Bioimage Data Analysis Workflows

Author : Kota Miura,Nataša Sladoje
Publisher : Springer Nature
Page : 178 pages
File Size : 40,5 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 : Kota Miura,Nataša Sladoje
Publisher : Springer Nature
Page : 218 pages
File Size : 47,6 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 : Natasa Sladoje,Kota Miura
Publisher : Unknown
Page : 176 pages
File Size : 40,7 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 : 49,9 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 : 46,7 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 : Radek Šachl,Mariana Amaro
Publisher : Springer Nature
Page : 529 pages
File Size : 48,7 Mb
Release : 2023-04-27
Category : Science
ISBN : 9783031303623

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Fluorescence Spectroscopy and Microscopy in Biology by Radek Šachl,Mariana Amaro Pdf

This book provides the reader with an updated comprehensive view of the rapidly developing and fascinating field of fluorescence spectroscopy and microscopy. In recent years, fluorescence spectroscopy and microscopy have experienced rapid technological development, which has enabled the detection and monitoring of single molecules with high spatial and temporal resolution. Thanks to these developments, fluorescence has become an even more popular method in physical, biological and related fields. This book guides the reader through both basic and advanced fluorescence spectroscopy and microscopy approaches with a focus on their applications in membrane and protein biophysics. Each of the four parts: A - Fluorescence Spectroscopy, B - Fluorescence Microscopy, C - Applications of Fluorescence Spectroscopy and Microscopy to biological membranes and D - Applications of Fluorescence Spectroscopy to protein studies are written by experts within the field. The book is intended for both complete beginners who want to quickly orient themselves in the large number of existing fluorescent methods, as well as for advanced readers who are interested in particular methods and their proper use.

Author : R ̄uta Navakauskien ̇e,Dalius Navakauskas,Veronika Borutinskait ̇e,Dalius Matuzevi ̆cius
Publisher : Springer Nature
Page : 453 pages
File Size : 55,5 Mb
Release : 2021-09-14
Category : Science
ISBN : 9783030687083

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Epigenetics and Proteomics of Leukemia by R ̄uta Navakauskien ̇e,Dalius Navakauskas,Veronika Borutinskait ̇e,Dalius Matuzevi ̆cius Pdf

This book reviews the current state of epigenetics and proteomics of leukemia and introduces the methods that are important to process and evaluate these factors in leukemia. In particular, epigenetic modifiers and their inhibitors in leukemia treatment as well as approaches to the epigenetic treatment of leukemia are covered. Various computational methods for proteome analysis are also described in detail, including 2DE fractionation and visualization, proteomic data processing, image acquisition and data anlaysis, and more. Protein localization in leukemia is also covered, in addition to the future of leukemia therapy. Epigenetics and Proteomics of Leukemia is an ideal book for advanced biomedical scientists and students, medical doctors and students, bioinformatics and health informatics researchers, computational biologists, structural biologists, systems biologists, and bioengineers.

Author : Emmanuel G. Reynaud,Pavel Tomancak
Publisher : John Wiley & Sons
Page : 421 pages
File Size : 41,8 Mb
Release : 2024-01-31
Category : Science
ISBN : 9783527803934

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

Light Sheet Fluorescence Microscopy An indispensable guide to a novel, revolutionary fluorescence microscopy technique! Light sheet 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 textbook: Serves as an easy-to-understand introduction to light sheet-based fluorescence 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 neuro-biologists, Light Sheet Fluorescence Microscopy offers a comprehensive overview of the most recent applications of this microscopy technique.

Author : Paul Verkade,Lucy Collinson
Publisher : John Wiley & Sons
Page : 245 pages
File Size : 45,7 Mb
Release : 2019-11-04
Category : Science
ISBN : 9781119086451

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Correlative Imaging by Paul Verkade,Lucy Collinson Pdf

Brings a fresh point of view to the current state of correlative imaging and the future of the field This book provides contributions from international experts on correlative imaging, describing their vision of future developments in the field based on where it is today. Starting with a brief historical overview of how the field evolved, it presents the latest developments in microscopy that facilitate the correlative workflow. It also discusses the need for an ideal correlative probe, applications in proteomic and elemental analysis, interpretation methods, and how correlative imaging can incorporate force microscopy, soft x-ray tomography, and volume electron microscopy techniques. Work on placing individual molecules within cells is also featured. Correlative Imaging: Focusing on the Future offers in-depth chapters on: correlative imaging from an LM perspective; the importance of sample processing for correlative imaging; correlative light and volume EM; correlation with scanning probe microscopies; and integrated microscopy. It looks at: cryo-correlative microscopy; correlative cryo soft X-ray imaging; and array tomography. Hydrated-state correlative imaging in vacuo, correlating data from different imaging modalities, and big data in correlative imaging are also considered. Brings a fresh view to one of the hottest topics within the imaging community: the correlative imaging field Discusses current research and offers expert thoughts on the field’s future developments Presented by internationally-recognized editors and contributors with extensive experience in research and applications Of interest to scientists working in the fields of imaging, structural biology, cell biology, developmental biology, neurobiology, cancer biology, infection and immunity, biomaterials and biomedicine Part of the Wiley–Royal Microscopical Society series Correlative Imaging: Focusing on the Future will appeal to those working in the expanding field of the biosciences, correlative microscopy and related microscopic areas. It will also benefit graduate students working in microscopy, as well as anyone working in the microscopy imaging field in biomedical research.

Author : Constantino Carlos Reyes-Aldasoro,Andrew Janowczyk,Mitko Veta,Peter Bankhead,Korsuk Sirinukunwattana
Publisher : Springer
Page : 192 pages
File Size : 47,8 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 : Hector Guerrero
Publisher : Springer
Page : 358 pages
File Size : 41,9 Mb
Release : 2018-12-14
Category : Business & Economics
ISBN : 9783030012793

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Excel Data Analysis by Hector Guerrero Pdf

This book offers a comprehensive and readable introduction to modern business and data analytics. It is based on the use of Excel, a tool that virtually all students and professionals have access to. The explanations are focused on understanding the techniques and their proper application, and are supplemented by a wealth of in-chapter and end-of-chapter exercises. In addition to the general statistical methods, the book also includes Monte Carlo simulation and optimization. The second edition has been thoroughly revised: new topics, exercises and examples have been added, and the readability has been further improved. The book is primarily intended for students in business, economics and government, as well as professionals, who need a more rigorous introduction to business and data analytics – yet also need to learn the topic quickly and without overly academic explanations.

Author : Claudia Kuntner,Bernhard Baumann,Adriana Tavares,Andreas Hess
Publisher : Frontiers Media SA
Page : 198 pages
File Size : 52,6 Mb
Release : 2020-12-16
Category : Science
ISBN : 9782889661725

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Status Go for Preclinical Imaging by Claudia Kuntner,Bernhard Baumann,Adriana Tavares,Andreas Hess Pdf

This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.

Author : Kheng Seang Lim
Publisher : Partridge Publishing Singapore
Page : 28 pages
File Size : 55,6 Mb
Release : 2019-03-29
Category : Medical
ISBN : 9781543750225

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Eeg Made Easy by Kheng Seang Lim Pdf

This EEG e-book aims to help beginners who find it difficult to understand EEG in text format. It is a supplement to EEG textbooks but is not a substitute to them. This is also suitable for busy neurologists who cannot remember the characteristics of various EEG patterns. The pocket-size and e-book formats allow for quick references. And most importantly, this is created for quick revisions before an EEG examination.

Author : Anonim
Publisher : Elsevier
Page : 3421 pages
File Size : 51,9 Mb
Release : 2018-08-21
Category : Medical
ISBN : 9780128114322

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Encyclopedia of Bioinformatics and Computational Biology by Anonim Pdf

Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

Author : Stephen J. Royle
Publisher : Unknown
Page : 200 pages
File Size : 53,6 Mb
Release : 2019
Category : Science
ISBN : 1621822788

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The Digital Cell by Stephen J. Royle Pdf

"Cell biology is becoming an increasingly quantitative field, as technical advances mean researchers now routinely capture vast amounts of data. This handbook is an essential guide to the computational approaches, image processing and analysis techniques, and basic programming skills that are now part of the skill set of anyone working in the field"--