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

作者： Li, Chen Ding, Changqin Li, Minghe Rong, Jiayue Ulcickas, James Simpson, Garth J. Purdue Univ Dept Chem W Lafayette IN 47907 USA

ISBN: (纸本)9781510632547

Conventional three-dimensional (3D) images of biological samples are typically assembled from a stack of two-dimensional images acquired sequentially at different focal planes. This time-consuming manner hinders the application of 3D imaging techniques to the investigation of fast biochemical dynamics and light-sensitive biological events. The concept of multifocus imaging, which enables simultaneous acquisition of images from multiple focal planes, was introduced to achieve rapid 3D imaging. In the present study, we achieved multifocus imaging through polarization wavefront shaping via a micro-retarder array which splits the incident linearly polarized light into three beamlets that are focused to three axially-offset focal planes with 100 itm separation. Append to an existing beam-scanning microscope, this multifocus system enables rapid 3D imaging compatible with a variety of optical microscopic approaches including laser transmittance, two-photon excited fluorescence, and second harmonic generation microscopy.

关键词： Multifocus imaging beam scanning microscopy polarization wavefront shaping Jones calculus

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FPGA Implementation of Spectral Fusing Gabor Domain Optical Coherence microscopy 27

FPGA Implementation of Spectral Fusing Gabor Domain Optical ...

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

作者： Meemon, Panomsak Lenaphet, Yutana Saetiew, Jadsada Suranaree Univ Technol Sch Phys Inst Sci Nakhon Ratchasima 30000 Thailand Suranaree Univ Technol Sch Elect Engn Inst Engn Nakhon Ratchasima 30000 Thailand

ISBN: (纸本)9781510632547

Gabor domain optical coherence microscopy (GD-OCM) is an emerging tomographic imaging technique that overcome the depth of focus (DOF) limit of high numerical objective lens by acquiring multiple cross-section images corresponded with different focal planes of the objective along an axial direction and combining them to form an invariant high resolution cross-section image. We previously reported an alternative processing method of GD-OCM called spectral fusing GD-OCM (SF-GD-OCM). SF-GD-OCM extracts in-focus information directly from acquired spectral interference signals. The advantage of SF-GD-OCM over the original GD-OCM is that the Gabor filtering and fusing can be implemented in an acquisition hardware instead of a host computer. Here, we have investigated the implementation of SF-GD-OCM by using FPGA frame grabber. The experimental setup of the acquisition system as well as the implementation of the spectral Gabor fusion in FPGA device have been developed and verified. Results show that the data processing of SF-GD-OCM in FPGA enabled acquisition device is possible and could lead to improvement in overall imaging speed of GD-OCM.

关键词： Gabor domain optical coherence microscopy Gabor fusion technique FPGA Extended depth of field

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The effect of post-acquisition data misalignments on the performance of STEM tomography

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ULTRAmicroscopy 2022年 235卷 113498-113498页

作者： Wang, Yi-Chi Wang, Zhong Lin Chinese Acad Sci Beijing Inst Nanoenergy & Nanosyst Beijing 101400 Peoples R China Univ Chinese Acad Sci Sch Nanosci & Technol Beijing 100049 Peoples R China Georgia Inst Technol Sch Mat Sci & Engn Atlanta GA 30332 USA

Scanning transmission electron microscopy (STEM) tomography is widely used to reveal three-dimensional (3D) structure of the specimens from nanometers to atomic resolution. Advances in transmission electron microscope enable high resolution and low dose data acquisition for 3D reconstruction to resolve 3D coordinates of single atoms. Meanwhile, the developments of reconstruction algorithms increase the reconstruction quality. However, the as-acquired raw datasets often require alignments before they can be used as inputs to feed a reconstruction algorithm. The effect of post-acquisition data misalignments on the final reconstruction quality of STEM tomography is less discussed. Here, using phantom datasets with a focus on atomic features, we simulate a range of misalignments on each alignment step and correlate the level of misalignments to the final reconstruction quality. The study pinpoints that accurate alignments of tilt angles and stack positions and minimizing scan distortion are important to the reconstruction quality, while the sequence of alignment steps do not affect the reconstruction quality. The study not only emphasizes the most important alignment steps that should be pay attention to for a high-quality 3D reconstruction, but also summarizes post-acquisition data alignment procedures as a primer for new practitioners to use STEM tomography.

关键词： Electron tomography three dimensional reconstruction scanning transmission electron microscopy image processing

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Evaluation of a combined two-color phase plate forming three-dimensional dark holes in super resolution microscopy 27

Evaluation of a combined two-color phase plate forming three...

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

作者： Nagai, Koumei Maruyama, Takashi Kodaira, Akira Kumagai, Hiroshi Bokor, Nandor Iketaki, Yoshinori NTT Adv Technol Corp 3-1 Morinosato Wakamiya Atsugi Kanagawa 2430124 Japan Kitasato Univ Sch Allied Hlth Sci Phys 1-15-1 Kitasato Sagamihara Kanagawa 2520373 Japan Budapest Univ Technol & Econ Dept Phys Budafoki Ut 8 H-1111 Budapest Hungary Olympus Corp 2-3 Kuboyama Cho Hachioji Tokyo 1928512 Japan

ISBN: (纸本)9781510632547

In this study, a combined two-color phase plate (CTPP) was designed for super-resolution microscopy based on up conversion fluorescence depletion (FD), fabricated, and evaluated. It is composed of two types of phase plates, a spiral phase plate and an annular phase plate. A two-color phase plate modulates the phase of the erase beam while maintaining the phase of the pump beam. SRM performed using the proposed CTPP is expected to enable super resolution in both the focal plane and in the optical axis direction. Despite its complex structure, a highly accurate CTPP was obtained by using the exposure and etching processes used in semiconductor manufacturing.

关键词： Super-resolution microscopy Phase modulation Fluorescence depletion Optical-axis resolution

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three-dimensional tomographic imaging and quantitative phase measurement using virtual phase conjugation 27

Three-dimensional tomographic imaging and quantitative phase...

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

作者： Kawashima, Satoshi Okamoto, Atsushi Maeda, Tomohiro Ogawa, Kazuhisa Tomita, Akihisa Osaki, Ryusuke Hayashi, Naoki Hokkaido Univ Grad Sch Informat Sci & Technol Kita Ku Kita14 Nishi9 Sapporo Hokkaido 0600814 Japan FUJIFILM Corp Minato Ku 7-3 Akasaka 9 Chome Tokyo 1070052 Japan

ISBN: (纸本)9781510632547

We have proposed virtual-phase-conjugation-based optical tomography (VPC-OT) using a virtual phase conjugation technology for single-shot and three-dimensional optical tomography. In VPC-OT, a random-spatial-phase-modulated probe beam is irradiated to the sample to be measured, and the complex amplitude of the signal composed of a superimposition of light reflected from each layer of the sample is measured. A three-dimensional tomogram of intensity and phase is obtained by reproducing the measured complex amplitude using a phase conjugate wave in a virtual optical system built in a computer. At this time, by changing the parameters of the virtual optical system, it becomes possible to obtain information of various tomographic planes from the data obtained with a single measurement. In the ideal virtual phase conjugate reproduction process, free space propagation can be assumed;however, in the actual measurement, due to the distortion of the waves and the surroundings of the sample to be measured, a mismatch will occur in modulation and demodulation, and the separation accuracy between different tomographic planes would be degraded. We perform an experiment to clarify the characteristics of VPC-OT in this situation. In this experiment, three-dimensional optical tomography is performed using an etching glass having a periodic structure of 30 mu m as a sample, and the phase distribution is measured quantitatively. Furthermore, by placing a cover glass in front of the object and performing the same measurement, we discuss the characteristics and performance of VPC-OT when there is an optical distortion around the sample to be measured.

关键词： Phase conjugation digital holography tomographic image processing tomography three-dimensional image acquisition wavefront encoding

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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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Compact spectrograph for hyperspectral imaging with overlapping fluorescent reporters 27

Compact spectrograph for hyperspectral imaging with overlapp...

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

作者： Hart, Nathan A. Gibbs, Holly C. Yeh, Alvin T. Texas A&M Univ Dept Biol Dept Biomed Engn College Stn TX 77843 USA

ISBN: (纸本)9781510632547

A compact, prismbased spectrograph was designed for 2-photon light sheet microscopy based on broadband, ultrashort optical pulses that corrects for chromatic aberrations and distortion. Gaussian or Bessel beams of broadband optical pulses may be used to create narrow cylindrical, nonlinear excitation volumes from which fluorophores emit characteristic spectra. In practice, a slit aperture is often used to optically section the excitation volume before being imaged onto the camera chip. Optical dispersion of the fluorescence in the transverse direction of the imaging slit allows for hyperspectral image acquisition. Hyperspectral imaging systems may be used to simultaneously image and segment multiple fluorescent reporters in biological tissue. However, current systems have properties which are undesirable for low-light microscopy including chromatic aberrations, distortion, low optical transmission, and large footprint which consumes precious laboratory real estate. Here, we present a novel spectrograph that has sufficient optical transmission, achromaticity, and distortion correction for microscopy of fluorescent reporters spanning the visible spectrum (400 650 nm). Across the spatial dimension of the excitation volume, the spectrograph has uniform separation of the spectral bands while maintaining a compact size and profile. A second order deconvolution algorithm is used to spectrally deconvolve overlapping fluorophores.

关键词： broadband excitation scanning plane microscopy multiplexed microscopy hyperspectral imaging spectral deconvolution

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

Three-Dimensional and Multidimensional Microscopy: Image Acq...

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three-dimensional and multidimensional microscopy: image acquisition and processing XXVII 2020

ISBN: (纸本)9781510632530

The proceedings contain 14 papers. The topics discussed include: multi-immersion open-top light-sheet microscopy;compact spectrograph for hyperspectral imaging with overlapping fluorescent reporters;computational super-resolution microscopy: leveraging noise model, regularization and sparsity to achieve highest resolution;wavelet-based characterization of the spatial relationship of nerve and collagen in neuropathic adipose tissue;multifocus imaging via polarization wavefront shaping;a study for accelerating the speed of all-in-focus image processing;excitation-scan mirror array system advancements to hyperspectral imaging applications;and 3D refractive index tomography with quantitative oblique back-illumination microscopy.

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Quantitative Characterization of Deformation and Damage in Shale Under Compression Utilizing Digital image Correlation

Quantitative Characterization of Deformation and Damage in S...

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2022 SPE/AAPG/SEG Unconventional Resources Technology Conference, URTC 2022

作者： Nath, Fatick Aguirre, Edgardo Aguirre, Gabriel Perez, Jose L. Netro, Cesar Borjas, Flavio Limon, Valeria School of Engineering Texas A&M International University LaredoTX United States

Shale formations are constantly facing challenges ensuring safe drilling and effective fracturing to unlock potential. One of the key influencing factors is accurately characterizing the deformation and damage due to its intrinsic lamination and natural fractures. Moreover, shale formations exhibit fine-scale heterogeneity while the conventional laboratory methods (LVDT, strain gauges, etc.) are unable to distinguish such variation. Besides, methods like acoustic emission (AE), X-ray, computed tomography (CT), and scanning electron microscopy (SEM) are lengthy, costly, and functional with only small test ranges. This study aims to investigate the damage and deformation characteristics in shale samples using three-dimensional digital image correlation (3D-DIC) to overcome such limitations. A set of samples from Wolfcamp, Mancos, and Eagle Ford shale are tested under uniaxial (D×L=2"×2") and diametrical (D×L=2"×1") compression using a precision 100kN Instron electromechanical load frame with a constant displacement of 0.05 mm/min. Specimens had distinct lamination and natural fractures. An ARAMIS 3D-DIC image acquisition system was positioned to monitor the samples at a rate of 2 frames per second in a non-contact manner while conducting the uniaxial and diametrical compression experiment. A black-in-white dot pattern is utilized on the specimen to track the deformation while loading. The ARAMIS 3D-DIC system is used for image processing, visualization, and analysis of the shale damage process with varying load conditions. DIC generated quantitative full-field strain maps with load (tension, compression, and shear) show all sequences in the damage process and strain evolution. The entire damage progress over time of shale samples is split into four stages: initial damage stage, linear elastic, elastic-plastic, and plastic damage stage, which are evaluated by damage variables. In uniaxial and diametrical compression, Eagle Ford shale exhibits central failure due to ten

关键词： Computerized tomography

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3D refractive index tomography with quantitative oblique back-illumination microscopy 27

3D refractive index tomography with quantitative oblique bac...

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

作者： Ledwig, Patrick B. Robles, Francisco E. Georgia Inst Technol Atlanta GA 30332 USA Emory Univ Sch Med Atlanta GA 30322 USA

ISBN: (纸本)9781510632547

We have recently developed quantitative oblique back-illumination microscopy (qOBM), which enables full-field quantitative phase imaging (QPI) of objects embedded in a thick scattering medium. This epi-mode technique makes use of multiple scattering as a source of transmissive illumination from within, allowing for rich structural detail based on optical path delay. We now produce quantitative 3D renderings of index of refraction with subcellular detail by computing a 3D transfer function of the entire optical system, including the multiply scattered illumination, and deconvolving it from a vertical stack of phase gradient contrast images. This approach allows truly non-invasive, label-free, tomographic quantitative reconstructions if index of refraction in thick scattering samples including thick tissue samples, at low cost and with simple operation, bringing QPI's unparalleled access to sub-cellular structural detail to previously unavailable domains of investigation.

关键词： back illumination quantitative phase thick sample refractive index multiple scattering differential phase contrast microscopy deconvolution

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