Scalable Image Analysis For Quantitative Microscopy

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Scalable Image Analysis for Quantitative Microscopy

Author : Friedrich Preußer
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (141 download)

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Book Synopsis Scalable Image Analysis for Quantitative Microscopy by : Friedrich Preußer

Download or read book Scalable Image Analysis for Quantitative Microscopy written by Friedrich Preußer and published by . This book was released on 2023* with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Englische Version: Since the invention of the microscope, microscopy images have generated new insights in biomedical research. While in the past these images were used for illustrative purposes, state-of-the-art microscopy images provide quantitative measurements. Moreover, modern microscopes are capable of autonomously producing large image datasets of increasing complexity, rendering manual analysis inefficient if not infeasible. Thus, extracting biologically relevant information from these datasets requires computational analysis using appropriate algorithms and software. While some analysis methods generalize to different microscope set-ups and types of images, others need to be well tailored to a particular problem. In this work, I present two new methods for automated image analysis of microscopy data. First, Fourier ring correlation-based quality estimation (FRC-QE) is a new metric for automated image quality estimation of 3D fluorescence microscopy acquisitions. I benchmarked the method in the context of evaluating clearing efficiency in human brain organoids. FRC-QE automates image quality control, a task that is often performed manually and thereby represents a bottleneck when scaling image-based experiments to thousand or more images. The method can estimate clearing efficiency across experimental replicates and clearing protocols. It generalizes to different microscopy modalities and efficiently scales to thousands of images. Second, I have developed a new method for behavioral imaging of C. elegans larvae. [...].

New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty

Author : Stegmaier, Johannes
Publisher : KIT Scientific Publishing
ISBN 13 : 3731505908
Total Pages : 264 pages
Book Rating : 4.7/5 (315 download)

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Book Synopsis New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty by : Stegmaier, Johannes

Download or read book New Methods to Improve Large-Scale Microscopy Image Analysis with Prior Knowledge and Uncertainty written by Stegmaier, Johannes and published by KIT Scientific Publishing. This book was released on 2017-02-08 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multidimensional imaging techniques provide powerful ways to examine various kinds of scientific questions. The routinely produced data sets in the terabyte-range, however, can hardly be analyzed manually and require an extensive use of automated image analysis. The present work introduces a new concept for the estimation and propagation of uncertainty involved in image analysis operators and new segmentation algorithms that are suitable for terabyte-scale analyses of 3D+t microscopy images.

New Methods to Improve Large-Scale Microscopy Image Analysis With Prior Knowledge and Uncertainty

Author : Johannes Stegmaier
Publisher :
ISBN 13 : 9781013281792
Total Pages : 260 pages
Book Rating : 4.2/5 (817 download)

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Book Synopsis New Methods to Improve Large-Scale Microscopy Image Analysis With Prior Knowledge and Uncertainty by : Johannes Stegmaier

Download or read book New Methods to Improve Large-Scale Microscopy Image Analysis With Prior Knowledge and Uncertainty written by Johannes Stegmaier and published by . This book was released on 2020-10-09 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: Multidimensional imaging techniques provide powerful ways to examine various kinds of scientific questions. The routinely produced data sets in the terabyte-range, however, can hardly be analyzed manually and require an extensive use of automated image analysis. The present work introduces a new concept for the estimation and propagation of uncertainty involved in image analysis operators and new segmentation algorithms that are suitable for terabyte-scale analyses of 3D+t microscopy images. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Quantitative Microscopy and Image Analysis

Author : David J. Diaz
Publisher : ASM International(OH)
ISBN 13 :
Total Pages : 148 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Quantitative Microscopy and Image Analysis by : David J. Diaz

Download or read book Quantitative Microscopy and Image Analysis written by David J. Diaz and published by ASM International(OH). This book was released on 1994 with total page 148 pages. Available in PDF, EPUB and Kindle. Book excerpt: Sponsored by Materials Characterization Committee of Materials Testing and Quality Control Division ASM Publication More precise data for quality control Accurate analysis of complex images Relationship between ultrasonic and metallographic measurements Correlation between 2- and 3- dimensional distributions. Sixteen selected papers examine theories, concepts and recent advances which will help you fill the need for more precise quality control and microstructure evaluation data through automatic image analysis. Computer-aided techniques now allow you to make fast, accurate quantification of morphological features recorded through optical metallography and scanning electron/transmission electron microscopy. Learn how accurate, reproducible measurements are being made from complex images which were previously difficult to analyze. Visual assessment of global properties and correlation with ultrasonic measurements are discussed. Subjects include: Mathematical Morphology Processing, Scanning Probe Microscopy, Infrared Sensing of Weld Penetration, Stereology of Anisotropic Microstructures Digital X-Ray Mapping.

Three-dimensional Quantitative Optical Microscopy Imaging Applied to Large Scale Digital Cell Analysis System

Author : Yuansheng Sun
Publisher :
ISBN 13 :
Total Pages : 242 pages
Book Rating : 4.:/5 (251 download)

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Book Synopsis Three-dimensional Quantitative Optical Microscopy Imaging Applied to Large Scale Digital Cell Analysis System by : Yuansheng Sun

Download or read book Three-dimensional Quantitative Optical Microscopy Imaging Applied to Large Scale Digital Cell Analysis System written by Yuansheng Sun and published by . This book was released on 2007 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Quantitative Imaging in Cell Biology

Author :
Publisher : Academic Press
ISBN 13 : 0124202012
Total Pages : 609 pages
Book Rating : 4.1/5 (242 download)

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Book Synopsis Quantitative Imaging in Cell Biology by :

Download or read book Quantitative Imaging in Cell Biology written by and published by Academic Press. This book was released on 2014-06-25 with total page 609 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume, number 123, of Methods in Cell Biology looks at methods for quantitative imaging in cell biology. It covers both theoretical and practical aspects of using optical fluorescence microscopy and image analysis techniques for quantitative applications. The introductory chapters cover fundamental concepts and techniques important for obtaining accurate and precise quantitative data from imaging systems. These chapters address how choice of microscope, fluorophores, and digital detector impact the quality of quantitative data, and include step-by-step protocols for capturing and analyzing quantitative images. Common quantitative applications, including co-localization, ratiometric imaging, and counting molecules, are covered in detail. Practical chapters cover topics critical to getting the most out of your imaging system, from microscope maintenance to creating standardized samples for measuring resolution. Later chapters cover recent advances in quantitative imaging techniques, including super-resolution and light sheet microscopy. With cutting-edge material, this comprehensive collection is intended to guide researchers for years to come. Covers sections on model systems and functional studies, imaging-based approaches and emerging studies Chapters are written by experts in the field Cutting-edge material

Image Analysis

Author : Donat P. Hader
Publisher : CRC Press
ISBN 13 : 9780849302398
Total Pages : 488 pages
Book Rating : 4.3/5 (23 download)

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Book Synopsis Image Analysis by : Donat P. Hader

Download or read book Image Analysis written by Donat P. Hader and published by CRC Press. This book was released on 2000-08-23 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Automatic image analysis has become an important tool in many fields of biology, medicine, and other sciences. Since the first edition of Image Analysis: Methods and Applications, the development of both software and hardware technology has undergone quantum leaps. For example, specific mathematical filters have been developed for quality enhancement of original images and for extraction of specific features of interest. Also, more complex programs have been developed for the analysis of object forms in distinguishing cancer cells from normal tissue cells. Just as significant, three-dimensional analysis of proteins, organelles, or macroscopic objects is even more complex. In addition, recent space-based experiments have optimized techniques for the extraction of movement parameters of numerous motile objects. The second edition of Image Analysis: Methods and Applications addresses all these new developments. Moreover, two new chapters have been added. One focuses on images on the internet, and the other discusses microscope image restoration. These chapters add significantly to the existing body of information on Internet communication protocol and environment as well as to that on image file formats considerations. The materials also include a list of internet Web sites that pertain to digital images and software along with those that relate to image processing. With these considerations in mind, Image Analysis: Methods and Application, Second Edition is of incalculable value to professionals, academics, and users of all aspects of image analysis in biology and other areas of science.

Computer-Assisted Microscopy

Author : John C. Russ
Publisher : Springer Science & Business Media
ISBN 13 : 1461305632
Total Pages : 461 pages
Book Rating : 4.4/5 (613 download)

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Book Synopsis Computer-Assisted Microscopy by : John C. Russ

Download or read book Computer-Assisted Microscopy written by John C. Russ and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 461 pages. Available in PDF, EPUB and Kindle. Book excerpt: The use of computer-based image analysis systems for all kinds of images, but especially for microscope images, has become increasingly widespread in recent years, as computer power has increased and costs have dropped. Software to perform each of the various tasks described in this book exists now, and without doubt additional algorithms to accomplish these same things more efficiently, and to perform new kinds of image processing, feature discrimination and measurement, will continue to be developed. This is likely to be true particularly in the field of three-dimensional imaging, since new microscopy methods are beginning to be used which can produce such data. It is not the intent of this book to train programmers who will assemble their own computer systems and write their own programs. Most users require only the barest of knowledge about how to use the computer, but the greater their understanding of the various image analysis operations which are possible, their advantages and limitations, the greater the likelihood of success in their application. Likewise, the book assumes little in the way of a mathematical background, but the researcher with a secure knowledge of appropriate statistical tests will find it easier to put some of these methods into real use, and have confidence in the results, than one who has less background and experience. Supplementary texts and courses in statistics, microscopy, and specimen preparation are recommended as necessary.

Scalable Interactive Visualization

Author : Achim Ebert
Publisher : MDPI
ISBN 13 : 3038428035
Total Pages : 245 pages
Book Rating : 4.0/5 (384 download)

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Book Synopsis Scalable Interactive Visualization by : Achim Ebert

Download or read book Scalable Interactive Visualization written by Achim Ebert and published by MDPI. This book was released on 2018-05-08 with total page 245 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "Scalable Interactive Visualization" that was published in Informatics

Digital Image Analysis of Microbes

Author : M. H. F. Wilkinson
Publisher : John Wiley & Sons
ISBN 13 : 9780471974406
Total Pages : 588 pages
Book Rating : 4.9/5 (744 download)

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Book Synopsis Digital Image Analysis of Microbes by : M. H. F. Wilkinson

Download or read book Digital Image Analysis of Microbes written by M. H. F. Wilkinson and published by John Wiley & Sons. This book was released on 1998-06-08 with total page 588 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing specific knowledge in the theory of image analysis, optics, fluorescence, and imaging devices in biomedical laboratories, this timely and indispensable volume focuses on the theory and applications of detection, morphometry, and motility measurement techniques applied to bacteria, fungi, yeasts and protozoa.

Microscope Image Processing

Author : Qiang Wu
Publisher : Elsevier
ISBN 13 : 0080558542
Total Pages : 585 pages
Book Rating : 4.0/5 (85 download)

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Book Synopsis Microscope Image Processing by : Qiang Wu

Download or read book Microscope Image Processing written by Qiang Wu and published by Elsevier. This book was released on 2010-07-27 with total page 585 pages. Available in PDF, EPUB and Kindle. Book excerpt: Digital image processing, an integral part of microscopy, is increasingly important to the fields of medicine and scientific research. This book provides a unique one-stop reference on the theory, technique, and applications of this technology. Written by leading experts in the field, this book presents a unique practical perspective of state-of-the-art microscope image processing and the development of specialized algorithms. It contains in-depth analysis of methods coupled with the results of specific real-world experiments. Microscope Image Processing covers image digitization and display, object measurement and classification, autofocusing, and structured illumination. Key Features: Detailed descriptions of many leading-edge methods and algorithms In-depth analysis of the method and experimental results, taken from real-life examples Emphasis on computational and algorithmic aspects of microscope image processing Advanced material on geometric, morphological, and wavelet image processing, fluorescence, three-dimensional and time-lapse microscopy, microscope image enhancement, MultiSpectral imaging, and image data management This book is of interest to all scientists, engineers, clinicians, post-graduate fellows, and graduate students working in the fields of biology, medicine, chemistry, pharmacology, and other related fields. Anyone who uses microscopes in their work and needs to understand the methodologies and capabilities of the latest digital image processing techniques will find this book invaluable. Presents a unique practical perspective of state-of-the-art microcope image processing and the development of specialized algorithms Each chapter includes in-depth analysis of methods coupled with the results of specific real-world experiments Co-edited by Kenneth R. Castleman, world-renowned pioneer in digital image processing and author of two seminal textbooks on the subject

Microscopic Image Analysis for Life Science Applications

Author : Jens Rittscher
Publisher : Artech House
ISBN 13 : 1596932376
Total Pages : 533 pages
Book Rating : 4.5/5 (969 download)

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Book Synopsis Microscopic Image Analysis for Life Science Applications by : Jens Rittscher

Download or read book Microscopic Image Analysis for Life Science Applications written by Jens Rittscher and published by Artech House. This book was released on 2008 with total page 533 pages. Available in PDF, EPUB and Kindle. Book excerpt: Here's a first-of-its-kind book that bridges the gap between biomedical imaging and the bioscience community. This unique resource gives you a detailed understanding of imaging platforms, fluorescence imaging, and fundamental image processing algorithms. Further, it guides you through application of advanced image analysis methods and techniques to specific biological problems. The book presents applications that span a wide range of scales, from the detection of signaling events in sub-cellular structures, to the automated analysis of tissue structures. Other critical areas discussed include the dynamics of cell populations and in vivo microscopy. This cutting-edge volume is supported with over 160 illustrations that support key topics throughout the book. CD-ROM Included! Contains full-color images and videos that further illustrate topics discussed in the book.

Quantitative Image Analysis of Microstructures

Author : Hans Eckart Exner
Publisher : I R Publications, Limited
ISBN 13 :
Total Pages : 260 pages
Book Rating : 4.:/5 (318 download)

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Book Synopsis Quantitative Image Analysis of Microstructures by : Hans Eckart Exner

Download or read book Quantitative Image Analysis of Microstructures written by Hans Eckart Exner and published by I R Publications, Limited. This book was released on 1988 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt:

The Image Processing Handbook

Author : John C. Russ
Publisher : CRC Press
ISBN 13 : 1498740286
Total Pages : 1035 pages
Book Rating : 4.4/5 (987 download)

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Book Synopsis The Image Processing Handbook by : John C. Russ

Download or read book The Image Processing Handbook written by John C. Russ and published by CRC Press. This book was released on 2018-09-03 with total page 1035 pages. Available in PDF, EPUB and Kindle. Book excerpt: Consistently rated as the best overall introduction to computer-based image processing, The Image Processing Handbook covers two-dimensional (2D) and three-dimensional (3D) imaging techniques, image printing and storage methods, image processing algorithms, image and feature measurement, quantitative image measurement analysis, and more. Incorporating image processing and analysis examples at all scales, from nano- to astro-, this Seventh Edition: Features a greater range of computationally intensive algorithms than previous versions Provides better organization, more quantitative results, and new material on recent developments Includes completely rewritten chapters on 3D imaging and a thoroughly revamped chapter on statistical analysis Contains more than 1700 references to theory, methods, and applications in a wide variety of disciplines Presents 500+ entirely new figures and images, with more than two-thirds appearing in color The Image Processing Handbook, Seventh Edition delivers an accessible and up-to-date treatment of image processing, offering broad coverage and comparison of algorithms, approaches, and outcomes.

Image Analysis in Histology

Author : Richard Wootton
Publisher : CUP Archive
ISBN 13 : 9780521434829
Total Pages : 466 pages
Book Rating : 4.4/5 (348 download)

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Book Synopsis Image Analysis in Histology by : Richard Wootton

Download or read book Image Analysis in Histology written by Richard Wootton and published by CUP Archive. This book was released on 1995-05-11 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a timely and useful introduction to the theory and practical application of image analysis in histology. This powerful research technique can be used to detect not only stored products in a cell (immunocytochemistry) but the synthetic machinery and the genes that control it (in situ hybridisation), as well as the specific binding sites that act as receptors for a molecule following its release (in vitro autoradiography). The book provides a good introduction for beginners before looking in greater detail at more advanced material in selected areas. The volume highlights the importance of technique in gathering quantitative information. The book is divided into four sections: introductory material, image acquisition, image processing, and applications. The applications areas include quantitative immunochemistry, quantification of nerves and neurotransmitters and automated grain counting in in situ hybridisation histochemistry.

Proceedings of the 2021 Indiana O’Brien Center Microscopy Workshop

Author : Bruce Molitoris
Publisher : Frontiers Media SA
ISBN 13 : 2889762300
Total Pages : 79 pages
Book Rating : 4.8/5 (897 download)

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Book Synopsis Proceedings of the 2021 Indiana O’Brien Center Microscopy Workshop by : Bruce Molitoris

Download or read book Proceedings of the 2021 Indiana O’Brien Center Microscopy Workshop written by Bruce Molitoris and published by Frontiers Media SA. This book was released on 2022-05-26 with total page 79 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Expansion Microscopy

Author : Fei Chen (Ph. D.)
Publisher :
ISBN 13 :
Total Pages : 107 pages
Book Rating : 4.:/5 (1 download)

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Book Synopsis Expansion Microscopy by : Fei Chen (Ph. D.)

Download or read book Expansion Microscopy written by Fei Chen (Ph. D.) and published by . This book was released on 2017 with total page 107 pages. Available in PDF, EPUB and Kindle. Book excerpt: Microscopy has facilitated the discovery of many biological insights by optically magnifying small structures in cells and tissues. However, the resolution of optical microscopy is limited by the diffraction of light to ~200-300 nm, comparable or larger to the size of many subcellular structures. In this thesis, we describe a suite of tools based on a novel super-resolution microscopy approach called Expansion microscopy. Expansion microscopy (ExM) physically expands tissues so that the resolution of ordinary microscopes is increased -5 times by leveraging the swelling properties of polyelectrolyte hydrogels. Ordinary microscopes used with ExM are more accessible and faster than the specialized optical systems designed to image beyond the diffraction limit (e.g., STORM/PALM, STED, SIM), while yielding similar performance. Expanded tissues are also optically clear, allowing for unprecedented super-resolution imaging in thick tissues and facile reagent diffusion into the sample. We have since developed a variant of ExM, called protein retention ExM, in which proteins are directly anchored to the swellable gel using a commercially available cross-linking molecule. This strategy enables ExM of genetically encoded fluorescent proteins and commercial fluorescently labeled secondary antibodies. With these advancements, ExM can be carried out with purely commercial reagents and represents a simple extension of standard histological methods used to prepare samples for imaging. Furthermore, we have developed a variant of the ExM technology that enables RNA molecules to be directly linked to the ExM gel network via a small molecule linker and isotropic expansion. This technology, termed ExFISH, enables visualization of RNAs with nanoscale precision and single molecule resolution. We have demonstrated that the covalent anchoring of RNA also enables robust repeated washing and probe hybridization steps, opening the door to combinatorial multiplexing strategies. By leveraging these benefits, we have further developed in situ analysis tools which allow for highly multiplexed imaging of RNA identity and location with nanoscale precision in intact tissues. Taken together, these tools allow for spatially mapping molecular information onto cell types and tissue structures which could be invaluable for spatially complex biological processes such as brain function, cancer heterogeneity and organismal development.