Download or read book Coded Computational Illumination and Detection for Three dimensional Fluorescence Microscopy written by Samuel J. Yang and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In vivo calcium imaging enables the optical monitoring of neural activity at the level of individual neurons in real time, necessitating the development of high speed, three-dimensional (3D) fluorescence microscopy techniques with at least single-neuron spatial resolution. Because a typical widefield microscope intrinsically produces only two-dimensional images, various illumination and detection coding strategies have been implemented to address the challenge of 3D fluorescence microscopy, utilizing either precisely structured and temporally scanned illumination patterns, such as in two-photon laser scanning microscopy or coding of the emission, as in light field microscopy, respectively. However, many single-focal illumination coding strategies have limited acquisition speeds, while detection-coding-only strategies requiring computational reconstruction of the 3D volume are limited by optical aberrations of the tissue. We present a 3D calcium imaging approach utilizing both multifocal scanned two-photon laser excitation for illumination coding and detection coding with the light field microscopy approach suitable for in vivo mammalian calcium imaging. A holographic 3D multifocal illumination pattern is targeted only towards pre-localized neurons avoiding the unnecessary illumination of other regions. The resulting fluorescence emission is coded and detected on an image sensor and deconvolution is used to recover the neural activity at each site. We present the design and optimization of such an imaging strategy, and validate the approach with experimental measurements. Finally, we demonstrate the application of this approach to in vivo mouse calcium imaging. The design and implementation of another technique, frame-projected independent fiber photometry, enabling the optical recording and control of neural activity in freely moving mammals with region-level spatial resolution, is presented in a dedicated chapter as well, including simultaneous recording from multiple brain regions in a mouse during social behavior, two-color activity recording, and optical optogenetic stimulation eliciting dynamics matching naturally observed patterns.
Download or read book Contribution to Three dimensional Fluorescence Microscopy Imaging Using Wavefront Encoding and Structured Illumination written by Nurmohammed Patwary and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Three-dimensional (3D) fluorescence microscopy (FM) is an integral part of biomedical research as it provides the necessary tool to investigate the interaction between the biomolecules in multiple dimensions (i.e. spatial, spectral, and temporal). This dissertation contributes toward two special types of FM: (i) computational optical sectioning microscopy (COSM), in which computational methods are used to improve the performance of the conventional imaging system, and (ii) structured illumination microscopy (SIM), which is used to increase the resolution of the optical microscope beyond the diffraction limit. A simplifying assumption of COSM is that the point spread function (PSF) does not change throughout the imaging volume; however, this assumption is not valid for optically thick samples (>5 µm), if the refractive index (RI) between the sample-mounting medium and the microscope objective (MO) lens’ immersion medium is different. Such cases require the use of computationally intensive depth-variant (DV) image restoration methods to avoid artifacts. To overcome this challenge, a wavefront encoded imaging system is developed, where we have demonstrated through simulation and experiment that a PSF does not change significantly up to a 60-µm imaging depth, which consequently improves the computational efficiency while restoring optically thick samples. Another contribution of this dissertation is investigating the impact of SA on SIM and the use of wavefront encoding to reduce the effect of SA on the SIM system. Data from the proof-of-concept setup was acquired and compared to the simulation to validate the implementations. Preliminary results demonstrate challenges that need to overcome, in order to be able to assess the impact of this approach on addressing SA satisfactorily. As an alternative approach, an image restoration method is developed and evaluated to improve the performance of SIM when the fringe visibility of the structured light is low, a condition that occurs when the sample is optically thick and/or the modulation frequency is high. Restoration results from simulated and experimental SIM raw images show improved signal to noise ratio (SNR) and adequate optical sectioning in 3D images, in which more details of fine structures are evident compared to results obtained with two existing computational methods.
Download or read book Computational Corrections for Three dimensional Wide Field Fluorescence Microscopy written by Bridget Martha Hanser and published by . This book was released on 2003 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Fluorescence Microscopy for Three Dimensional Reconstruction written by Hayato Ikoma and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: With rapidly increasing computational power, computational fluorescence microscopy is advancing the frontier of biological imaging. Computational algorithms tailored for specific experimental settings are demanded to solve given tasks such as denoising, spectral unmixing, 3D localization and reconstruction, and ptychography. In this thesis, we present the reconstruction of dense and sparse three dimensional fluorescent volumes. In the first half, we present a volumetric reconstruction method designed for 3D fluorescence imaging of biological samples in the low-light regime. Our method deconvolves a captured focal stack through optimization. As deconvolution is an ill-posed problem, the uniqueness of the solution is imposed through regularization. We formulate the objective function as a sum of a data fidelity term and a regularization term, and minimize it using the alternating direction method of multipliers algorithm. The data fidelity is accurately evaluated with a negative log-likelihood function based on a mixed Poisson-Gaussian model of photon shot noise and camera read noise, which are both present in low-light imaging. Among several possible regularization strategies, we show that a Hessian-based regularizer is most effective for describing locally smooth features present in biological specimens. We demonstrate its performance for fixed and live cell imaging, showing its applicability as a tool for biological research. In the second half, we introduce a hybrid optical-electronic computing approach to three dimensional localization microscopy. Driven by artificial intelligence, this approach learns a set of depth-dependent point spread functions (PSFs) and a localization network jointly in an end-to-end fashion, co-designing an optical imaging system and a neural network. We also present a custom grayscale lithography process to fabricate freeform diffractive optical elements that optically implement the designed PSFs and outline several biological experiments with fixed and live cells that demonstrate the efficacy of the proposed computational microscopy approach.
Download or read book Fluorescence Confocal Laser Scanning Microscopy for Three dimensional Imaging of Living Biological Specimens written by David Ray Sandison and published by . This book was released on 1993 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Enabling Real time Light field 3D Fluorescence Microscopy Through Computational Microscopy and Deep Learning written by Josué Page Vizcaíno and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Three dimensional Computational Imaging with Holographic Microscopy Data written by Mohammad Mehdi DaneshPanah and published by . This book was released on 2007 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Optical Phase Imaging written by Cheng Liu and published by Springer Nature. This book was released on 2022-04-11 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, computational optical phase imaging techniques are presented along with Matlab codes that allow the reader to run their own simulations and gain a thorough understanding of the current state-of-the-art. The book focuses on modern applications of computational optical phase imaging in engineering measurements and biomedical imaging. Additionally, it discusses the future of computational optical phase imaging, especially in terms of system miniaturization and deep learning-based phase retrieval.
Download or read book Fourier Ptychographic Imaging written by Guoan Zheng and published by Morgan & Claypool Publishers. This book was released on 2016-06-30 with total page 94 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book demonstrates the concept of Fourier ptychography, a new imaging technique that bypasses the resolution limit of the employed optics. In particular, it transforms the general challenge of high-throughput, high-resolution imaging from one that is coupled to the physical limitations of the optics to one that is solvable through computation. Demonstrated in a tutorial form and providing many MATLAB® simulation examples for the reader, it also discusses the experimental implementation and recent developments of Fourier ptychography. This book will be of interest to researchers and engineers learning simulation techniques for Fourier optics and the Fourier ptychography concept.
Download or read book Fast Image Restoration in Light sheet Fluorescence Microscopy with Extended Depth of Field Using GPUs written by David Castillo Andreo and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Light sheet fluorescence microscopy (LSFM) is used in many biological research experiments that require fast three-dimensional (3D) imaging up to a few volumes per second. Wavefront coding (WFC) microscopy provides LSFM with 3D real-time imaging capabilities introducing a controlled aberration that extends the depth of field (DOF) of the microscope objective. Resulting images, however, are blurred and need to be processed to recover the original sharpness in a CPU-intensive deconvolution which makes real-time visualization unattainable. We present computational tools based on GPU parallel computing to achieve real-time deconvolution and visualization of the images obtained with WFC light-sheet microscopy.
Download or read book Improved Imaging in Three dimensional Fluorescence Microscopy written by Wen-chieh Lin and published by . This book was released on 1993 with total page 97 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book An Experimental and Computational Study of Binary Optical Elements for Aberration Correction in Three dimensional Fluorescence Microscopy written by Christian Kevin Sieracki and published by . This book was released on 1995 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Medical Image Computing and Computer Assisted Intervention MICCAI 2012 written by Nicholas Ayache and published by Springer Science & Business Media. This book was released on 2012-09-22 with total page 807 pages. Available in PDF, EPUB and Kindle. Book excerpt: The three-volume set LNCS 7510, 7511, and 7512 constitutes the refereed proceedings of the 15th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2012, held in Nice, France, in October 2012. Based on rigorous peer reviews, the program committee carefully selected 252 revised papers from 781 submissions for presentation in three volumes. The first volume includes 91 papers organized in topical sections on abdominal imaging, computer-assisted interventions and robotics; computer-aided diagnosis and planning; image reconstruction and enhancement; analysis of microscopic and optical images; computer-assisted interventions and robotics; image segmentation; cardiovascular imaging; and brain imaging: structure, function and disease evolution.
Download or read book Deep Learning Enabled Computational Imaging in Optical Microscopy and Air Quality Monitoring written by Yichen Wu and published by . This book was released on 2019 with total page 182 pages. Available in PDF, EPUB and Kindle. Book excerpt: Exponential advancements in computational resources and algorithms have given birth to the new paradigm in imaging that rely on computation to digitally reconstruct and enhance images. These computational imaging modalities have enabled higher resolution, larger throughput and/or automatic detection capabilities for optical microscopy. An example is lens-less digital holographic microscope, which enables snapshot imaging of volumetric samples over wide field-of-view without using imaging lenses. Recent developments in the field of deep learning have further opened up exciting avenues for computational imaging, which offer unprecedented performance thanks to their capability to robustly learn content-specific complex image priors. This dissertation introduces a novel and universal modeling framework of deep learning -based image reconstruction technique to tackle various challenges in optical microscopic imaging, including digital holography reconstructions and 3D fluorescence microscopy. Firstly, auto-focusing and phase recovery in holography reconstruction are conventionally challenging and time-consuming to digitally perform. A convolutional neural network (CNN) based approach was developed that solves both problems rapidly in parallel, enabling extended depth-of-field holographic reconstruction with significantly improved time complexity from O(mn) to O(1). Secondly, to fuse advantages of snapshot volumetric capability in digital holography and speckle- and artifact-free image contrast in bright-field microscopy, a CNN was used to transform across microscopy modalities from holographic image reconstructions to their equivalent high contrast bright-field microscopic images. Thirdly, 3D fluorescence microscopy generally requires axial scanning. A CNN was trained to learn defocuses of fluorescence and digitally refocusing a single 2D fluorescence image onto user-defined 3D surfaces within the sample volume, which extends depth-of-field of fluorescence microscopy by 20-fold without any axial scanning, additional hardware, or a trade-off of imaging resolution or speed. This enables high-speed volumetric imaging and digital aberration correction for live samples. Based on deep learning powered computational microscopy, a hand-held device was also developed to measure the particulate matters and bio-aerosols in the air using the lens-less digital holographic microscopic imaging geometry. This device, named c-Air, demonstrates accurate, high-throughput and automatic detection, sizing and classification of the particles in the air, which opens new opportunities in deep learning based environmental sensing and personalized and/or distributed air quality monitoring.
Download or read book Analog and Digital Holography with MATLAB written by Georges T. Nehmetallah and published by SPIE-International Society for Optical Engineering. This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Holography is the only truly three-dimensional imaging method available, and MATLAB has become the programming language of choice for engineering and physics students. Whereas most books solely address the theory behind these 3D imaging techniques, this monograph concentrates on the exact code needed to perform complex mathematical and physical operations.
Download or read book Coded Optical Imaging written by Jinyang Liang and published by Springer Nature. This book was released on with total page 697 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Computational Fluorescence Lifetime Imaging Microscopy for Biomedical Sciences written by Yayao Ma and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence lifetime imaging microscopy (FLIM) is a powerful imaging technique that enables the visualization of biological samples at the molecular level by measuring the fluorescence decay rate of fluorescent probes. This provides critical information about molecular interactions, environmental changes, and localization within biological systems. However, creating high-resolution lifetime maps using conventional FLIM systems can be challenging, as it often requires extensive scanning that can significantly lengthen acquisition times. This issue is further compounded in three-dimensional (3D) imaging because it demands additional scanning along the depth axis. To tackle this challenge, we developed two novel computational imaging techniques. The first technique is compressed FLIM based on a compressed sensing scheme. By leveraging the compressibility of biological scenes in a specific domain, we simultaneously record the time-lapse fluorescence decay upon pulsed laser excitation within a large field of view. The resultant system can acquire a widefield fluorescence lifetime image within a single camera exposure, eliminating the motion artifact and minimizing the photobleaching and phototoxicity. The imaging speed, limited only by the readout speed of the camera, is up to 100 Hz. We demonstrated the utility of compressed FLIM in imaging various transient dynamics at the microscopic scale. The second technique is light field tomographic FLIM (LIFT-FLIM). This approach allows for the acquisition of volumetric fluorescence lifetime images in a highly data-efficient manner, significantly reducing the number of scanning steps required compared to conventional point-scanning or line-scanning FLIM imagers. Moreover, LIFT-FLIM enables the measurement of highdimensional data using low-dimensional detectors, which are typically low-cost and feature a higher temporal bandwidth. We demonstrated LIFT-FLIM using a linear single-photon avalanche diode array on various biological systems, showcasing unparalleled single-photon detection sensitivity. Additionally, we expanded the functionality of our method to spectral FLIM and demonstrated its application in high-content multiplexed imaging of lung organoids. LIFT-FLIM has the potential to open up new avenues in both basic and translational biomedical research.
