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three-dimensional and multidimensional microscopy: image acquisition and processing xxvi 2019

ISBN: (纸本)9781510624085

The proceedings contain 20 papers. The topics discussed include: fluorescence recovery after photobleaching (FRAP) with simultaneous fluorescence lifetime and time-resolved fluorescence anisotropy imaging (FLIM & tr-FAIM);evaluation of a high-speed multispectral light source for stroboscopic differential imaging for endocardial examination of daphnia magna;fast stimulated Raman projection tomography with iterative reconstruction from sparse projections;Monte Carlo model for speckle contrast imaging;model-based iterative reconstruction for spectral-domain optical coherence tomography;and feasibility study of limited-angle reconstruction based in vivo optical projection tomography.

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Distributed and networked analysis of volumetric image data for remote collaboration of microscopy image analysis

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Journal of Medical Imaging 2025年第2期12卷 024001页

作者： Chen, Alain Han, Shuo Lee, Soonam Fu, Chichen Yang, Changye Wu, Liming Winfree, Seth Dunn, Kenneth W. Salama, Paul Delp, Edward J. Purdue University School of Electrical and Computer Engineering Video and Image Processing Laboratory West LafayetteIN United States National Institute of Allergy and Infectious Diseases Rocky Mountain Laboratories HamiltonMT United States Indiana University School of Medicine IndianapolisIN United States Purdue University at Indianapolis School of Electrical and Computer Engineering IndianapolisIN United States

Purpose: The advancement of high-content optical microscopy has enabled the acquisition of very large three-dimensional (3D) image datasets. The analysis of these image volumes requires more computational resources than a biologist may have access to in typical desktop or laptop computers. This is especially true if machine learning tools are being used for image analysis. With the increased amount of data analysis and computational complexity, there is a need for a more accessible, easy-to-use, and efficient network-based 3D image processing system. The distributed and networked analysis of volumetric image data (DINAVID) system was developed to enable remote analysis of 3D microscopy images for biologists. Approach: We present an overview of the DINAVID system and compare it to other tools currently available for microscopy image analysis. DINAVID is designed using open-source tools and has two main sub-systems, a computational system for 3D microscopy image processing and analysis and a 3D visualization system. Results: DINAVID is a network-based system with a simple web interface that allows biologists to upload 3D volumes for analysis and visualization. DINAVID enables the image access model of a center hosting image volumes and remote users analyzing those volumes, without the need for remote users to manage any computational resources. Conclusions: The DINAVID system, designed and developed using open-source tools, enables biologists to analyze and visualize 3D microscopy volumes remotely without the need to manage computational resources. DINAVID also provides several image analysis tools, including pre-processing and several segmentation models. © 2025 Society of Photo-Optical Instrumentation Engineers (SPIE).

关键词： Photointerpretation

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Refractive index properties of the retina accessed by multi-wavelength digital holographic microscopy 26

Refractive index properties of the retina accessed by multi-...

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

作者： Barroso, Alvaro Ketelhut, Steffi Heiduschka, Peter Nettels-Hackert, Gerburg Schnekenburger, Juergen Kemper, Bjoern Univ Munster Med Fac Biomed Technol Ctr Mendelstr 17 D-48149 Munster Germany Univ Munster Dept Ophtalmol Med Ctr Domagkstr 15 D-48149 Munster Germany

ISBN: (纸本)9781510624092

The refractive index (RI) of the retina and its dispersion are essential parameters in ophthalmologic imaging. However, the spatial RI distribution in retinal tissue is difficult to access. We explored the capabilities of multispectral quantitative phase imaging (QPI) with digital holographic microscopy (DHM) for label-free refractive index characterization of dissected murine retina. The retrieved tissue refractive indices are in agreement with previously reported values for living cells and dissected tissues. Moreover, the detected spatial refractive index distributions correlate with results from complementary conducted OCT investigations. In summary, multispectral DHM is a promising tool for label-free characterization of optical retina properties.

关键词： digital holographic microscopy quantitative phase imaging multi-wavelength hyperspectral imaging retina refractive index

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Enhanced spectral lightfield fusion microscopy via deep computational optics for whole-slide pathology 26

Enhanced spectral lightfield fusion microscopy via deep comp...

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

作者： Kazemzadeh, Farnoud Li-Chang, Hector Wong, Alexander Univ Waterloo Waterloo ON Canada Waterloo Artificial Intelligence Inst Waterloo ON Canada Royal Victoria Reg Hlth Ctr Barrie ON Canada

ISBN: (纸本)9781510624092

Lensfree on-chip microscopy, which harnesses holography principles to capture interferometric light-field encodings without the need of lenses, is an emerging microscopy modality with widespread interest given the large field-of-view (FOV) compared to lens-based microscopy systems. In particular, there is a growing interest on the development of high-quality lensfree on-chip color microscopy. In this study, we propose a multi-laser spectral lightfield fusion microscopy using deep computational optics for achieving lensfree on-chip color microscopy. We will demonstrate that leveraging deep computational optics can enable imaging resolution beyond the diffraction limit without the use of any complex hardware-based super-resolution techniques, such as aperture scanning. The capabilities of the microscope are examined for whole-slide pathology. The superior imaging resolution of the instrument is demonstrated by imaging of a series of biological specimens demonstrating the true color imaging capability of the instrument while showcasing the large FOV of the instrument.

关键词： on-chip microscopy deep computational optics light-field fusion

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Temporal focusing-based multiphoton excitation fluorescence images with background noise cancellation via Hilbert-Huang transform 26

Temporal focusing-based multiphoton excitation fluorescence ...

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

作者： Hu, Yvonne Yuling Luo, Yuan-Rong Lin, Chun-Yu Chang, Chia-Yuan Chen, Shean-Jen Natl Cheng Kung Univ Dept Photon Tainan Taiwan Natl Cheng Kung Univ Dept Engn Sci Tainan Taiwan Natl Cheng Kung Univ Dept Mech Engn Tainan Taiwan Natl Chiao Tung Univ Inst Imaging & Biomed Photon Coll Photon Tainan Taiwan

ISBN: (纸本)9781510624092

Temporal focusing multiphoton excitation microscopy has wide field-of-view and optical sectioning. By using digital micromirror device, it provides patterned illumination. However, without filling the back aperture of objective lens, the axial confinement is limited to micron-meters, leading the out-of-focus fluorophores excited and image blurred. In this study, Hilbert-Huang transform is proposed to reduce the background noise. The empirical mode decomposition is first applied to disassemble the image into intrinsic mode functions and then reconstruct by Hilbert transform after diminishing background residues. The axial confinement can be enhanced from 2.79 mu m to 0.73 mu m with structure frequency in 1.06 mu m(-1).

关键词： Temporal focusing Digital micromirror device Structured illumination microscopy Hilbert-Huang transform

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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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three-dimensional Fluorescence Imaging with an Automated Light-field Microscope 26

Three-dimensional Fluorescence Imaging with an Automated Lig...

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

作者： Steinbrener, J. Pribosek, J. Baumgart, M. Bereczki, T. Harms, K. Ripper, D. Tortschanoff, A. Kenda, A. CTR Carinthian Tech Res AG Europastr 12 A-9524 Villach Austria IMC Fachhsch Krems GmbH Piaristengasse 1 A-3500 Krems Austria Mol Devices Austria GmbH Lagerhausstr 45 A-5071 Salzburg Austria

ISBN: (纸本)9781510624092

In addition to the two-dimensional intensity distribution in the image plane, light field microscopes capture information about the angle of the incident radiation. This information can be used to extract depth information about the object, calculate all-in-focus images and perform three-dimensional reconstructions from a single exposure. In combination with automated microscopy setups, this makes the technique a promising tool for high-throughput, three-dimensional cell assay evaluation which could substantially improve drug development and screening. To this end, we have developed a novel generalized calibration and three-dimensional reconstruction scheme for a light-field fluorescence microscope setup. The scheme can handle Keplerian and Galilean light field camera configurations added to infinity corrected microscopes configured to be telecentric as well as non-telecentric or hypercentric. The latter provides a significant advantage over the state of the art as it allows for an application specific optimization of lateral and axial resolution, field-of-view, and depth-of-focus. The reconstruction itself is performed iteratively using an expectation maximization algorithm. Super-resolved reconstructions can be achieved by including experimentally measured point-spread-functions. To reduce the required computational power, sparsity and periodicity of the system matrix relating object space to light field space is exploited. This is particularly challenging for the non-telecentric cases, where the voxel size of the reconstructed object space depends on the axial coordinate. We provide details on the experimental setup and the reconstruction algorithm, and present results on the experimental verification of theoretical performance parameters as well as successful reconstructions of fluorescent beads and three-dimensional cell spheroids.

关键词： Light-field microscopy 3D fluorescence imaging Reconstruction algorithms

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Projection multiplexing for enhanced acquisition speed in holographic tomography 26

Projection multiplexing for enhanced acquisition speed in ho...

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

作者： Kus, Arkadiusz Baczewska, Maria Ziemczonok, Michal Kujawinska, Malgorzata Warsaw Univ Technol Inst Micromech & Photon Sw Boboli 8 St PL-02525 Warsaw Poland

ISBN: (纸本)9781510624092

In holographic tomography (HT), the 3D refractive index distribution within weakly-scattering, phase-only biological object is retrieved. This key property of the technique is one of its most significant strengths compared to labelling-based methods of cell analysis such as fluorescence microscopy. As a consequence, however, it is required to acquire a set of holograms at several viewing directions, which hinders the measurement speed. In this paper we explore the prospect of multiplexing projections in order to decrease the number of scanning positions required for the full measurements. The presented analysis is based on experimental data acquired in a limited-angle holographic tomography system and emulates the performance of a spatial-light-modulator-based system in which multiple projections may be acquired simultaneously by generating a distribution of multiple point sources in the Fourier plane of the condenser lens. For this reason, the increase in acquisition speed strictly depends on the number of multiplexed holograms and results in decreased reconstruction quality. The performance of the system is demonstrated and analyzed with biological objects - human keratinocyte cells.

关键词： Holographic tomography optical diffraction tomography tomographic phase microscopy quantitative phase imaging 3D refractive index hologram multiplexing

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Compressed ultrafast transmission electron microscopy: a simulation study 26

Compressed ultrafast transmission electron microscopy: a sim...

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

作者： Liu, Xianglei Zhang, Shian Yurtsever, Aycan Liang, Jinyang Inst Natl Rech Sci Ctr Energie Mat Telecommun 1650 Blvd Lionel Boulet Varennes PQ J3X 1S2 Canada East China Normal Univ State Key Lab Precis Spect 3663 North Zhongshan Rd Shanghai 200062 Peoples R China

ISBN: (纸本)9781510624092

Bringing ultrafast temporal resolution to transmission electron microscopy (TEM) has historically been challenging. Despite significant recent progress in this direction, it remains difficult to achieve sub-nanosecond temporal resolution with a single electron pulse imaging. To address this limitation, here, we propose a methodology that combines laser-assisted TEM with computational imaging methodologies based on compressed sensing (CS). In this technique, a two-dimensional (2D) transient event [i.e. (x, y) frames that vary in time] is recorded through a CS paradigm. The 2D streak image generated on a camera is used to reconstruct the datacube of the ultrafast event, with two spatial and one temporal dimensions, via a CS-based image reconstruction algorithm. Using numerical simulation, we find that the reconstructed results are in good agreement with the ground truth, which demonstrates the applicability of CS-based computational imaging methodologies to laser-assisted TEM. Our proposed method, complementing the existing ultrafast stroboscopic and nanosecond single-shot techniques, opens up the possibility for single-shot, spatiotemporal imaging of irreversible structural phenomena with sub-nanosecond temporal resolution.

关键词： Transmission electron microscopy ultrafast imaging compressed sensing streak imaging

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Model-based iterative reconstruction for spectral-domain optical coherence tomography 26

Model-based iterative reconstruction for spectral-domain opt...

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

作者： Mason, Jonathan H. Reinwald, Yvonne Yang, Ying Waters, Sarah El Haj, Alicia Bagnaninchi, Pierre O. Univ Edinburgh MRC Ctr Regenerat Med 5 Little France Dr Edinburgh Midlothian Scotland Nottingham Trent Univ Coll Sci & Technol Dept Engn Nottingham England Keele Univ Inst Sci & Technol Med Keele Staffs England Univ Oxford Math Inst Oxford England Univ Birmingham Healthcare Technol Inst Birmingham W Midlands England

ISBN: (纸本)9781510624092

Spectral domain optical coherence tomography (OCT) offers high resolution multidimensional imaging, but generally suffers from defocussing, intensity falloff and shot noise, causing artifacts and image degradation along the imaging depth. In this work, we develop an iterative statistical reconstruction technique, based upon the interferometric synthetic aperture microscopy (ISAM) model with additive noise, to actively compensate for these effects. For the ISAM re-sampling, we use a non uniform FFT with Kaiser-Bessel interpolation, offering efficiency and high accuracy. We then employ an accelerated gradient descent based algorithm, to minimize the negative log-likelihood of the model, and include spatial or wavelet sparsity based penalty functions, to provide appropriate regularization for given image structures. We evaluate our approach with titanium oxide micro-bead and cucumber samples with a commercial spectral domain OCT system, under various subsampling regimes, and demonstrate superior image quality over traditional reconstruction and ISAM methods.

关键词： OCT ISAM demonstrate ISAM optical coherence tomography Demonstrate Spectral domain image quality image degradation

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