An Introduction To High Content Screening: Imaging Technology, Assay Development, and Data Analysis in Biology and Drug Discovery

Marc Notes: Includes bibliographical references and index.; This guide instructs readers on the fundamentals of high content screening (HCS) techniques, focussing on practical and widely-used techniques such as image processing and multiparametric assays. Jacket Description/Back: Master the Power of High Content ScreeningAlthough the level of interest and investment in high content (HC) technologies is growing rapidly, new users have been missing a standard and accessible introduction to the field. This book fills that need as a practical resource for HC techniques. Using a collaborative and interdisciplinary author base with experience in the pharmaceutical industry and academia, this book focuses on the fundamental concepts, rather than advanced material. The major objectives for the book are to educate people about the basic principles underlying HC screening that are rarely (or never) discussed in many publications in the field, and to provide the technical training needed to enable readers to design and implement their own HC screens. These objectives are met through the main text of the book, a tutorial chapter and a detailed appendix.- Instructs readers on the fundamentals of high content screening (HCS) techniques- Focuses on practical and widely-used techniques like image processing and multiparametric assays- Breaks down HCS into individual modules for training and connects them at the end- Includes a tutorial chapter that works through sample HCS assays, glossary, and detailed appendicesBiographical Note: Steven Haney is a Senior Research Advisor and Group Leader at Eli Lilly and Company. He edited the book "High Content Screening: Science, Techniques, and Applications" (Wiley, 2008). Douglas Bowman is an Associate Scientific Fellow at Takeda Pharmaceuticals. Arijit Chakravarty is the Director of Modeling and Simulation (DMPK) at Takeda Pharmaceuticals. Anthony Davies is Center Director, Translational Cell Imaging, Queensland University Of Technology, Queensland, Australia. Caroline Shamu is the Director of the ICCB-Longwood Screening Facility at Harvard Medical School. Table of Contents: PREFACE xviiCONTRIBUTORS xix1 Introduction 1"Steven A. Haney"1.1 The Beginning of High Content Screening, 11.2 Six Skill Sets Essential for Running HCS Experiments, 41.3 Integrating Skill Sets into a Team, 71.4 A Few Words on Experimental Design, 81.5 Conclusions, 9Key Points, 9Further Reading, 10References, 10SECTION I FIRST PRINCIPLES 112 Fluorescence and Cell Labeling 13"Anthony Davies and Steven A. Haney"2.1 Introduction, 132.2 Anatomy of Fluorescent Probes, Labels, and Dyes, 142.3 Stokes' Shift and Biological Fluorophores, 152.4 Fluorophore Properties, 162.5 Localization of Fluorophores Within Cells, 182.6 Multiplexing Fluorescent Reagents, 262.7 Specialized Imaging Applications Derived from Complex Properties of Fluorescence, 272.8 Conclusions, 30Key Points, 31Further Reading, 31References, 313 Microscopy Fundamentals 33"Steven A. Haney, Anthony Davies, and Douglas Bowman"3.1 Introducing HCS Hardware, 333.2 Deconstructing Light Microscopy, 373.3 Using the Imager to Collect Data, 433.4 Conclusions, 45Key Points, 45Further Reading, 46References, 464 Image Processing 47"John Bradley, Douglas Bowman, and Arijit Chakravarty"4.1 Overview of Image Processing and Image Analysis in HCS, 474.2 What is a Digital Image?, 484.3 "Addressing" Pixel Values in Image Analysis Algorithms, 484.4 Image Analysis Workflow, 494.5 Conclusions, 60Key Points, 60Further Reading, 60References, 60SECTION II GETTING STARTED 635 A General Guide to Selecting and Setting Up a High Content Imaging Platform 65"Craig Furman, Douglas Bowman, Anthony Davies, Caroline Shamu, and Steven A. Haney"5.1 Determining Expectations of the HCS System, 655.2 Establishing an HC Platform Acquisition Team, 665.3 Basic Hardware Decisions, 675.4 Data Generation, Analysis, and Retention, 725.5 Installation, 735.6 Managing the System, 755.7 Setting Up Workflows for Researchers, 775.8 Conclusions, 78Key Points, 79Further Reading, 796 Informatics Considerations 81"Jay Copeland and Caroline Shamu"6.1 Informatics Infrastructure for High Content Screening, 816.2 Using Databases to Store HCS Data, 866.3 Mechanics of an Informatics Solution, 896.4 Developing Image Analysis Pipelines: Data Management Considerations, 956.5 Compliance With Emerging Data Standards, 996.6 Conclusions, 101Key Points, 102Further Reading, 102References, 1027 Basic High Content Assay Development 103"Steven A. Haney and Douglas Bowman"7.1 Introduction, 1037.2 Initial Technical Considerations for Developing a High Content Assay, 1037.3 A Simple Protocol to Fix and Stain Cells, 1077.4 Image Capture and Examining Images, 1097.5 Conclusions, 111Key Points, 112Further Reading, 112Reference, 112SECTION III ANALYZING DATA 1138 Designing Metrics for High Content Assays 115"Arijit Chakravarty, Steven A. Haney, and Douglas Bowman"8.1 Introduction: Features, Metrics, Results, 1158.2 Looking at Features, 1168.3 Metrics and Results: The Metric is the Message, 1208.4 Types of High Content Assays and Their Metrics, 1218.5 Metrics to Results: Putting it all Together, 1268.6 Conclusions, 128Key Points, 128Further Reading, 129References, 1299 Analyzing Well-Level Data 131"Steven A. Haney"9.1 Introduction, 1319.2 Reviewing Data, 1329.3 Plate and Control Normalizations of Data, 1349.4 Calculation of Assay Statistics, 1359.5 Data Analysis: Hit Selection, 1389.6 IC 50 Determinations, 1399.7 Conclusions, 143Key Points, 143Further Reading, 143References, 14410 Analyzing Cell-Level Data 145"Steven A. Haney, Lin Guey, and Arijit Chakravarty"10.1 Introduction, 14510.2 Understanding General Statistical Terms and Concepts, 14610.3 Examining Data, 14910.4 Developing a Data Analysis Plan, 15510.5 Cell-Level Data Analysis: Comparing Distributions Through Inferential Statistics, 15810.6 Analyzing Normal (or Transformed) Data, 15910.7 Analyzing Non-Normal Data, 16010.8 When to Call For Help, 16210.9 Conclusions, 162Key Points, 162Further Reading, 163References, 163SECTION IV ADVANCED WORK 16511 Designing Robust Assays 167"Arijit Chakravarty, Douglas Bowman, Anthony Davies, Steven A. Haney, and Caroline Shamu"11.1 Introduction, 16711.2 Common Technical Issues in High Content Assays, 16711.3 Designing Assays to Minimize Trouble, 17211.4 Looking for Trouble: Building in Quality Control, 17711.5 Conclusions, 179Key Points, 180Further Reading, 180References, 18012 Automation and Screening 181"John Donovan, Arijit Chakravarty, Anthony Davies, Steven A. Haney, Douglas Bowman, John Ringeling, and Ben Knight"12.1 Introduction, 18112.2 Some Preliminary Considerations, 18112.3 Laboratory Options, 18312.4 The Automated HCS Laboratory, 18612.5 Conclusions, 192Key Points, 192Further Reading, 19313 High Content Analysis for Tissue Samples 195"Kristine Burke, Vaishali Shinde, Alice McDonald, Douglas Bowman, and Arijit Chakravarty"13.1 Introduction, 19513.2 Design Choices in Setting Up a High Content Assay in Tissue, 19613.3 System Configuration: Aspects Unique to Tissue-Based HCS, 19913.4 Data Analysis, 20313.5 Conclusions, 207Key Points, 207Further Reading, 207References, 208SECTION V HIGH CONTENT ANALYTICS 20914 Factoring and Clustering High Content Data 211"Steven A. Haney"14.1 Introduction, 21114.2 Common Unsupervised Learning Methods, 21214.3 Preparing for an Unsupervised Learning Study, 21814.4 Conclusions, 228Key Points, 228Further Reading, 228References, 22915 Supervised Machine Learning 231"Jeff Palmer and Arijit Chakravarty"15.1 Introduction, 23115.2 Foundational Concepts, 23215.3 Choosing a Machine Learning Algorithm, 23415.4 When Do You Need Machine Learning, and How Do You Use IT?, 24315.5 Conclusions, 244Key Points, 244Further Reading, 244Appendix A Websites and Additional Information on Instruments, Reagents, and Instruction 247Appendix B A Few Words About One Letter: Using R to Quickly Analyze HCS Data 249"Steven A. Haney"B.1 Introduction, 249B.2 Setting Up R, 250B.3 Analyzing Data in R, 253B.4 Where to Go Next, 261Further Reading, 263Appendix C Hypothesis Testing for High Content Data: A Refresher 265"Lin Guey and Arijit Chakravarty"C.1 Introduction, 265C.2 Defining Simple Hypothesis Testing, 266C.3 Simple Statistical Tests to Compare Two Groups, 269C.4 Statistical Tests on Groups of Samples, 276C.5 Introduction to Regression Models, 280C.6 Conclusions, 285Key Concepts, 286Further Reading, 286GLOSSARY 287TUTORIAL 295INDEX 323

Contributor Bio:  Haney, Steven A Steven A. Haney, PhD, is a Principal Scientist in the Department of Biological Technologies at Wyeth Research, where he has developed programs for oncology drug development, built a HCS program for use in target validation and drug discovery, and prepared gene family-based target validation strategies. Dr. Haney has authored many peer-reviewed articles and has spoken at numerous conferences on HCS. Contributor Bio:  Bowman, Doug Bowman is a Grand Ole Opry performer who comes from an established family of country singers.