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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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Automatic detection of alignment errors in cryo-electron tomography

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JOURNAL OF STRUCTURAL BIOLOGY 2025年第1期217卷 108153页

作者： de Isidro-Gomez, F. P. Vilas, J. L. Carazo, J. M. Sorzano, C. O. S. Campus Univ Autonoma Ctr Nacl Biotecnol CNB CSIC Biocomp Unit Darwin 3 Madrid 28049 Spain Univ Autonoma Madrid Madrid 28049 Spain

Cryo-electron tomography is an imaging technique that allows the study of the three-dimensional structure of a wide range of biological samples, from entire cellular environments to purified specimens. This technique collects a series of images from different views of the specimen by tilting the sample stage in the microscope. Subsequently, this information is combined into a three-dimensional reconstruction. To obtain reliable representations of the specimen of study, it is mandatory to define the acquisition geometry accurately. This is achieved by aligning all tilt images to a standard reference scheme. Errors in this step introduce artifacts into the final reconstructed tomograms, leading to loss of resolution and making them unsuitable for detailed sample analysis. This publication presents algorithms for automatically assessing the alignment quality of the tilt series and their classification based on the residual errors provided by the alignment algorithms. If no alignment information is available, a set of algorithms for calculating the residual vectors focused on fiducial markers is also presented. This software is accessible as part of the Xmipp software package and the Scipion framework.

关键词： Cryo-electron tomography Tilt-series alignment Electron tomography Electron microscopy image processing Structural biology

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Multi-immersion open-top light-sheet microscopy 27

Multi-immersion open-top light-sheet microscopy

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

作者： Glaser, Adam K. Liu, Jonathan T. C. Univ Washington Dept Mech Engn Seattle WA 98195 USA

We present an easy-to-use multi-immersion open-top light-sheet microscope designed specifically for high-throughput imaging of a diverse set of tissues prepared with a variety of clearing protocols.

ISBN: (纸本)9781510632547

We present an easy-to-use multi-immersion open-top light-sheet microscope designed specifically for high-throughput imaging of a diverse set of tissues prepared with a variety of clearing protocols.

关键词： light-sheet microscopy selective-plane illumination microscopy fluorescence microscopy

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Computational super-resolution microscopy: leveraging noise model, regularization and sparsity to achieve highest resolution 27

Computational super-resolution microscopy: leveraging noise ...

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

作者： Xing, Jian Chen, Simeng Becker, Stephen Yu, Jiun-Yann Cogswell, Carol Univ Colorado Dept Elect Comp & Energy Engn Boulder CO 80309 USA Univ Colorado Dept Appl Math Boulder CO 80309 USA

ISBN: (纸本)9781510632547

We report progress in algorithm development for a computation-based super-resolution microscopy technique. Building upon previous results, we examine our recently implemented microscope system and construct alternative processing algorithms. Based on numerical simulations results, we evaluate the performance of each algorithm and determine the one most suitable for our super-resolution microscope.

关键词： Super-resolution microscopy regularization computational microscopy

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3,3′-thiodipropanol as a refractive index matching mounting medium for fluorescence microscopy 27

3,3′-thiodipropanol as a refractive index matching mounting...

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

作者： Alata Tejedo, Milvia Iris Martinez Cervantes, Juan Carlos Piazza, Valeria Ctr Invest Opt AC Loma Bosque 115 Guanajuato Mexico

ISBN: (纸本)9781510632547

In this work, several tests of the performance of 3,3'-thiodipropanol (TDP) as a mounting medium for fluorescence microscopy of biological samples were performed. Besides optical properties like the dispersion curve of TDP and the effect of the embedding medium on the fluorescence of commonly used dyes, the interaction with biological specimens, including the labeling of filamentous actin with fluorescent phalloidins, was tested: TDP showed to represent an interesting alternative to commercial mounting media. By mixing TDP with 2,2'-thiodiethanol (TDE), it was possible not only to fine tune the refractive index of the resulting solution, but to preserve the compatibility with fluorescent phalloidins.

关键词： Mounting media fluorescence microscopy filamentous actin

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A study for accelerating the speed of all-in-focus image processing 27

A study for accelerating the speed of all-in-focus image pro...

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

作者： Wang, Lihui Tabata, Satoshi Takeuchi, Hirotoshi Ishikawa, Masatoshi Guangdong Acad Sci Guangdong Inst Semicond Ind Technol 363 Changxing Rd Guangzhou 510650 Peoples R China Univ Tokyo Grad Sch Informat Sci & Technol Bunkyo Ku 7-3-1 Hongo Tokyo 1138656 Japan

ISBN: (纸本)9781510632547

To capture an all-in-focus and 3D depth image, shape from focus method is widely used. The phase accuracy of the image candidates should be processed and adjusted beforehand Phase only correction method was employed in this work and to accelerate the processing speed, the image processing by Fast Fourier Transform (FFT) was optimized Meanwhile, the processing task was assigned in several parallel threads so that the performance would be improved. The method was used on a variable focus imaging system, and, as a result, the processing speed was improved to around 2.5-fps.

关键词： all-in-focus shape from focus phase-only correction method 3D imaging variable focus system

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Multifocus imaging via polarization wavefront shaping 27

Multifocus imaging via polarization wavefront shaping

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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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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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