Bioimage Data Analysis Workflows ‒ Advanced Components and Methods
Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

Author: Kota Miura

Publisher: Springer Nature

Published: 2022-09-28

Total Pages: 218

ISBN-13: 3030763943

DOWNLOAD EBOOK

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.

Bioimage Data Analysis Workflows
Bioimage Data Analysis Workflows

Author: Kota Miura

Publisher: Springer Nature

Published: 2019-10-17

Total Pages: 178

ISBN-13: 3030223868

DOWNLOAD EBOOK

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.

Bioimage Data Analysis Workflows
Bioimage Data Analysis Workflows

Author: Natasa Sladoje

Publisher:

Published: 2020-10-08

Total Pages: 176

ISBN-13: 9781013271922

DOWNLOAD EBOOK

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.

Standard and Super-Resolution Bioimaging Data Analysis
Standard and Super-Resolution Bioimaging Data Analysis

Author: Ann Wheeler

Publisher: John Wiley & Sons

Published: 2017-10-12

Total Pages: 285

ISBN-13: 1119096936

DOWNLOAD EBOOK

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.

Comprehensive Medicinal Chemistry III
Comprehensive Medicinal Chemistry III

Author:

Publisher: Elsevier

Published: 2017-06-03

Total Pages: 4609

ISBN-13: 0128032014

DOWNLOAD EBOOK

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

Advanced Statistical Methods for the Analysis of Large Data-Sets
Advanced Statistical Methods for the Analysis of Large Data-Sets

Author: Agostino Di Ciaccio

Publisher: Springer Science & Business Media

Published: 2012-03-05

Total Pages: 464

ISBN-13: 3642210376

DOWNLOAD EBOOK

The theme of the meeting was “Statistical Methods for the Analysis of Large Data-Sets”. In recent years there has been increasing interest in this subject; in fact a huge quantity of information is often available but standard statistical techniques are usually not well suited to managing this kind of data. The conference serves as an important meeting point for European researchers working on this topic and a number of European statistical societies participated in the organization of the event. The book includes 45 papers from a selection of the 156 papers accepted for presentation and discussed at the conference on “Advanced Statistical Methods for the Analysis of Large Data-sets.”

Quantitative Bioimaging
Quantitative Bioimaging

Author: Raimund J. Ober

Publisher: CRC Press

Published: 2020-12-15

Total Pages: 693

ISBN-13: 0429892128

DOWNLOAD EBOOK

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.

Chemical Engineering Computation with MATLAB®
Chemical Engineering Computation with MATLAB®

Author: Yeong Koo Yeo

Publisher: CRC Press

Published: 2020-12-15

Total Pages: 849

ISBN-13: 1000284883

DOWNLOAD EBOOK

Chemical Engineering Computation with MATLAB®, Second Edition continues to present basic to advanced levels of problem-solving techniques using MATLAB as the computation environment. The Second Edition provides even more examples and problems extracted from core chemical engineering subject areas and all code is updated to MATLAB version 2020. It also includes a new chapter on computational intelligence and: Offers exercises and extensive problem-solving instruction and solutions for various problems Features solutions developed using fundamental principles to construct mathematical models and an equation-oriented approach to generate numerical results Delivers a wealth of examples to demonstrate the implementation of various problem-solving approaches and methodologies for problem formulation, problem solving, analysis, and presentation, as well as visualization and documentation of results Includes an appendix offering an introduction to MATLAB for readers unfamiliar with the program, which will allow them to write their own MATLAB programs and follow the examples in the book Provides aid with advanced problems that are often encountered in graduate research and industrial operations, such as nonlinear regression, parameter estimation in differential systems, two-point boundary value problems and partial differential equations and optimization This essential textbook readies engineering students, researchers, and professionals to be proficient in the use of MATLAB to solve sophisticated real-world problems within the interdisciplinary field of chemical engineering. The text features a solutions manual, lecture slides, and MATLAB program files._

Artificial Intelligence and Machine Learning for Digital Pathology
Artificial Intelligence and Machine Learning for Digital Pathology

Author: Andreas Holzinger

Publisher: Springer Nature

Published: 2020-06-24

Total Pages: 351

ISBN-13: 3030504026

DOWNLOAD EBOOK

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.