Standard and Super-Resolution Bioimaging Data Analysis (eBook, PDF)

A Primer
Redaktion: Wheeler, Ann; Henriques, Ricardo

• Format: PDF

Produktbeschreibung

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.

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Produktdetails

• Verlag: Jossey-Bass
• Seitenzahl: 312
• Erscheinungstermin: 12. Oktober 2017
• Englisch
• ISBN-13: 9781119096924
• Artikelnr.: 52555524

Autorenporträt

ANN WHEELER, PhD, is Head of the Advanced Imaging Resource at the MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, UK. RICARDO HENRIQUES, PhD, is Head of the Quantitative Imaging and NanoBioPhysics research group at the MRC Laboratory for Molecular Cell Biology, University College London, UK.

Inhaltsangabe

List of Contributors xi

Foreword xiii

1 Digital Microscopy: Nature to Numbers 1
Ann Wheeler

1.1 Acquisition 4

1.1.1 First Principles: How Can Images Be Quantified? 4

1.1.2 Representing Images as a Numerical Matrix Using a Scientific Camera 6

1.1.3 Controlling Pixel Size in Cameras 8

1.2 Initialisation 11

1.2.1 The Sample 12

1.2.2 Pre?]Processing 12

1.2.3 Denoising 12

1.2.4 Filtering Images 14

1.2.5 Deconvolution 16

1.2.6 Registration and Calibration 19

1.3 Measurement 21

1.4 Interpretation 23

1.5 References 29

2 Quantification of Image Data 31
Jean?]Yves Tinevez

2.1 Making Sense of Images 31

2.1.1 The Magritte Pipe 31

2.1.2 Quantification of Image Data Via Computers 33

2.2 Quantifiable Information 35

2.2.1 Measuring and Comparing Intensities 35

2.2.2 Quantifying Shape 36

2.2.3 Spatial Arrangement of Objects 41

2.3 Wrapping Up 45

2.4 References 46

3 Segmentation in Bioimaging 47
Jean?]Yves Tinevez

3.1 Segmentation and Information Condensation 47

3.1.1 A Priori Knowledge 48

3.1.2 An Intuitive Approach 49

3.1.3 A Strategic Approach 51

3.2 Extracting Objects 52

3.2.1 Detecting and Counting Objects 52

3.2.2 Automated Segmentation of Objects 60

3.3 Wrapping Up 74

3.4 References 79

4 Measuring Molecular Dynamics and Interactions by Förster Resonance Energy Transfer (FRET) 83
Aliaksandr Halavatyi and Stefan Terjung

4.1 FRET?]Based Techniques 83

4.1.1 Ratiometric Imaging 84

4.1.2 Acceptor Photobleaching 85

4.1.3 Other FRET Measurement Techniques 85

4.1.4 Alternative Methods to Measure Interactions 87

4.2 Experimental Design 89

4.2.1 Ratiometric Imaging of FRET?]Based Sensors 90

4.2.2 Acceptor Photobleaching 91

4.3 FRET Data Analysis 92

4.3.1 Ratiometric Imaging 92

4.3.2 Acceptor Photobleaching 93

4.3.3 Data Averaging and Statistical Analysis 93

4.4 Computational Aspects of Data Processing 94

4.4.1 Software Tools 94

4.4.2 FRET Data Analysis with Fiji 94

4.5 Concluding Remarks 95

4.6 References 96

5 FRAP and Other Photoperturbation Techniques 99
Aliaksandr Halavatyi and Stefan Terjung

5.1 Photoperturbation Techniques in Cell Biology 99

5.1.1 Scientific Principles Underpinning FRAP 100

5.1.2 Other Photoperturbation Techniques 103

5.2 FRAP Experiments 106

5.2.1 Selecting Fluorescent Tags 107

5.2.2 Optimisation of FRAP Experiments 107

5.2.3 Storage of Experimental Data 109

5.3 FRAP Data Analysis 109

5.3.1 Quantification of FRAP Intensities 112

5.3.2 Normalisation 113

5.3.3 In Silico Modelling of FRAP Data 115

5.3.4 Fitting Recovery Curves 120

5.3.5 Evaluating the Quality of FRAP Data and Analysis Results 121

5.3.6 Data Averaging and Statistical Analysis 122

5.3.7 Software for FRAP Data Processing 123

5.4 Procedures for Quantitative FRAP Analysis with Freeware Software Tools 127

5.4.1 Quantification of Intensity Traces with Fiji 127

5.4.2 Processing FRAP Recovery Curves with FRAPAnalyser 128

5.5 Notes 130

5.6 Concluding Remarks 131

5.7 References 132

5A Case Study: Analysing COPII Turnover During ER Exit 135

5A.1 Quantitative FRAP A