Author: Bridget Martha HanserPublisher:
ISBN:
Category :
Languages : en
Pages : 396
Book Description
Computational Corrections for Three-dimensional Wide Field Fluorescence Microscopy
Author: Bridget Martha HanserPublisher:
ISBN:
Category :
Languages : en
Pages : 396
Book Description
Coded Computational Illumination and Detection for Three-dimensional Fluorescence Microscopy
Author: Samuel J. YangPublisher:
ISBN:
Category :
Languages : en
Pages :
Book Description
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.
An Experimental and Computational Study of Binary Optical Elements for Aberration Correction in Three-dimensional Fluorescence Microscopy
Author: Christian Kevin SierackiPublisher:
ISBN:
Category : Fluorescence microscopy
Languages : en
Pages : 206
Book Description
Computational Fluorescence Microscopy for Three Dimensional Reconstruction
Author: Hayato IkomaPublisher:
ISBN:
Category :
Languages : en
Pages :
Book Description
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.
Enabling Real-time Light-field 3D Fluorescence Microscopy Through Computational Microscopy and Deep Learning
Author: Josué Page VizcaínoContribution to Three-dimensional Fluorescence Microscopy Imaging Using Wavefront Encoding and Structured Illumination
Author: Nurmohammed PatwaryPublisher:
ISBN:
Category :
Languages : en
Pages :
Book Description
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.
Computational Optical Phase Imaging
Author: Cheng LiuPublisher: Springer Nature
ISBN: 9811916411
Category : Science
Languages : en
Pages : 311
Book Description
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.
Three-dimensional Reconstruction Methods for Micro-rotation Fluorescence Microscopy
Author: Danai LaksameethanasanPublisher:
ISBN: 9789512297542
Category :
Languages : en
Pages : 59
Book Description
Three-dimensional Microscopy
Author: Guide to Yeast Genetics and Molecular and Cell Biology, Part C
Author: Gerald R. FinkPublisher: Gulf Professional Publishing
ISBN: 9780121822545
Category : Science
Languages : en
Pages : 786
Book Description
This volume and its companion, Volume 350, are specifically designed to meet the needs of graduate students and postdoctoral students as well as researchers, by providing all the up-to-date methods necessary to study genes in yeast. Procedures are included that enable newcomers to set up a yeast laboratory and to master basic manipulations. Relevant background and reference information given for procedures can be used as a guide to developing protocols in a number of disciplines. Specific topics addressed in this book include cytology, biochemistry, cell fractionation, and cell biology.