Bioimage Data Analysis Workflows Advanced Components And Methods

Author : Kota Miura,Nataša Sladoje
Publisher : Springer Nature
Page : 218 pages
File Size : 44,6 Mb
Release : 2022-09-28
Category : Science
ISBN : 9783030763947

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Bioimage Data Analysis Workflows ‒ Advanced Components and Methods by Kota Miura,Nataša Sladoje Pdf

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images.

Author : Kota Miura,Nataša Sladoje
Publisher : Springer Nature
Page : 178 pages
File Size : 52,9 Mb
Release : 2019-10-17
Category : Medical
ISBN : 9783030223861

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Bioimage Data Analysis Workflows by Kota Miura,Nataša Sladoje Pdf

This Open Access textbook provides students and researchers in the life sciences with essential practical information on how to quantitatively analyze data images. It refrains from focusing on theory, and instead uses practical examples and step-by step protocols to familiarize readers with the most commonly used image processing and analysis platforms such as ImageJ, MatLab and Python. Besides gaining knowhow on algorithm usage, readers will learn how to create an analysis pipeline by scripting language; these skills are important in order to document reproducible image analysis workflows. The textbook is chiefly intended for advanced undergraduates in the life sciences and biomedicine without a theoretical background in data analysis, as well as for postdocs, staff scientists and faculty members who need to perform regular quantitative analyses of microscopy images.

Author : Natasa Sladoje,Kota Miura
Publisher : Unknown
Page : 176 pages
File Size : 40,6 Mb
Release : 2020-10-08
Category : Science
ISBN : 1013271920

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Bioimage Data Analysis Workflows by Natasa Sladoje,Kota Miura Pdf

This Open Access textbook provides students and researchers in the life sciences with essential practical information on how to quantitatively analyze data images. It refrains from focusing on theory, and instead uses practical examples and step-by step protocols to familiarize readers with the most commonly used image processing and analysis platforms such as ImageJ, MatLab and Python. Besides gaining knowhow on algorithm usage, readers will learn how to create an analysis pipeline by scripting language; these skills are important in order to document reproducible image analysis workflows. The textbook is chiefly intended for advanced undergraduates in the life sciences and biomedicine without a theoretical background in data analysis, as well as for postdocs, staff scientists and faculty members who need to perform regular quantitative analyses of 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.

Author : Ann Wheeler,Ricardo Henriques
Publisher : John Wiley & Sons
Page : 312 pages
File Size : 51,7 Mb
Release : 2017-10-12
Category : Science
ISBN : 9781119096924

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Standard and Super-Resolution Bioimaging Data Analysis by Ann Wheeler,Ricardo Henriques Pdf

A comprehensive guide to the art and science of bioimaging data acquisition, processing and analysis Standard and Super-Resolution Bioimaging Data Analysis gets newcomers to bioimage data analysis quickly up to speed on the mathematics, statistics, computing hardware and acquisition technologies required to correctly process and document data. The past quarter century has seen remarkable progress in the field of light microscopy for biomedical science, with new imaging technologies coming on the market at an almost annual basis. Most of the data generated by these systems is image-based, and there is a significant increase in the content and throughput of these imaging systems. This, in turn, has resulted in a shift in the literature on biomedical research from descriptive to highly-quantitative. Standard and Super-Resolution Bioimaging Data Analysis satisfies the demand among students and research scientists for introductory guides to the tools for parsing and processing image data. Extremely well illustrated and including numerous examples, it clearly and accessibly explains what image data is and how to process and document it, as well as the current resources and standards in the field. A comprehensive guide to the tools for parsing and processing image data and the resources and industry standards for the biological and biomedical sciences Takes a practical approach to image analysis to assist scientists in ensuring scientific data are robust and reliable Covers fundamental principles in such a way as to give beginners a sound scientific base upon which to build Ideally suited for advanced students having only limited knowledge of the mathematics, statistics and computing required for image data analysis An entry-level text written for students and practitioners in the bioscience community, Standard and Super-Resolution Bioimaging Data Analysis de-mythologises the vast array of image analysis modalities which have come online over the past decade while schooling beginners in bioimaging principles, mathematics, technologies and standards.

Author : Florian Levet,Florian Jug,Virginie Uhlmann
Publisher : Frontiers Media SA
Page : 147 pages
File Size : 55,9 Mb
Release : 2022-06-23
Category : Science
ISBN : 9782889764068

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Methods and Tools for Bioimage Analysis by Florian Levet,Florian Jug,Virginie Uhlmann Pdf

Author : Anonim
Publisher : Elsevier
Page : 4609 pages
File Size : 40,9 Mb
Release : 2017-06-03
Category : Technology & Engineering
ISBN : 9780128032015

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Comprehensive Medicinal Chemistry III by Anonim Pdf

Comprehensive Medicinal Chemistry III, Eight Volume Set provides a contemporary and forward-looking critical analysis and summary of recent developments, emerging trends, and recently identified new areas where medicinal chemistry is having an impact. The discipline of medicinal chemistry continues to evolve as it adapts to new opportunities and strives to solve new challenges. These include drug targeting, biomolecular therapeutics, development of chemical biology tools, data collection and analysis, in silico models as predictors for biological properties, identification and validation of new targets, approaches to quantify target engagement, new methods for synthesis of drug candidates such as green chemistry, development of novel scaffolds for drug discovery, and the role of regulatory agencies in drug discovery. Reviews the strategies, technologies, principles, and applications of modern medicinal chemistry Provides a global and current perspective of today's drug discovery process and discusses the major therapeutic classes and targets Includes a unique collection of case studies and personal assays reviewing the discovery and development of key drugs

Author : Emmanuel G. Reynaud,Pavel Tomancak
Publisher : John Wiley & Sons
Page : 421 pages
File Size : 42,5 Mb
Release : 2024-04-08
Category : Science
ISBN : 9783527341351

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Light Sheet Fluorescence Microscopy by Emmanuel G. Reynaud,Pavel Tomancak Pdf

An indispensable guide to a novel, revolutionary fluorescence microscopy technique! Light sheet-based fluorescence microscopy has revolutionized microscopy, since it allows scientists to perform experiments in an entirely different manner and to record data that had not been accessible before. With contributions from noted experts in the fields of physics, biology, and computer science, Light Sheet Fluorescence Microscopy is a unique guide that offers a practical approach to the subject, including information on the basics of light sheet fluorescence microscopy, instrumentation, applications, sample preparation, and data analysis. Comprehensive in scope, the book is filled with the cutting-edge methods as well as valuable insider tips. Grounded in real-world applications, the book includes chapters from major manufacturers that explores their recent systems and developments. In addition, the book hightlights a discussion of a “do-it-yourself” light sheet microscope, making the technique affordable for every laboratory. This important book: Serves as an easy-to-understand introduction to light sheet-based fluroescence Includes numerous tips and tricks for advanced practitioners Provides in-depth information on hardware and software solutions for a straightforward implementation of light sheet fluorescence microscopy in the lab Includes chapters from the major manufacturers including Zeiss, Leica, Lavision Biotech, Phase View, and Asi Aimed at cell biologists, biophysicists, developmental biologists, and neurobiologists, Light Sheet-based Fluorescence Microscopy offers a comprehensive overview of the and the most recent applications of this microscopy technique.

Author : Raimund J. Ober,E. Sally Ward,Jerry Chao
Publisher : CRC Press
Page : 693 pages
File Size : 43,8 Mb
Release : 2020-12-15
Category : Medical
ISBN : 9780429892127

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Quantitative Bioimaging by Raimund J. Ober,E. Sally Ward,Jerry Chao Pdf

Quantitative bioimaging is a broad interdisciplinary field that exploits tools from biology, chemistry, optics, and statistical data analysis for the design and implementation of investigations of biological processes. Instead of adopting the traditional approach of focusing on just one of the component disciplines, this textbook provides a unique introduction to quantitative bioimaging that presents all of the disciplines in an integrated manner. The wide range of topics covered include basic concepts in molecular and cellular biology, relevant aspects of antibody technology, instrumentation and experimental design in fluorescence microscopy, introductory geometrical optics and diffraction theory, and parameter estimation and information theory for the analysis of stochastic data. Key Features: Comprises four parts, the first of which provides an overview of the topics that are developed from fundamental principles to more advanced levels in the other parts. Presents in the second part an in-depth introduction to the relevant background in molecular and cellular biology and in physical chemistry, which should be particularly useful for students without a formal background in these subjects. Provides in the third part a detailed treatment of microscopy techniques and optics, again starting from basic principles. Introduces in the fourth part modern statistical approaches to the determination of parameters of interest from microscopy data, in particular data generated by single molecule microscopy experiments. Uses two topics related to protein trafficking (transferrin trafficking and FcRn-mediated antibody trafficking) throughout the text to motivate and illustrate microscopy techniques. An online appendix providing the background and derivations for various mathematical results presented or used in the text is available at http://www.routledge.com/9781138598980.

Author : Winnok H. De Vos,Sebastian Munck,Jean-Pierre Timmermans
Publisher : Springer
Page : 272 pages
File Size : 50,7 Mb
Release : 2016-05-20
Category : Science
ISBN : 9783319285498

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Focus on Bio-Image Informatics by Winnok H. De Vos,Sebastian Munck,Jean-Pierre Timmermans Pdf

This volume of Advances Anatomy Embryology and Cell Biology focuses on the emerging field of bio-image informatics, presenting novel and exciting ways of handling and interpreting large image data sets. A collection of focused reviews written by key players in the field highlights the major directions and provides an excellent reference work for both young and experienced researchers.

Author : Ole Tange
Publisher : Lulu.com
Page : 114 pages
File Size : 41,5 Mb
Release : 2018-03-12
Category : Computers
ISBN : 9781387509881

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GNU Parallel 2018 by Ole Tange Pdf

GNU Parallel is a UNIX shell tool for running jobs in parallel. Learn how to use GNU Parallel from the developer of GNU Parallel.

Author : Erik R. Ranschaert,Sergey Morozov,Paul R. Algra
Publisher : Springer
Page : 373 pages
File Size : 55,9 Mb
Release : 2019-01-29
Category : Medical
ISBN : 9783319948782

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Artificial Intelligence in Medical Imaging by Erik R. Ranschaert,Sergey Morozov,Paul R. Algra Pdf

This book provides a thorough overview of the ongoing evolution in the application of artificial intelligence (AI) within healthcare and radiology, enabling readers to gain a deeper insight into the technological background of AI and the impacts of new and emerging technologies on medical imaging. After an introduction on game changers in radiology, such as deep learning technology, the technological evolution of AI in computing science and medical image computing is described, with explanation of basic principles and the types and subtypes of AI. Subsequent sections address the use of imaging biomarkers, the development and validation of AI applications, and various aspects and issues relating to the growing role of big data in radiology. Diverse real-life clinical applications of AI are then outlined for different body parts, demonstrating their ability to add value to daily radiology practices. The concluding section focuses on the impact of AI on radiology and the implications for radiologists, for example with respect to training. Written by radiologists and IT professionals, the book will be of high value for radiologists, medical/clinical physicists, IT specialists, and imaging informatics professionals.

Author : Elena Rebollo,Manel Bosch
Publisher : Humana
Page : 467 pages
File Size : 48,5 Mb
Release : 2020-09-04
Category : Medical
ISBN : 1493996886

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Computer Optimized Microscopy by Elena Rebollo,Manel Bosch Pdf

This volume explores open-source based image analysis techniques to provide a state-of-the-art collection of workflows covering current bioimage analysis problematics, including colocalization, particle counting, 3D structural analysis, ratio imaging and FRET quantification, particle tracking, high-content screening or machine learning. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and scripts, step-by-step, readily reproducible image analysis protocols, and tips on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, Computer Optimized Microscopy: Methods and Protocols is a valuable resource for both novice and experienced researchers who are interested in learning more about this developing field.

Author : Constantino Carlos Reyes-Aldasoro,Andrew Janowczyk,Mitko Veta,Peter Bankhead,Korsuk Sirinukunwattana
Publisher : Springer
Page : 192 pages
File Size : 45,9 Mb
Release : 2019-07-03
Category : Computers
ISBN : 9783030239374

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Digital Pathology by Constantino Carlos Reyes-Aldasoro,Andrew Janowczyk,Mitko Veta,Peter Bankhead,Korsuk Sirinukunwattana Pdf

This book constitutes the refereed proceedings of the 15th European Congress on Digital Pathology, ECDP 2019, held in Warwick, UK in April 2019. The 21 full papers presented in this volume were carefully reviewed and selected from 30 submissions. The congress theme will be Accelerating Clinical Deployment, with a focus on computational pathology and leveraging the power of big data and artificial intelligence to bridge the gaps between research, development, and clinical uptake.

Author : Andreas Holzinger,Randy Goebel,Michael Mengel,Heimo Müller
Publisher : Springer Nature
Page : 351 pages
File Size : 48,5 Mb
Release : 2020-06-24
Category : Computers
ISBN : 9783030504021

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Artificial Intelligence and Machine Learning for Digital Pathology by Andreas Holzinger,Randy Goebel,Michael Mengel,Heimo Müller Pdf

Data driven Artificial Intelligence (AI) and Machine Learning (ML) in digital pathology, radiology, and dermatology is very promising. In specific cases, for example, Deep Learning (DL), even exceeding human performance. However, in the context of medicine it is important for a human expert to verify the outcome. Consequently, there is a need for transparency and re-traceability of state-of-the-art solutions to make them usable for ethical responsible medical decision support. Moreover, big data is required for training, covering a wide spectrum of a variety of human diseases in different organ systems. These data sets must meet top-quality and regulatory criteria and must be well annotated for ML at patient-, sample-, and image-level. Here biobanks play a central and future role in providing large collections of high-quality, well-annotated samples and data. The main challenges are finding biobanks containing ‘‘fit-for-purpose’’ samples, providing quality related meta-data, gaining access to standardized medical data and annotations, and mass scanning of whole slides including efficient data management solutions.

Author : Anil V. Parwani
Publisher : Springer Nature
Page : 253 pages
File Size : 41,8 Mb
Release : 2021-10-29
Category : Medical
ISBN : 9783030833329

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Whole Slide Imaging by Anil V. Parwani Pdf

This book provides up-to-date and practical knowledge in all aspects of whole slide imaging (WSI) by experts in the field. This includes a historical perspective on the evolution of this technology, technical aspects of making a great whole slide image, the various applications of whole slide imaging and future applications using WSI for computer-aided diagnosis The goal is to provide practical knowledge and address knowledge gaps in this emerging field. This book is unique because it addresses an emerging area in pathology for which currently there is only limited information about the practical aspects of deploying this technology. For example, there are no established selection criteria for choosing new scanners and a knowledge base with the key information. The authors of the various chapters have years of real-world experience in selecting and implementing WSI solutions in various aspects of pathology practice. This text also discusses practical tips and pearls to address the selection of a WSI vendor, technology details, implementing this technology and provide an overview of its everyday uses in all areas of pathology. Chapters include important information on how to integrate digital slides with laboratory information system and how to streamline the “digital workflow” with the intent of saving time, saving money, reducing errors, improving efficiency and accuracy, and ultimately benefiting patient outcomes. Whole Slide Imaging: Current Applications and Future Directions is designed to present a comprehensive and state-of the-art approach to WSI within the broad area of digital pathology. It aims to give the readers a look at WSI with a deeper lens and also envision the future of pathology imaging as it pertains to WSI and associated digital innovations.