Biomedical Image Analysis Recipes in MATLAB

As its title suggests, this innovative book has been written for life scientists needing to analyse their data sets, and programmers, wanting a better understanding of the types of experimental images life scientists investigate on a regular basis. Each chapter presents one self-contained biomedical experiment to be analysed. Part I of the book presents its two basic ingredients: essential concepts of image analysis and Matlab. In Part II, algorithms and techniques are shown as series of "recipes" or solved examples that show how specific techniques are applied to a biomedical experiments like Western Blots, Histology, Scratch Wound Assays and Fluoresence. Each recipe begins with simple techniques that gradually advance in complexity. Part III presents some advanced techniques for the generation of publication quality figures. The book does not assume any computational or mathematical expertise.

• A practical, clearly-written introduction to biomedical image analysis that provides the tools for life scientists and engineers to use when solving problems in their own laboratories.
• Presents the basic concepts of MATLAB software and uses it throughout to show how it can execute flexible and powerful image analysis programs tailored to the specific needs of the problem.
• Within the context of four biomedical cases, it shows algorithms and techniques as series of "recipes", or solved examples that show how a particular technique is applied in a specific experiment.
• Companion website containing example datasets, MATLAB files and figures from the book.

Preface vii

Acknowledgements ix

About the Companion Website xi

1 The Basic Ingredients 1

2 Introduction to Images 45

3 Introduction to Colour 71

4 Western Blots 79

5 Scratch Wound Assays 135

6 Bright Field Microscopy 215

7 Fluorescence Microscopy 291

8 Creating Publication-Quality Figures from Matlab 343

Index 401

Constantino Carlos Reyes-Aldasoro (BSEE UNAM, Mexico, MSc Imperial College London, UK, PhD Warwick, UK) is an interdisciplinary scientist with skills that span from microscopy to image analysis of biomedical data sets to advanced computer programming. His teaching experience is also wide ranging from Engineering, Physics and Computing to Medicine and Radiology. His research concentrates on Biomedical Image Analysis of Cancer, Microcirculation and Inflammation. He has published numerous journal/conference papers in both Biological and Engineering fields, which have been cited in more than 500 publications. He is a senior member of the Institute of Electrical and Electronics Engineers and executive committee member of the British
Association for Cancer Research.

As its title suggests, this innovative book has been written for life scientists needing to analyse their data sets, and programmers, wanting a better understanding of the types of experimental images life scientists investigate on a regular basis. Each chapter presents one self-contained biomedical experiment to be analysed. Part I of the book presents its two basic ingredients: essential concepts of image analysis and Matlab. In Part II, algorithms and techniques are shown as series of ‘recipes’ or solved examples that show how specific techniques are applied to a biomedical experiments like Western Blots, Histology, Scratch Wound Assays and Fluoresence. Each recipe begins with simple techniques that gradually advance in complexity. Part III presents some advanced techniques for the generation of publication quality figures. The book does not assume any computational or mathematical expertise.

• A practical, clearly-written introduction to biomedical image analysis that provides the tools for life scientists and engineers to use when solving problems in their own laboratories.

• Presents the basic concepts of MATLAB® software and uses it throughout to show how it can execute flexible and powerful image analysis programmes tailored to the specific needs of the problem.

• Within the context of four biomedical cases, it shows algorithms and techniques as series of ‘recipes’, or solved examples that show how a particular technique is applied in a specific experiment.

• Companion website containing example datasets, MATLAB® files and figures from the book.