Computational Methods and Tools for Reproducible and Scalable Bioimage Analysis PDF Download

Author: Markus Daniel Herrmann
Publisher:
ISBN:
Category :
Languages : en
Pages :

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Author: Kota Miura
Publisher: Springer Nature
ISBN: 3030763943
Category : Science
Languages : en
Pages : 218

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Book Description
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: Birgit Möller
Publisher:
ISBN:
Category :
Languages : en
Pages : 0

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Image analysis, spot detection, segmentation, active contours, machine learning, Alida, MiToBo, life sciences, cells, roots.

Author: Kota Miura
Publisher: Springer Nature
ISBN: 3030223868
Category : Medical
Languages : en
Pages : 178

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Book Description
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: Bruce Molitoris
Publisher: Frontiers Media SA
ISBN: 2889762300
Category : Science
Languages : en
Pages : 79

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Author: Winnok H. De Vos
Publisher: Springer
ISBN: 3319285491
Category : Science
Languages : en
Pages : 277

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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: Michael Nielsen
Publisher: Princeton University Press
ISBN: 0691202850
Category : Science
Languages : en
Pages : 272

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How the internet and powerful online tools are democratizing and accelerating scientific discovery Reinventing Discovery argues that we are living at the dawn of the most dramatic change in science in more than three hundred years. This change is being driven by powerful cognitive tools, enabled by the internet, which are greatly accelerating scientific discovery. There are many books about how the internet is changing business, the workplace, or government. But this is the first book about something much more fundamental: how the internet is transforming our collective intelligence and our understanding of the world. From the collaborative mathematicians of the Polymath Project to the amateur astronomers of Galaxy Zoo, Reinventing Discovery tells the exciting story of the unprecedented new era in networked science. It will interest anyone who wants to learn about how the online world is revolutionizing scientific discovery—and why the revolution is just beginning.

Author: Alex A.T. Bui
Publisher: Springer Science & Business Media
ISBN: 1441903852
Category : Technology & Engineering
Languages : en
Pages : 454

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Medical Imaging Informatics provides an overview of this growing discipline, which stems from an intersection of biomedical informatics, medical imaging, computer science and medicine. Supporting two complementary views, this volume explores the fundamental technologies and algorithms that comprise this field, as well as the application of medical imaging informatics to subsequently improve healthcare research. Clearly written in a four part structure, this introduction follows natural healthcare processes, illustrating the roles of data collection and standardization, context extraction and modeling, and medical decision making tools and applications. Medical Imaging Informatics identifies core concepts within the field, explores research challenges that drive development, and includes current state-of-the-art methods and strategies.

Author: Ann Wheeler
Publisher: John Wiley & Sons
ISBN: 1119096936
Category : Science
Languages : en
Pages : 285

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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: Felix Bronner
Publisher: Elsevier
ISBN: 0323149995
Category : Science
Languages : en
Pages : 448

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Cell Shape: Determinants, Regulation, and Regulatory Role is written to help readers understand cell shape and its regulation. It provides insight into how the shape of a cell is determined at a molecular level. It also discusses how the shape of the cell, as a signal, controls gene expression and modulates intercellular interaction. Divided into four parts encompassing 13 chapters, this volume begins with an overview of the mechanism of shape determination. It then explores how the cytoskeleton, the extracellular matrix, and biochemical force transduction may affect or respond to cell shape control. Other chapters focus on the mechanical modeling of cell shape and the biochemical reactions underlying cell motility. The text also describes the results of the molecular studies that have provided important information on the composition of the cytoskeleton. The final chapter reviews the shape changes that happen during embryogenesis. It also considers how the polarity of the embryo is determined. This book is a valuable resource for biologists, embryologists, and cell biologists.