Download or read book Optical Methods for Deep tissue Imaging Precise Mapping of Cellular Topography and Single molecule Stoichiometry Analysis written by Avtar Singh and published by . This book was released on 2016 with total page 516 pages. Available in PDF, EPUB and Kindle. Book excerpt: Fluorescence microscopy and spectroscopy have proven crucial to biological investigations because of their superior contrast, molecular specificity, gentle nature and diverse information content. However, despite these key advantages, the technologies are continually evolving to address limitations in spatiotemporal resolution, imaging depth, quantification, multiplexing and other areas. This thesis describes wide-ranging efforts to understand the capabilities of fluorescence-based methods and to push the boundaries of biophysical measurement through new instrumentation and analysis strategies. We begin with an investigation into the depth limit of two-photon microscopy and its dependence on tissue scattering. A customized sample cell and two-detector measurement chamber are used to study the influence of fundamental objective lens parameters on fluorescence excitation and emission in turbid media. The results advocate the use of large field-of-view objectives with low excitation numerical aperture (NA) and high collection NA, encouraging the development of novel detection geometries and objective lens designs that decouple these latter two parameters. The advent of super-resolution imaging has inspired a surge of innovation aimed at combatting longstanding problems in the field of microscopy. One especially challenging goal has been to develop methods with molecular-scale precision in the axial dimension. While interferometric approaches such as scanning angle interference microscopy (SAIM) have yielded the necessary precision, their ability to capture livecell dynamics has remained limited. A second project details an azimuthal scanning platform that boosts SAIM temporal resolution by an order of magnitude without compromising on spatial information. Furthermore, our scanning instrumentation serves as versatile platform for general-purpose quantitative biological imaging. A major caveat of single molecule imaging is the in vitro nature of many experiments. A third set of experiments aims to bridge the gap between traditional single molecule work and a biological relevant setting. We develop a new strategy to assemble protein complexes at physiological concentrations and dilute them to single molecule levels without any exogenous chemical agents. Fluorescence correlation spectroscopy and stepwise photobleaching are then used to study the oligomeric character of individual complexes without removing them from their native environment. Although we demonstrate the utility of our approach through subunit stoichiometry measurements, it represents a generalizable strategy to extend single molecule imaging to the cellular mileu.
Download or read book Handbook of Tissue Optical Clearing written by Valery V. Tuchin and published by CRC Press. This book was released on 2022-02-04 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biomedical photonics is currently one of the fastest growing fields, connecting research in physics, optics, and electrical engineering coupled with medical and biological applications. It allows for the structural and functional analysis of tissues and cells with resolution and contrast unattainable by any other methods. However, the major challenges of many biophotonics techniques are associated with the need to enhance imaging resolution even further to the sub-cellular level as well as translate them for in vivo studies. The tissue optical clearing method uses immersion of tissues into optical clearing agents (OCAs) that reduces the scattering of tissue and makes tissue more transparent and this method has been successfully used ever since. This book is a self-contained introduction to tissue optical clearing, including the basic principles and in vitro biological applications, from in vitro to in vivo tissue optical clearing methods, and combination of tissue optical clearing and various optical imaging for diagnosis. The chapters cover a wide range of issues related to the field of tissue optical clearing: mechanisms of tissue optical clearing in vitro and in vivo; traditional and innovative optical clearing agents; recent achievements in optical clearing of different tissues (including pathological tissues) and blood for optical imaging diagnosis and therapy. This book provides a comprehensive account of the latest research and possibilities of utilising optical clearing as an instrument for improving the diagnostic effectiveness of modern optical diagnostic methods. The book is addressed to biophysicist researchers, graduate students and postdocs of biomedical specialties, as well as biomedical engineers and physicians interested in the development and application of optical methods in medicine. Key features: The first collective reference to collate all known knowledge on this topic Edited by experts in the field with chapter contributions from subject area specialists Brings together the two main approaches in immersion optical clearing into one cohesive book
Download or read book Advanced Biophotonics written by Ruikang K. Wang and published by CRC Press. This book was released on 2013-07-23 with total page 735 pages. Available in PDF, EPUB and Kindle. Book excerpt: Despite a number of books on biophotonics imaging for medical diagnostics and therapy, the field still lacks a comprehensive imaging book that describes state-of-the-art biophotonics imaging approaches intensively developed in recent years. Addressing this shortfall, Advanced Biophotonics: Tissue Optical Sectioning presents contemporary methods and applications of biophotonics imaging. Gathering research otherwise scattered in numerous physical, chemical, biophysical, and biomedical journals, the book helps researchers, bioengineers, and medical doctors understand major recent bioimaging technologies and the underlying biophotonics science. Well-known international experts explore a variety of "hot" biomedical optics and biophotonics problems, including the use of photoacoustic imaging to investigate the molecular and cellular processes in living systems. The book also covers Monte Carlo modeling, tissue optics and tissue optical clearing, nonlinear optical microscopy, various aspects of optical coherence tomography, multimodal tomography, adaptive optics, and signal imaging. With 58 color images, this book represents a valuable contribution to the biomedical and biophotonics literature. Designed for researchers and practitioners in biophotonics, the book is also a useful resource for scientists in laser physics and technology, fiber optics, spectroscopy, materials science, biology, and medicine as well as students studying biomedical physics and engineering, biomedical optics, and biophotonics.
Download or read book Imaging from Cells to Animals In Vivo written by Margarida Barroso and published by CRC Press. This book was released on 2020-12-03 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book offers an overview of imaging techniques used to investigate cells and tissue in their native environment. It covers the range of imaging approaches used, as well as the application of those techniques to the study of biological processes in cells and whole tissues within living organisms.
Download or read book Optical Imaging Techniques in Cell Biology Second Edition written by Guy Cox and published by CRC Press. This book was released on 2012-06-04 with total page 319 pages. Available in PDF, EPUB and Kindle. Book excerpt: Optical Imaging Techniques in Cell Biology, Second Edition covers the field of biological microscopy, from the optics of the microscope to the latest advances in imaging below the traditional resolution limit. It includes the techniques—such as labeling by immunofluorescence and fluorescent proteins—which have revolutionized cell biology. Quantitative techniques such as lifetime imaging, ratiometric measurement, and photoconversion are all covered in detail. Expanded with a new chapter and 40 new figures, the second edition has been updated to cover the latest developments in optical imaging techniques. Explanations throughout are accurate, detailed, but as far as possible non-mathematical. This edition includes appendices with useful practical protocols, references, and suggestions for further reading. Color figures are integrated throughout.
Download or read book Optical Imaging in Human Disease and Biological Research written by Xunbin Wei and published by Springer Nature. This book was released on 2021-05-29 with total page 309 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book introduces readers to the basic principle of optical imaging technologies. Focusing on human disease diagnostics using optical imaging methods, it provides essential information for researchers in various fields and discusses the latest trends in optical imaging. In recent decades, there has been a huge increase in imaging technologies and their applications in human diseases diagnostics, including magnetic resonance imaging, x-ray computed tomography, and nuclear tomographic imaging. This book promotes further developments to extend optical imaging to a wider range of disease diagnostics. It is a valuable resource for researchers and students in the field of biomedical optics, as well as for clinicians.
Download or read book Diffuse Optical Tomography written by Huabei Jiang and published by CRC Press. This book was released on 2018-09-03 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by an authority involved in the field since its nascent stages, Diffuse Optical Tomography: Principles and Applications is a long-awaited profile of a revolutionary imaging method. Diffuse Optical Tomography (DOT) provides spatial distributions of intrinsic tissue optical properties or molecular contrast agents through model-based reconstruction algorithms using NIR measurements along or near the boundary of tissue. Despite the practical value of DOT, many engineers from electrical or applied mathematics backgrounds do not have a sufficient understanding of its vast clinical applications and portability value, or its uncommon advantages as a tool for obtaining functional, cellular, and molecular parameters. A collection of the author’s research and experience, this book fuses historical perspective and experiential anecdotes with fundamental principles and vital technical information needed to successfully apply this technology—particularly in medical imaging. This reference finally outlines how to use DOT to create experimental image systems and adapt the results of laboratory studies for use in clinical applications including: Early-stage detection of breast tumors and prostate cancer "Real-time" functional brain imaging Joint imaging to treat progressive diseases such as arthritis Monitoring of tumor response New contrast mechanisms and multimodality methods This book covers almost every aspect of DOT—including reconstruction algorithms based on nonlinear iterative Newton methods, instrumentation and calibration methods in both continuous-wave and frequency domains, and important issues of imaging contrast and spatial resolution. It also addresses phantom experiments and the development of various image-enhancing schemes, and it describes reconstruction methods based on contrast agents and fluorescence DOT. Offering a concise description of the particular problems involved in optical tomography, this reference illustrates DOT’s fundamental foundations and the principle of image reconstruction. It thoroughly explores computational methods, forward mathematical models, and inverse strategies, clearly illustrating solutions to key equations.
Download or read book Multimodal Optical Diagnostics of Cancer written by Valery V. Tuchin and published by Springer Nature. This book was released on 2020-10-23 with total page 605 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an in-depth description and discussion of different multi-modal diagnostic techniques for cancer detection and treatment using exact optical methods, their comparison, and combination. Coverage includes detailed descriptions of modern state of design for novel methods of optical non-invasive cancer diagnostics; multi-modal methods for earlier cancer diagnostic enhancing the probability of effective cancer treatment; modern clinical trials with novel methods of clinical cancer diagnostics; medical and technical aspects of clinical cancer diagnostics, and long-term monitoring. Biomedical engineers, cancer researchers, and scientists will find the book to be an invaluable resource. Introduces optical imaging strategies; Focuses on multimodal optical diagnostics as a fundamental approach; Discusses novel methods of optical non-invasive cancer diagnostics.
Download or read book Engineering New Capabilities Into Optical Microscopes written by Matthew D. Lew and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The labeling of specific biological structures with single fluorescent molecules has ushered in a new era of imaging technology: super-resolution optical microscopy with resolution far beyond the diffraction limit down to some tens of nm. With the features of these exquisite tools in mind, this Dissertation discusses optical strategies for measuring the three-dimensional (3D) position and orientation of single molecules with nanoscale precision and several super-resolution imaging studies of structures in living cells. The concepts of single-molecule imaging, super-resolution microscopy, the engineering of optical point spread functions (PSFs), and quantitative analysis of single-molecule fluorescence images are introduced. The various computational methods and experimental apparatuses developed during the course of my graduate work are also discussed. Next, a new engineered point spread function, called the Corkscrew PSF, is shown for 3D imaging of point-like emitters. This PSF has been demonstrated to measure the location of nanoscale objects with 2-6 nm precision in 3D throughout a 3.2-micrometer depth range. Characterization and application of the Double-Helix (DH) PSF for super-resolution imaging of structures within mammalian and bacterial cells is discussed. The DH-PSF enables 3D single-molecule imaging within living cells with precisions of tens of nanometers throughout a ~2-micrometer depth range. Finally, the impact of single-molecule emission patterns and molecular orientation on optical imaging is treated, with particular emphasis on multiple strategies for improving the accuracy of super-resolution imaging. The DH microscope is shown to be well-suited for accurately and simultaneously measuring the 3D position and orientation of single molecules.
Download or read book Computational Optical Biomedical Spectroscopy and Imaging written by Sarhan M. Musa and published by CRC Press. This book was released on 2015-01-28 with total page 437 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational Optical Biomedical Spectroscopy and Imaging covers recent discoveries and research in the field by some of the best inventors and researchers in the world. It also presents useful computational methods and applications used in optical biomedical spectroscopy and imaging. Topics covered include:New trends in immunohistochemical, genome
Download or read book Single molecule Localization Microscopy and Applications to Visualize the Accessible Genome with ATAC see written by Maurice Youzong Lee and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: It has been thirty years since the first experimental observation of a single molecule, and thirteen years since the first few single-molecule super-resolution fluorescence microscopy methods were first published. Since these two key milestones, scientists have been developing and applying new optical methods to better understand the world around us, whether it is in crystals at cryogenic temperatures or in the crowded environment within living cells. In single-molecule localization microscopy, we first use fluorescent molecules to label the biological structure we are interested in studying. Next, instead of imaging all the fluorescent molecules at the same time in a single camera frame, we can use chemical means to make the molecules stochastically blink on and off. In this manner, instead of separating the overlapping fluorescent spots (or point spread functions) from each single emitter in space, we can now separate them temporally. Next, we can perform a process called superlocalization to measure their precise molecular coordinates in each camera frame, before recombining them spatially to create a super-resolution reconstruction. In my dissertation, I will describe how I have developed new capabilities for single-molecule localization microscopy and how I combined our super-resolution imaging methods with a new accessible chromatin labeling scheme to try to image the accessible genome in the nucleus. First, I will describe my attempts in using an engineered point spread function (PSF) called the corkscrew PSF to image labeled structures in 3D, but with a faster acquisition rate with a higher density of emitters per camera frame and fewer overlapping PSFs as compared to other engineered PSFs. From my work, I found that we had to use real-time Z drift correction to ensure that the amount of spherical aberration in our optical systems do not change while imaging a sample. A varying amount of spherical aberration changes the behavior of the corkscrew PSF over the imaging period which makes it challenging to accurately and precisely measure the locations of the emitters. Second, I will describe how I have fabricated a transmissive fixed dielectric phase mask that encodes for the Tetrapod PSF for use in our 4f optical systems. Microfabrication is a process that has to be done properly to create a functioning end product. I have tried to describe it with as many details as possible in Chapter 4. The fixed phase masks that I fabricated encode for a Tetrapod PSF that has an effective working axial range of 6 μm and work for emission wavelengths of 660 nm or 550 nm, and they have been used in multiple projects in the lab that resulted in several publications. Finally, I will describe how I have used our super-resolution imaging methods to visualize the accessible genome in the nucleus that has been labeled with a biochemical labeling method known as Assay of Transposase-Accessible Chromatin with visualization (ATAC-see). The two-meter long human genome is heavily compacted into a ten-micron-wide nucleus. But a part of the genome has to remain accessible to the biomolecular machinery that carry out gene regulation, transcription, and DNA repair. It would be useful if we could image the accessible genome within the nucleus and compare this map of accessible chromatin with other maps of labeled biomolecules. ATAC-see labels accessible chromatin in the nucleus with fluorophores. We can image the labeled fluorescence distribution with single-molecule localization microscopy to obtain super-resolution images of the underlying structure of accessible chromatin in the nucleus. This project had many twists and turns but I did make several interesting observations that may help to improve the ATAC-see labeling method so that future scientists may be able to accurately and reproducibly image the accessible genome in the nucleus. One observation was that ATAC-see appears to preferentially label the periphery of the nucleus. Another observation is that the Tn5 monomers do not readily dimerize after binding to the fluorescently-labeled dsDNA sequencing adapters. This greatly reduces the concentration of effective labels by about 30 times. Two ways to promote dimerization may be to use a peptide linker to connect two Tn5 monomers together or to connect the dsDNA sequencing adapters via extending the "reverse" strand.
Download or read book Tissue Optics written by Valeriĭ Viktorovich Tuchin and published by SPIE-International Society for Optical Engineering. This book was released on 2000 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt: This tutorial text explores light-scattering techniques developed for studies of tissues and optical cell ensembles. It discusses results of theoretical and experimental investigations into photon transport in tissues and describes methods for solving direct and inverse scattering problems involving different types of tissues and fluids (opaque vs transparent).
Download or read book Optical Methods in Cell Physiology written by Paul De Weer and published by Wiley-Interscience. This book was released on 1986 with total page 506 pages. Available in PDF, EPUB and Kindle. Book excerpt: A book for physiologists, biologists and biochemists studying cell physiology. Included are major optical techniques and bases for designing experiments and choosing appropriate instrumentation, along with discussions on methods and results of optical techniques applied to research through image enhancement, probes for membrane potential, intracellular indicators for Ca and pH, and photobleaching and photoactivation techniques. Also included are schematic drawings and numerous references.
Download or read book Comprehensive Biophysics written by and published by Academic Press. This book was released on 2012-04-12 with total page 3533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biophysics is a rapidly-evolving interdisciplinary science that applies theories and methods of the physical sciences to questions of biology. Biophysics encompasses many disciplines, including physics, chemistry, mathematics, biology, biochemistry, medicine, pharmacology, physiology, and neuroscience, and it is essential that scientists working in these varied fields are able to understand each other's research. Comprehensive Biophysics, Nine Volume Set will help bridge that communication gap. Written by a team of researchers at the forefront of their respective fields, under the guidance of Chief Editor Edward Egelman, Comprehensive Biophysics, Nine Volume Set provides definitive introductions to a broad array of topics, uniting different areas of biophysics research - from the physical techniques for studying macromolecular structure to protein folding, muscle and molecular motors, cell biophysics, bioenergetics and more. The result is this comprehensive scientific resource - a valuable tool both for helping researchers come to grips quickly with material from related biophysics fields outside their areas of expertise, and for reinforcing their existing knowledge. Biophysical research today encompasses many areas of biology. These studies do not necessarily share a unique identifying factor. This work unites the different areas of research and allows users, regardless of their background, to navigate through the most essential concepts with ease, saving them time and vastly improving their understanding The field of biophysics counts several journals that are directly and indirectly concerned with the field. There is no reference work that encompasses the entire field and unites the different areas of research through deep foundational reviews. Comprehensive Biophysics fills this vacuum, being a definitive work on biophysics. It will help users apply context to the diverse journal literature offering, and aid them in identifying areas for further research Chief Editor Edward Egelman (E-I-C, Biophysical Journal) has assembled an impressive, world-class team of Volume Editors and Contributing Authors. Each chapter has been painstakingly reviewed and checked for consistent high quality. The result is an authoritative overview which ties the literature together and provides the user with a reliable background information and citation resource
Download or read book Deep Tissue Imaging with Short wave Infrared Light and Adaptive Optics written by Fei Xia and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Imaging with high spatial resolution and high specificity within intact tissues at depth has long been a critical research objective for implementation in biological studies. The development of imaging tools with the capability of deep imaging at cellular resolution would allow for more realistic and complicated biological hypotheses to be tested in their natural environment - intravitally. The most challenging aspects of such tool developments involve light scattering and aberration, which cause the light to distort along its propagation direction, limiting both its imaging depth and resolution. This thesis attempts to provide several solutions to overcomes these challenges. To overcome light scattering, imaging within the short-wave infrared region (SWIR, wavelength 1 - 2.5 micrometers) is explored in chapters 2-4. In chapter 2 and 3, reflectance confocal and fluorescence confocal microscopy are demonstrated providing 2-4 times deeper penetration than any previously reported work and preclude the possibility of using one-photon confocal microscopy for deep imaging, a method that has been rarely discussed. Furthermore, a study on the impact of staining inhomogeneity on the depth limit of fluorescence confocal microscopy also demonstrated the potential of confocal microscopy combined with SWIR and low staining inhomogeneity to achieve unprecedented imaging depth. After demonstrating the deep imaging capability of one-photon imaging at depth with a SWIR light source, a multimodal system combining three-photon, third-harmonic, and optical coherence microscopy (OCM) is demonstrated in chapter 4. This multimodal system was able to achieve simultaneous imaging depth comparable to imaging with multiple contrast mechanisms in terms of the fluorescence, the harmonic signal, and the backscattering. Furthermore, this multimodal system provided complementary information about the mouse in vivo and represented a powerful intravital biological imaging tool. To overcome light aberration, adaptive optical methods are demonstrated in chapters 5-7. In chapter 5, a sensorless, adaptive optics, and indirect wavefront sensing system is demonstrated to improve SWIR-excited three-photon imaging, achieving about 7x signal enhancement in the mouse hippocampus area. This method is based on using the nonlinear three-photon fluorescence signal as feedback and involves light exposure during the optimization process. To reduce light exposure, a more direct wavefront sensing method is explored using a SWIR OCM system to directly sense the complex field of a biological sample in chapter 6. The advantage of this system, including its potential high-speed wavefront sensing and offline wavefront estimation, and its limitations with respect to phase stability are discussed. Finally, in chapter 7, a direct wavefront sensing method based on a cheap silicon wavefront sensor is presented. This method provides a convenient approach for aberration measurement with any experiment that involves SWIR ultrafast laser. This thesis shows the great promise to achieve high-resolution deep tissue imaging at a larger depth by combining longer wavelength at short-wave infrared region and adaptive optics. It is anticipated that this thesis work will open doors to much more exciting biological research in the near future.
Download or read book Cell Imaging Techniques written by Douglas Taatjes and published by Humana Press. This book was released on 2012-10-02 with total page 550 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cell Imaging is rapidly evolving as new technologies and new imaging advances continue to be introduced. In the second edition of Cell Imaging Techniques: Methods and Protocols expands upon the previous editions with current techniques that includes confocal microscopy, transmission electron microscopy, atomic force microscopy, and laser microdissection. With new chapters covering colocalization analysis of fluorescent probes, correlative light and electron microscopy, environmental scanning electron microscopy, light sheet microscopy, intravital microscopy, high throughput microscopy, and stereological techniques. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls Authoritative and cutting-edge, Cell Imaging Techniques: Methods and Protocols, Second Edition is an easily accessible volume of protocols to be used with a variety of imaging-based equipment likely available in a core imaging facility.
Download or read book Handbook of Coherent Domain Optical Methods written by Valeriĭ Viktorovich Tuchin and published by Birkhäuser. This book was released on with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt:
