSLM. When collecting optical sections using a CSLM the detected intensity decreases the deeper in the specimen the section is collected. This is due to absorption, scattering and bleaching. For the special case of a single microsphere it is of interest to find out how this combined effect is distributed within the sphere for a certain distribution of the fluorescent stain. When this distribution is known the attenuation can be compensated for. In the simulation the distribution of the stain is supposed to be the result of a diffusion process and all attenuation is supposed to arise from absorption only. The attenuation for a certain volume element (voxel) is supposed to occur from absorption in the voxels above, within the cone formed by the focused excitation light beam. A basic assumption is that the attenuation within each voxel is a fraction of the fluorescent intensity within that same voxel. A simulation program has been written where the parameters of the diffusion process within the microsphere can be controlled. Also the parameters for the attenuation calculation can be set, e.g. the assumed fraction of fluorescent intensity that act as attenuation. 3D datasets can be generated for visualization. Also intensity profiles can be generated along a diameter of the simulated sphere in the depth direction, since the intensity distribution is circularly symmetric in the lateral directions. Some comparisons are made to real microspheres, and the parameters are adjusted for closest resemblance. This adjustment can be done manually but an implementation using non-linear fitting of data is also presented. The

关键词： simulation light attenuation confocal microscopy micro sphere

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3D reconstruction methods using line-scanning microscopy with a linear sensor

3D reconstruction methods using line-scanning microscopy wit...

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European conference on Biomedical Optics, ECBO 2013

作者： Macedo, Milton P. Correiaa, C.M.B.A. Center of Instrumentation Department of Physics University of Coimbra Coimbra Portugal ISEC Instituto Superior de Engenharia de Coimbra Coimbra Portugal

ISBN: (纸本)9780819496461

Line-scanning microscopy is a technique with ability to deliver images with an higher acquisition rate than confocal microscopy. But it is accomplished at expense of the degradation of resolution for details parallel to sensor if slit detectors are used. With a linear image sensor it is possible to attenuate or even cancel this effect through the use of information stored in each pixel / light distribution across line pixels of the sensor. In spite of its great potential the use of linear image sensors and in particular the development of three-dimensional (3D) reconstruction methods that take into account its specificity is scarce. This led to our motivation to build a laboratory prototype of a bench stage-scanning microscope using a linear image sensor. We aim at improving lateral resolution isotropy but also image visualization and 3D mesh reconstruction using different optical setups particularly illumination modes, e.g., widefield and line-illumination. The versatility of the laboratory prototype namely its software for image acquisition, processing and visualization is important to attain this goal in the sense that it provides excellent means to develop and test algorithms. Several algorithms for 3D reconstruction were developed and are presented and discussed in this paper. Results of the application of these 3D reconstruction methods show the improvements on lateral resolution isotropy and depth discrimination achieved using algorithms integrating sensor geometry or spatial sampling rate. Also it is evidenced the impact of an insufficient spatial sampling rate from 3D mesh reconstructions. © 2013 OSA-SPIE.

关键词： Pixels

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Optimization of the design of a multiple-photon excitation laser scanning fluorescence imaging system.

Optimization of the design of a multiple-photon excitation l...

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

作者： Wokosin, DL White, JG Univ. of Wisconsin/Madison (United States)

ISBN: (纸本)0819423955

Multi-photon (two or more photon) excitation imaging offers three significant advantages compared to laser-scanning confocal fluorescence microscopy for 3-D and 4-D fluorescence microscopy: considerable reduction in total sample excitation, increased depth penetration, and increased detection sensitivity. All-solid-state ultra-fast lasers offer tremendous potential for affordable, reliable, ''turn-key'' multi-photon excitation sources. We have been developing a multi-photon system that utilizes an all-solid-state Nd:YLF excitation source. We have been evaluating the potential of this source for biological microscopy and have been optimizing system parameters for this application area. We have found that the 1047 nm radiation from these lasers can excite by two-photon fluorescence many commonly used fluorophores that are normally excited from blue to yellow light. In addition, we have found that this wavelength readily excites several normally UV excited fluorophores by the mechanism of three-photon excitation. The Nd:YLF laser has proven reliable in operation with nearly 6000 hours logged without significant loss of power. However, the original system produced rather long pulses for multi-photon excitation (300 fs) and a beam shape that was not ideal. We have recently commissioned the development of an improved pulse compressor from the manufacturers that gives narrower pulses (120 fs), improved beam shape, and a smaller insertion loss. This optimized excitation system has 6 times more potential two-photon excited fluorescence and 22 times more potential three-photon excited fluorescence than the prototype system. In addition, by optimizing coatings in the excitation and signal paths, we have improved the descanned detection sensitivity by 20% for two-photon excited fluorescence and 315% for three-photon excited fluorescence. The excitation optical transfer efficiency (1047 nm) of our imaging system is currently 60% to the back aperture of the objective. The emissio

关键词： 3-D 4-D laser scanning fluorescence microscopy confocal three-photon excitation two-photon excitation non-descanned emission collection

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On-line 3-dimensional confocal imaging in vivo

On-line 3-dimensional confocal imaging in vivo

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Proceedings of the 1999 IEEE Engineering in Medicine and Biology 21st Annual conference and the 1999 Fall Meeting of the Biomedical Engineering Society (1st Joint BMES / EMBS)

作者： Li, J. Jester, J.V. Cavanagh, H.D. Petroll, W.M. Univ of Texas Southwestern Medical Cent Dallas United States

ISBN: (纸本)0780356756

Tandem Scanning Confocal microscopy (TSCM) is ideal for in vivo corneal imaging, but currently requires time-consuming off-line image processing. To overcome this limitation, we have developed a novel PC-based TSCM system. The system is the first to provide interactive 3-D on-line image acquisition and analysis of in vivo confocal images.

关键词： Medical imaging

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3D image acquisition and Display: Technology, Perception and Applications, 3D 2021

3D Image Acquisition and Display: Technology, Perception and...

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

ISBN: (纸本)9781557528209

The proceedings contain 41 papers. The topics discussed include: focus stacking and 3D visualization in multispectral microscopy of thick samples;Hough transform processing in 3D object detection and visualization;visible and long wave infrared imaging in degraded environments using three dimensional polarimetric integral imaging;overview of optical signal detection in turbid water using temporally encoded polarimetric integral imaging;photophoretic optical trap display test rigs;an overview of hand gesture recognition in degraded environments using three-dimensional integral imaging and deep neural networks;generation of 3D light field with reconfigurable time-dimension characteristics based on integral imaging;and autostereoscopic 3D display based on liquid crystal screen with binocular viewpoints tracking.

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OPTIMIZATION AND DEVELOPMENT OF X-RAY microscopy TECHNIQUE FOR INVESTIGATION OF THERMAL BARRIER COATING

OPTIMIZATION AND DEVELOPMENT OF X-RAY MICROSCOPY TECHNIQUE F...

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conference and Exhibition on Materials Science and Technology (MS and T)

作者： Asadizanjani, Navid Shahbazmohammadi, Sina Jordan, Eric H. Univ Connecticut Storrs CT 06269 USA

ISBN: (纸本)9781119183853;9781119183877

Full understanding of the cracking behavior of thermal barrier coatings (TBCs), requires a three-dimensional (3D) characterization of all layers. Common microscopy techniques are based on 2D cross section images and fail provide 3D information and because such methods are destructive it is not possible to watch the growth or linking of specific cracks. Collecting a series of two-dimensional (2D) cross-section images to generate the 3D volume is both time consuming and will not allow tracking the growth of cracks but instead provides only statistical information that also relies of assuming all samples behave the same way. X-ray tomography or micro-CT is as a valuable nondestructive method which can potentially provide us with the unique opportunity to track changes of the same location and hence same crack as a function of time during thermal cycling. X-ray tomography presents a number of challenges including the relatively high attenuation of x-rays in the TBC and substrate. There are various nontrivial parameters yet to be optimized for a successful tomography. Sample size and several interdependent image acquisition parameters are the most significant factors determining the quality of imaging. Also, it is necessary to achieve repeatable image processing and develop algorithms that can extract quantitative information;otherwise, X-ray microscopy remains merely qualitative. Here we seek to establish a reliable procedure to acquire meaningful repeatable quantitative 3D information of TBC samples. It is shown that parameters have to be optimized based on the region of interest in TBC samples, that is, there are different parameters to be tuned for the TGO thickness measurement, recording of interfacial surface geometry change, evolution of cracks in the ceramic top coat and study of bond coat compositional integrity. These optimized parameters are explained and verified. In addition, a sample analysis with a repeatability check has also been performed to ensure the

关键词： Cracks

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Establishing multi-modality datasets with the incorporation of 3D histopathology for soft tissue classification

Establishing multi-modality datasets with the incorporation ...

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Medical Imaging 2006 conference

作者： de Ryk, Jessica Thiesse, Jacqueline Reinhardt, Joseph M. Hoffman, Eric A. McLennan, Geoffrey Univ Iowa 200 Hawkins Dr Iowa City IA 52242 USA

ISBN: (纸本)0819464236

The development of multi-modality image analysis has gained increasing popularity over recent years. Multi-modality image databases are being developed to benefit patient clinical care, research and education. The incorporation of histopathology in these multi-modality datasets is complicated by the large differences in image quality, content and spatial association. We have developed a novel system, the large-scale image microtome array (LIMA), to bridge the gap between non-structurally destructive and destructive imaging such that reliable registration and incorporation of three-dimensional (3D) histopathology can be achieved. We have developed registration algorithms to align the micro-CT, LIMA and histopathology data to a common coordinate system. Using this multi-modality image dataset we have developed a classification algorithm to identify on a pixel basis, the tissue types present. The output from the classification processing is a 3D color coded map of tissue distributions. The resulting complete dataset provides an abundance of valuable information relating to the tissue sample including density, anatomical structure, color, texture and cellular information in three dimensions. In this study we have chosen to use normal and diseased lung tissue, however the flexibility of the image acquisition and subsequent processing algorithms makes it applicable to any soft organ tissue.

关键词： 3D histopathology microscopy computed micro-tomography thin-plate spline registration classification

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A DEFORMABLE 3D ZEBRAFISH MODEL FOR BRIGHT-FIELD microscopy image SIMULATION 18

A DEFORMABLE 3D ZEBRAFISH MODEL FOR BRIGHT-FIELD MICROSCOPY ...

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18th International conference on Interfaces and Human Computer Interaction 2024, IHCI 2024, the 17th International conference on Game and Entertainment Technologies 2024, GET 2024 and the 18th International conference on Computer Graphics, Visualization, Computer Vision and image processing 2024, CGVCVIP 2024, Part of the 18th Multi conference on Computer Science and Information Systems 2024, MCCSIS 2024

作者： Jámbor, Richárd Tanács, Attila Dept. of Image Processing and Computer Graphics Institute of Informatics University of Szeged Árpád tér 2. SzegedH-6720 Hungary

ISBN: (纸本)9789898704580

Due to their rapid reproduction, development, and similar genetic structure to humans, zebrafish are popular animals in various biological research. Their small size and body transparency make them convenient to examine under a bright-field light microscope. However, these provide 2-dimensional projected images, which makes 3D measurements difficult. Usual approaches try to reconstruct 3D structures from series of projected images, that is not always an option. In our paper we propose an approach to model the images acquisition process including the 3D parametric deformable model of the zebrafish and the light conditions in the microscopy environment. Our goal is to simulate images that look similar to the real ones using only a few parameters. © 2024 Interfaces and Human Computer Interaction. All Rights Reserved.

关键词： Invertebrates

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Hyperspectral holographic fourier-microscopy

Hyperspectral holographic fourier-microscopy

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Digital Holography and Three-dimensional Imaging, DH 2014

作者： Kalenkov, G.S. Kalenkov, S.G. Shtanko, A.E. 141700 9 Institutskiy per Dolgoprudny Moscow Region Russia 107023 B. Semenovskaya 38 Moscow Russia Moscow State University of Technology 'Stankin' 127994 Vadkovskiy per. 1 Moscow Russia

New lens free holographic image acquisition method in polychromatic, unpolarized light is presented. Hyperspectral amplitude and average-phase profile images of standard microscope samples obtained experimentally are ... 详细信息

ISBN: (纸本)9781557523082

关键词： Noise abatement

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GPU-based visualization techniques for 3D microscopic imaging data

GPU-based visualization techniques for 3D microscopic imagin...

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conference on Computational Imaging V

作者： Wang, Qiqi Sun, Yinlong Robinson, J. Paul Purdue Univ Dept Comp Sci W Lafayette IN 47907 USA Purdue Univ Dept Biomed Engn W Lafayette IN 47907 USA

ISBN: (纸本)9780819466112

Three-dimensional (3D) microscopic imaging techniques such as confocal microscopy have become a common tool in measuring cellular structures. While computer volume visualization has advanced into a sophisticated level in medical applications, much fewer studies have been made on data acquired by the 3D microscopic imaging techniques. To optimize the visualization of such data, it is important to consider the data characteristics such as thin data volume. It is also interesting to apply the new GPU (graphics processing unit) technology to interactive volume rendering of the data. In this paper, we discuss several texture-based techniques to visualize confocal microscopy data by considering the data characteristics and with support of GPU. One simple technique generates one set of 2D textures along the axial direction of image acquisition. An improved technique uses three sets of 2D textures in the three principal directions, and creates the rendered image via a weighted sum of the images generated by blending the individual texture sets. In addition, we propose a new approach based on stencil such that textures are blended based on a stencil control. Given the viewing condition, a texel needs to be drawn only when its corresponding projection on the image plane is inside a stencil area. Finally, we have explored the use of multiple-channel datasets for flexible classification of objects. These studies are useful to optimize the visualization of 3D microscopic imaging data.

关键词： volume visualization interactive rendering GPU-based techniques texture blending stencil techniques 3D microscopic imaging confocal microscopy

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