Imaging cellular and molecular biological functions: with 13 tables
Gespeichert in:
| Format: | Elektronisch E-Book |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Berlin [u.a.]
Springer
2007
|
| Schriftenreihe: | Principles and Practice
|
| Schlagworte: | |
| Online-Zugang: | UBR01 Volltext Inhaltsverzeichnis |
| Beschreibung: | 1 Online-Ressource |
| ISBN: | 9783540713319 |
| DOI: | 10.1007/978-3-540-71331-9 |
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| 245 | 1 | 0 | |a Imaging cellular and molecular biological functions |b with 13 tables |c Spencer L. Shorte ... eds. |
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Datensatz im Suchindex
| _version_ | 1804137225788588032 |
|---|---|
| adam_text | Contents
Preface v
I Considerations for Routine Imaging
1 Entering the Portal: Understanding the Digital Image
Recorded Through a Microscope 3
Kristin L. Hazelwood, Scott G. Olenych, John D. Griffin,
Judith A. Cathcart, and Michael W. Davidson
1.1 Introduction 3
1.2 Historical Perspective 4
1.3 Digital Image Acquisition: Analog to
Digital Conversion 4
1.4 Spatial Resolution in Digital Images 6
1.5 The Contrast Transfer Function 8
1.6 Image Brightness and Bit Depth 10
1.7 Image Histograms 11
1.8 Fundamental Properties of CCD Cameras 12
1.9 CCD Enhancing Technologies 16
1.10 CCD Performance Measures 17
1.11 Multidimensional Imaging 21
1.12 The Point Spread Function 24
1.13 Digital Image Display and Storage 28
1.14 Imaging Modes in Optical Microscopy 29
1.15 Summary 39
1.16 Internet Resources 41
References 41
2 Quantitative Biological Image Analysis 45
Erik Meijering and Gert van Cappellen
2.1 Introduction 45
2.2 Definitions and Perspectives 46
2.3 Image Preprocessing 48
2.3.1 Image Intensity Transformation 50
2.3.2 Local Image Filtering 50
ix
x Contents
2.3.3 Geometrical Image Transformation 53
2.3.4 Image Restoration 55
2.4 Advanced Processing for Image Analysis 57
2.4.1 Colocalization Analysis 58
2.4.2 Neuron Tracing and Quantification 58
2.4.3 Particle Detection and Tracking 60
2.4.4 Cell Segmentation and Tracking 62
2.5 Higher Dimensional Data Visualization 63
2.5.1 Volume Rendering 64
2.5.2 Surface Rendering 64
2.6 Software Tools and Development 66
References 68
3 The Open Microscopy Environment: A Collaborative
Data Modeling and Software Development Project
for Biological Image Informatics 71
Jason R. Swedlow
3.1 Introduction 71
3.1.1 What Is OME? 72
3.1.2 Why OME What Is the Problem? 72
3.2 OME Specifications and File Formats 74
3.2.1 OME Data Model 74
3.2.2 OME XML, OME TIFF and Bio Formats 76
3.3 OME Data Management and Analysis Software 77
3.3.1 OME Server and Web User Interface 77
3.3.2 OMERO Server, Client and Importer 84
3.3.3 Developing Usable Tools for Imaging 89
3.4 Conclusions and Future Directions 90
References 90
4 Design and Function of a Light Microscopy Facility 93
Kurt I. Anderson, Jeremy Sanderson, and Jan Peychl
4.1 Introduction 93
4.2 Users 95
4.3 Staff 96
4.3.1 Workplace Safety 96
4.3.2 User Training 97
4.3.3 Equipment Management 97
4.4 Equipment 98
4.4.1 Large Equipment 98
4.4.2 Small Equipment 99
4.4.3 Tools 100
4.4.4 Imaging Facility Layout 100
4.5 Organization 103
4.5.1 Equipment Booking Database 103
Contents xi
4.5.2 Fee for Service 106
4.5.3 Cost Matrix 107
4.5.4 Advisory Committees Ill
4.6 Summary 112
References 113
II Advanced Methods and Concepts
5 Quantitative Colocalisation Imaging: Concepts,
Measurements, and Pitfalls 117
Martin Oheim and Dongdong Li
5.1 Introduction 117
5.1.1 One Fluorophore, One Image? 124
5.1.2 A Practical Example of Dual Band Detection 135
5.2 Quantifying Colocalisation 137
5.2.1 Colour Merging 137
5.2.2 Pixel Based Techniques 139
5.2.3 Object Based Techniques 147
5.3 Conclusions 150
References 151
6 Quantitative FRET Microscopy of Live Cells 157
Adam D. Hoppe
6.1 Introduction 157
6.2 Introductory Physics of FRET 158
6.3 Manifestations of FRET in Fluorescence Signals 160
6.3.1 Spectral Change (Sensitized Emission) 160
6.3.2 Fluorescence Lifetime 161
6.3.3 Polarization 162
6.3.4 Accelerated Photobleaching 162
6.4 Molecular Interaction Mechanisms That Can Be
Observed by FRET 163
6.4.1 Conformational Change 164
6.4.2 Molecular Association 164
6.4.3 Molecular Assembly 164
6.5 Measuring Fluorescence Signals in the Microscope 165
6.6 Methods for FRET Microscopy 167
6.6.1 Photobleaching Approaches 168
6.6.2 Sensitized Emission 170
6.6.3 Spectral Fingerprinting and Matrix Notation for FRET. ... 173
6.6.4 Polarization 174
6.7 Fluorescence Lifetime Imaging Microscopy for FRET 175
6.8 Data Display and Interpretation 176
6.9 FRET Based Biosensors 177
xii Contents
6.10 FRET Microscopy for Analyzing Interaction Networks
in Live Cells 178
6.11 Conclusion 180
References 180
7 Fluorescence Photobleaching and Fluorescence Correlation
Spectroscopy: Two Complementary Technologies
To Study Molecular Dynamics in Living Cells 183
Malte Wachsmuth and Klaus Weisshart
7.1 Introduction 183
7.1.1 FRAP and Other Photobleaching Methods 184
7.1.2 FCS and Other Fluctuation Analysis Methods 186
7.1.3 Comparing and Combining Techniques 187
7.2 Fundamentals 189
7.2.1 Fluorescent Labelling 189
7.2.2 Microscope Setup 191
7.2.3 Diffusion and Binding in Living Cells 193
7.2.4 Fluorescence, Blinking, and Photobleaching 194
7.2.5 Two Photon Excitation 195
7.3 How To Perform a FRAP Experiment 196
7.3.1 The Principle of Imaging Based FRAP 196
7.3.2 Choosing and Optimising the Experimental Parameters .... 197
7.3.3 Quantitative Evaluation 200
7.3.4 Controls and Potential Artefacts 203
7.4 How To Perform an FCS Experiment 205
7.4.1 The Principle of FCS 205
7.4.2 Instrument Alignment and Calibration 208
7.4.3 Setting Up an Experiment 212
7.4.4 Types of Applications 213
7.4.5 Potential Artefacts 215
7.5 How To Perform a CP Experiment 217
7.5.1 The Principle of CP 217
7.5.2 Choosing and Optimising the Experimental Parameters .... 218
7.5.3 Quantitative Evaluation 219
7.5.4 Controls and Potential Artefacts 220
7.6 Quantitative Treatment 221
7.6.1 Fluorescence Recovery After Photobleaching 221
7.6.2 Fluorescence Correlation Spectroscopy 223
7.6.3 Continuous Fluorescence Photobleaching 226
7.7 Conclusion 227
References 227
8 Single Fluorescent Molecule Tracking in Live Cells 235
Ghislain G. Cabal, Jost Enninga, and Musa M. Mhlanga
8.1 Introduction 235
Contents xiii
8.2 Tracking of Single Chromosomal Loci 236
8.2.1 General Remarks 236
8.2.2 In Vivo Single Loci Tagging via Operator/Repressor
Recognition 237
8.2.3 The Design of Strains Containing TetO Repeats
and Expressing TetR GFP 238
8.2.4 In Vivo Microscopy for Visualization of Single Tagged
Chromosomal Loci 244
8.2.5 Limits and Extension of Operator/Repressor Single
Loci Tagging System 246
8.3 Single Molecule Tracking of mRNA 247
8.3.1 Overview 247
8.3.2 The MS2 GFP System 247
8.3.3 The Molecular Beacon System 248
8.3.4 Setting Up the Molecular Beacon System for
the Detection of mRNA 250
8.3.5 Ensuring the Observed Fluorescent Particles in Vivo
Consist of Single Molecules of mRNA 251
8.4 Single Particle Tracking for Membrane Proteins 253
8.4.1 Overview 253
8.4.2 Quantum Dots As Fluorescent Labels for
Biological Samples 254
8.4.3 Functionalizing Quantum Dots To Label
Specific Proteins 255
8.4.4 Tracking the Glycin Receptor 1 at the Synaptic Cleft
Using Quantum Dots 257
8.5 Tracking Analysis and Image Processing of Data from
Particle Tracking in Living Cells 258
8.6 Conclusion 258
8.7 Protocols for Laboratory Use 259
8.7.1 Protocol: Single Molecule Tracking of Chromosomal
Loci in Yeast 259
8.7.2 Protocol: Single Molecule Tracking of
mRNA Experiment Using Molecular Beacons 259
References 261
9 From Live Cell Microscopy to Molecular Mechanisms:
Deciphering the Functions of Kinetochore Proteins 265
Khuloud Jaqaman, Jonas F. Dorn, and Gaudenz Danuser
9.1 Introduction 265
9.2 Biological Problem: Deciphering the Functions of
Kinetochore Proteins 268
9.3 Experimental Design 269
9.4 Extraction of Dynamics from Images 273
9.4.1 Mixture Model Fitting 274
xiv Contents
9.4.2 Tag Tracking 275
9.4.3 Multitemplate Matching 275
9.5 Characterization of Dynamics 276
9.5.1 Confined Brownian Motion Model 277
9.5.2 Simple Microtubule Dynamic Instability Model 278
9.5.3 Autoregressive Moving Average Model 279
9.5.4 Descriptor Sensitivity and Completeness 280
9.6 Quantitative Genetics of the Yeast Kinetochore 282
9.7 Conclusion 284
References 284
III Cutting Edge Applications Utilities
10 Towards Imaging the Dynamics of Protein Signalling 289
Lars Kaestner and Peter Lipp
10.1 Spatiotemporal Aspects of Protein Signalling Dynamics 289
10.2 How To Be Fast While Maintaining the Resolution 290
10.3 How To Make Proteins Visible 299
10.4 Concepts To Image Protein Dynamics 303
10.5 Concepts To Image Protein Protein Interactions 305
10.6 Concepts To Image Biochemistry with Fluorescent Proteins 309
References 311
11 New Technologies for Imaging and Analysis
of Individual Microbial Cells 313
Byron F. Brehm Stecher
11.1 Introduction 313
11.2 Live Cell Imaging 314
11.3 Imaging Infection 315
11.4 Imaging Single Molecules (Within Single Cells) 318
11.5 Measuring Discrete Cell Properties and Processes 319
11.6 Wetware 321
11.7 Hardware and Applications 323
11.7.1 Nonphotonic Microscopies 323
11.7.2 Image Analysis 324
11.7.3 Spectroscopic Methods 325
11.8 Fluorescence Correlation Spectroscopy 326
11.9 A Picture is Worth a Thousand Dots New Developments
in Flow Cytometry 330
11.10 Strength in Numbers Highly Parallel Analysis
Using Cellular Arrays 334
11.11 Nontactile Manipulation of Individual Cells and
Wall less Test Tubes 335
11.12 Conclusions 337
References 338
Contents xv
12 Imaging Parasites in Vivo 345
Rogerio Amino, Blandine Franke Fayard, Chris Janse,
Andrew Waters, Robert Menard, and Freddy Frischknecht
12.1 Introduction 345
12.2 The Life Cycle of Malaria Parasites 346
12.3 A Very Brief History of Light Microscopy
and Malaria Parasites 348
12.4 In Vivo Imaging of Luminescent Parasites 349
12.5 In Vivo Imaging of Fluorescent Parasites 350
12.6 Imaging Malaria Parasites in the Mosquito 351
12.7 Imaging Malaria Parasites in the Mammalian Host 354
12.8 Towards Molecular Imaging in Vivo 358
12.9 A Look at Other Parasites 359
12.10 Conclusion 360
References 360
13 Computer Assisted Systems for Dynamic 3D Reconstruction
and Motion Analysis of Living Cells 365
David R. Soil, Edward Voss, Deborah Wessels, and Spencer Kuhl
13.1 Introduction 365
13.2 Approaches to 3D Reconstruction and Motion Analysis 366
13.3 Obtaining Optical Sections for 3D Reconstruction 368
13.4 Outlining 368
13.5 Reconstructing 3D Faceted Images and Internal Architecture. . . 373
13.6 Quantitative Analyses of Behavior 373
13.7 3D DIASemb 375
13.8 Resolving Filopodia 377
13.9 The Combined Use of LSCM and 3D DIAS 380
13.10 Reasons for 3D Dynamic Image Reconstruction Analysis 381
References 382
14 High Throughput/High Content Automated Image
Acquisition and Analysis 385
Gabriele Gradl, Chris Hinnah, Achim Kirsch, Jiirgen Muller,
Dana Nojima, and Julian Wolcke
14.1 The Driving Forces for High Throughput/High Content
Automated Imaging 385
14.2 Confocal Imaging in High Throughput The Principles
Available 386
14.3 Resolution and Sensitivity 389
14.4 Measurements 392
14.5 Where Is the Signal and How To Focus? 393
14.6 Plates and Lenses 394
14.7 Image Analysis 395
14.8 Throughput: How To Acquire and Analyze Data Rapidly 399
xvi Contents
14.9 Screening Examples 401
References 404
15 Cognition Network Technology A Novel Multimodal
Image Analysis Technique for Automatic Identification
and Quantification of Biological Image Contents 407
Maria Athelogou, Giinter Schmidt, Arno Schape,
Martin Baatz, and Gerd Binnig
15.1 Introduction 407
15.2 Cognition Network Technology and Cognition
Network Language 409
15.2.1 Cognition Networks 409
15.2.2 Input Data and Image Object Hierarchy 410
15.2.3 Features and Variables 411
15.2.4 Classes and Classification 413
15.2.5 Processes 414
15.2.6 Domains 414
15.2.7 Using CNT CNL for Image Analysis 415
15.2.8 Application Notes 417
15.3 Discussion 421
References 421
16 High Content Phenotypic Cell Based Assays 423
Eugenio Fava, Eberhard Krausz, Rico Barsacchi,
Ivan Baines, and Marino Zerial
16.1 A New Tool for Biological Research and Drug Discovery 423
16.2 What Is High Content Screening and How Can
Biologists Use It? 424
16.3 Assay Design: First Think, Then Act 425
16.4 Assay Optimization 426
16.5 Cell Culture 426
16.6 Cell Vessels 428
16.7 Cellular Imaging 428
16.8 Autofluorescence 430
16.9 Image Analysis 431
16.10 Transfection Optimization for RNAi Based Assays 431
16.11 Escapers and Silencing Efficiency 432
16.12 Toxicity 435
16.13 Off Target or Unspecific Reactions 436
16.14 Assay Quality 437
16.15 Assay Validation 438
16.16 Conclusion and Outlook 440
References 440
Index 443
|
| adam_txt |
Contents
Preface v
I Considerations for Routine Imaging
1 Entering the Portal: Understanding the Digital Image
Recorded Through a Microscope 3
Kristin L. Hazelwood, Scott G. Olenych, John D. Griffin,
Judith A. Cathcart, and Michael W. Davidson
1.1 Introduction 3
1.2 Historical Perspective 4
1.3 Digital Image Acquisition: Analog to
Digital Conversion 4
1.4 Spatial Resolution in Digital Images 6
1.5 The Contrast Transfer Function 8
1.6 Image Brightness and Bit Depth 10
1.7 Image Histograms 11
1.8 Fundamental Properties of CCD Cameras 12
1.9 CCD Enhancing Technologies 16
1.10 CCD Performance Measures 17
1.11 Multidimensional Imaging 21
1.12 The Point Spread Function 24
1.13 Digital Image Display and Storage 28
1.14 Imaging Modes in Optical Microscopy 29
1.15 Summary 39
1.16 Internet Resources 41
References 41
2 Quantitative Biological Image Analysis 45
Erik Meijering and Gert van Cappellen
2.1 Introduction 45
2.2 Definitions and Perspectives 46
2.3 Image Preprocessing 48
2.3.1 Image Intensity Transformation 50
2.3.2 Local Image Filtering 50
ix
x Contents
2.3.3 Geometrical Image Transformation 53
2.3.4 Image Restoration 55
2.4 Advanced Processing for Image Analysis 57
2.4.1 Colocalization Analysis 58
2.4.2 Neuron Tracing and Quantification 58
2.4.3 Particle Detection and Tracking 60
2.4.4 Cell Segmentation and Tracking 62
2.5 Higher Dimensional Data Visualization 63
2.5.1 Volume Rendering 64
2.5.2 Surface Rendering 64
2.6 Software Tools and Development 66
References 68 '
3 The Open Microscopy Environment: A Collaborative
Data Modeling and Software Development Project
for Biological Image Informatics 71
Jason R. Swedlow
3.1 Introduction 71
3.1.1 What Is OME? 72
3.1.2 Why OME What Is the Problem? 72
3.2 OME Specifications and File Formats 74
3.2.1 OME Data Model 74
3.2.2 OME XML, OME TIFF and Bio Formats 76
3.3 OME Data Management and Analysis Software 77
3.3.1 OME Server and Web User Interface 77
3.3.2 OMERO Server, Client and Importer 84
3.3.3 Developing Usable Tools for Imaging 89
3.4 Conclusions and Future Directions 90
References 90
4 Design and Function of a Light Microscopy Facility 93
Kurt I. Anderson, Jeremy Sanderson, and Jan Peychl
4.1 Introduction 93
4.2 Users 95
4.3 Staff 96
4.3.1 Workplace Safety 96
4.3.2 User Training 97
4.3.3 Equipment Management 97
4.4 Equipment 98
4.4.1 Large Equipment 98
4.4.2 Small Equipment 99
4.4.3 Tools 100
4.4.4 Imaging Facility Layout 100
4.5 Organization 103
4.5.1 Equipment Booking Database 103
Contents xi
4.5.2 Fee for Service 106
4.5.3 Cost Matrix 107
4.5.4 Advisory Committees Ill
4.6 Summary 112
References 113
II Advanced Methods and Concepts
5 Quantitative Colocalisation Imaging: Concepts,
Measurements, and Pitfalls 117
Martin Oheim and Dongdong Li
5.1 Introduction 117
5.1.1 One Fluorophore, One Image? 124
5.1.2 A Practical Example of Dual Band Detection 135
5.2 Quantifying Colocalisation 137
5.2.1 'Colour Merging' 137
5.2.2 Pixel Based Techniques 139
5.2.3 Object Based Techniques 147
5.3 Conclusions 150
References 151
6 Quantitative FRET Microscopy of Live Cells 157
Adam D. Hoppe
6.1 Introduction 157
6.2 Introductory Physics of FRET 158
6.3 Manifestations of FRET in Fluorescence Signals 160
6.3.1 Spectral Change (Sensitized Emission) 160
6.3.2 Fluorescence Lifetime 161
6.3.3 Polarization 162
6.3.4 Accelerated Photobleaching 162
6.4 Molecular Interaction Mechanisms That Can Be
Observed by FRET 163
6.4.1 Conformational Change 164
6.4.2 Molecular Association 164
6.4.3 Molecular Assembly 164
6.5 Measuring Fluorescence Signals in the Microscope 165
6.6 Methods for FRET Microscopy 167
6.6.1 Photobleaching Approaches 168
6.6.2 Sensitized Emission 170
6.6.3 Spectral Fingerprinting and Matrix Notation for FRET. . 173
6.6.4 Polarization 174
6.7 Fluorescence Lifetime Imaging Microscopy for FRET 175
6.8 Data Display and Interpretation 176
6.9 FRET Based Biosensors 177
xii Contents
6.10 FRET Microscopy for Analyzing Interaction Networks
in Live Cells 178
6.11 Conclusion 180
References 180
7 Fluorescence Photobleaching and Fluorescence Correlation
Spectroscopy: Two Complementary Technologies
To Study Molecular Dynamics in Living Cells 183
Malte Wachsmuth and Klaus Weisshart
7.1 Introduction 183
7.1.1 FRAP and Other Photobleaching Methods 184
7.1.2 FCS and Other Fluctuation Analysis Methods 186
7.1.3 Comparing and Combining Techniques 187
7.2 Fundamentals 189
7.2.1 Fluorescent Labelling 189
7.2.2 Microscope Setup 191
7.2.3 Diffusion and Binding in Living Cells 193
7.2.4 Fluorescence, Blinking, and Photobleaching 194
7.2.5 Two Photon Excitation 195
7.3 How To Perform a FRAP Experiment 196
7.3.1 The Principle of Imaging Based FRAP 196
7.3.2 Choosing and Optimising the Experimental Parameters . 197
7.3.3 Quantitative Evaluation 200
7.3.4 Controls and Potential Artefacts 203
7.4 How To Perform an FCS Experiment 205
7.4.1 The Principle of FCS 205
7.4.2 Instrument Alignment and Calibration 208
7.4.3 Setting Up an Experiment 212
7.4.4 Types of Applications 213
7.4.5 Potential Artefacts 215
7.5 How To Perform a CP Experiment 217
7.5.1 The Principle of CP 217
7.5.2 Choosing and Optimising the Experimental Parameters . 218
7.5.3 Quantitative Evaluation 219
7.5.4 Controls and Potential Artefacts 220
7.6 Quantitative Treatment 221
7.6.1 Fluorescence Recovery After Photobleaching 221
7.6.2 Fluorescence Correlation Spectroscopy 223
7.6.3 Continuous Fluorescence Photobleaching 226
7.7 Conclusion 227
References 227
8 Single Fluorescent Molecule Tracking in Live Cells 235
Ghislain G. Cabal, Jost Enninga, and Musa M. Mhlanga
8.1 Introduction 235
Contents xiii
8.2 Tracking of Single Chromosomal Loci 236
8.2.1 General Remarks 236
8.2.2 In Vivo Single Loci Tagging via Operator/Repressor
Recognition 237
8.2.3 The Design of Strains Containing TetO Repeats
and Expressing TetR GFP 238
8.2.4 In Vivo Microscopy for Visualization of Single Tagged
Chromosomal Loci 244
8.2.5 Limits and Extension of Operator/Repressor Single
Loci Tagging System 246
8.3 Single Molecule Tracking of mRNA 247
8.3.1 Overview 247
8.3.2 The MS2 GFP System 247
8.3.3 The Molecular Beacon System 248
8.3.4 Setting Up the Molecular Beacon System for
the Detection of mRNA 250
8.3.5 Ensuring the Observed Fluorescent Particles in Vivo
Consist of Single Molecules of mRNA 251
8.4 Single Particle Tracking for Membrane Proteins 253
8.4.1 Overview 253
8.4.2 Quantum Dots As Fluorescent Labels for
Biological Samples 254
8.4.3 Functionalizing Quantum Dots To Label
Specific Proteins 255
8.4.4 Tracking the Glycin Receptor 1 at the Synaptic Cleft
Using Quantum Dots 257
8.5 Tracking Analysis and Image Processing of Data from
Particle Tracking in Living Cells 258
8.6 Conclusion 258
8.7 Protocols for Laboratory Use 259
8.7.1 Protocol: Single Molecule Tracking of Chromosomal
Loci in Yeast 259
8.7.2 Protocol: Single Molecule Tracking of
mRNA Experiment Using Molecular Beacons 259
References 261
9 From Live Cell Microscopy to Molecular Mechanisms:
Deciphering the Functions of Kinetochore Proteins 265
Khuloud Jaqaman, Jonas F. Dorn, and Gaudenz Danuser
9.1 Introduction 265
9.2 Biological Problem: Deciphering the Functions of
Kinetochore Proteins 268
9.3 Experimental Design 269
9.4 Extraction of Dynamics from Images 273
9.4.1 Mixture Model Fitting 274
xiv Contents
9.4.2 Tag Tracking 275
9.4.3 Multitemplate Matching 275
9.5 Characterization of Dynamics 276
9.5.1 Confined Brownian Motion Model 277
9.5.2 Simple Microtubule Dynamic Instability Model 278
9.5.3 Autoregressive Moving Average Model 279
9.5.4 Descriptor Sensitivity and Completeness 280
9.6 Quantitative Genetics of the Yeast Kinetochore 282
9.7 Conclusion 284
References 284
III Cutting Edge Applications Utilities
10 Towards Imaging the Dynamics of Protein Signalling 289
Lars Kaestner and Peter Lipp
10.1 Spatiotemporal Aspects of Protein Signalling Dynamics 289
10.2 How To Be Fast While Maintaining the Resolution 290
10.3 How To Make Proteins Visible 299
10.4 Concepts To Image Protein Dynamics 303
10.5 Concepts To Image Protein Protein Interactions 305
10.6 Concepts To Image Biochemistry with Fluorescent Proteins 309
References 311
11 New Technologies for Imaging and Analysis
of Individual Microbial Cells 313
Byron F. Brehm Stecher
11.1 Introduction 313
11.2 Live Cell Imaging 314
11.3 Imaging Infection 315
11.4 Imaging Single Molecules (Within Single Cells) 318
11.5 Measuring Discrete Cell Properties and Processes 319
11.6 "Wetware" 321
11.7 Hardware and Applications 323
11.7.1 Nonphotonic Microscopies 323
11.7.2 Image Analysis 324
11.7.3 Spectroscopic Methods 325
11.8 Fluorescence Correlation Spectroscopy 326
11.9 A Picture is Worth a Thousand Dots New Developments
in Flow Cytometry 330
11.10 Strength in Numbers Highly Parallel Analysis
Using Cellular Arrays 334
11.11 Nontactile Manipulation of Individual Cells and
"Wall less Test Tubes" 335
11.12 Conclusions 337
References 338
Contents xv
12 Imaging Parasites in Vivo 345
Rogerio Amino, Blandine Franke Fayard, Chris Janse,
Andrew Waters, Robert Menard, and Freddy Frischknecht
12.1 Introduction 345
12.2 The Life Cycle of Malaria Parasites 346
12.3 A Very Brief History of Light Microscopy
and Malaria Parasites 348
12.4 In Vivo Imaging of Luminescent Parasites 349
12.5 In Vivo Imaging of Fluorescent Parasites 350
12.6 Imaging Malaria Parasites in the Mosquito 351
12.7 Imaging Malaria Parasites in the Mammalian Host 354
12.8 Towards Molecular Imaging in Vivo 358
12.9 A Look at Other Parasites 359
12.10 Conclusion 360
References 360
13 Computer Assisted Systems for Dynamic 3D Reconstruction
and Motion Analysis of Living Cells 365
David R. Soil, Edward Voss, Deborah Wessels, and Spencer Kuhl
13.1 Introduction 365
13.2 Approaches to 3D Reconstruction and Motion Analysis 366
13.3 Obtaining Optical Sections for 3D Reconstruction 368
13.4 Outlining 368
13.5 Reconstructing 3D Faceted Images and Internal Architecture. . . 373
13.6 Quantitative Analyses of Behavior 373
13.7 3D DIASemb 375
13.8 Resolving Filopodia 377
13.9 The Combined Use of LSCM and 3D DIAS 380
13.10 Reasons for 3D Dynamic Image Reconstruction Analysis 381
References 382
14 High Throughput/High Content Automated Image
Acquisition and Analysis 385
Gabriele Gradl, Chris Hinnah, Achim Kirsch, Jiirgen Muller,
Dana Nojima, and Julian Wolcke
14.1 The Driving Forces for High Throughput/High Content
Automated Imaging 385
14.2 Confocal Imaging in High Throughput The Principles
Available 386
14.3 Resolution and Sensitivity 389
14.4 Measurements 392
14.5 Where Is the Signal and How To Focus? 393
14.6 Plates and Lenses 394
14.7 Image Analysis 395
14.8 Throughput: How To Acquire and Analyze Data Rapidly 399
xvi Contents
14.9 Screening Examples 401
References 404
15 Cognition Network Technology A Novel Multimodal
Image Analysis Technique for Automatic Identification
and Quantification of Biological Image Contents 407
Maria Athelogou, Giinter Schmidt, Arno Schape,
Martin Baatz, and Gerd Binnig
15.1 Introduction 407
15.2 Cognition Network Technology and Cognition
Network Language 409
15.2.1 Cognition Networks 409
15.2.2 Input Data and Image Object Hierarchy 410
15.2.3 Features and Variables 411
15.2.4 Classes and Classification 413
15.2.5 Processes 414
15.2.6 Domains 414
15.2.7 Using CNT CNL for Image Analysis 415
15.2.8 Application Notes 417
15.3 Discussion 421
References 421
16 High Content Phenotypic Cell Based Assays 423
Eugenio Fava, Eberhard Krausz, Rico Barsacchi,
Ivan Baines, and Marino Zerial
16.1 A New Tool for Biological Research and Drug Discovery 423
16.2 What Is High Content Screening and How Can
Biologists Use It? 424
16.3 Assay Design: First Think, Then Act 425
16.4 Assay Optimization 426
16.5 Cell Culture 426
16.6 Cell Vessels 428
16.7 Cellular Imaging 428
16.8 Autofluorescence 430
16.9 Image Analysis 431
16.10 Transfection Optimization for RNAi Based Assays 431
16.11 Escapers and Silencing Efficiency 432
16.12 Toxicity 435
16.13 Off Target or Unspecific Reactions 436
16.14 Assay Quality 437
16.15 Assay Validation 438
16.16 Conclusion and Outlook 440
References 440
Index 443 |
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| index_date | 2024-07-02T19:09:26Z |
| indexdate | 2024-07-09T21:08:55Z |
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| language | English |
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| spelling | Imaging cellular and molecular biological functions with 13 tables Spencer L. Shorte ... eds. Berlin [u.a.] Springer 2007 1 Online-Ressource txt rdacontent c rdamedia cr rdacarrier Principles and Practice Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Cytologie (DE-588)4070177-3 gnd rswk-swf Bildgebendes Verfahren (DE-588)4006617-4 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Molekularbiologie (DE-588)4039983-7 s Bildgebendes Verfahren (DE-588)4006617-4 s DE-604 Cytologie (DE-588)4070177-3 s Shorte, Spencer L. Sonstige oth Erscheint auch als Druck-Ausgabe, Hardcover 3-540-71330-1 Erscheint auch als Druck-Ausgabe, Hardcover 978-3-540-71330-2 https://doi.org/10.1007/978-3-540-71331-9 Verlag Volltext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016215483&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Imaging cellular and molecular biological functions with 13 tables Molekularbiologie (DE-588)4039983-7 gnd Cytologie (DE-588)4070177-3 gnd Bildgebendes Verfahren (DE-588)4006617-4 gnd |
| subject_GND | (DE-588)4039983-7 (DE-588)4070177-3 (DE-588)4006617-4 (DE-588)4143413-4 |
| title | Imaging cellular and molecular biological functions with 13 tables |
| title_auth | Imaging cellular and molecular biological functions with 13 tables |
| title_exact_search | Imaging cellular and molecular biological functions with 13 tables |
| title_exact_search_txtP | Imaging cellular and molecular biological functions with 13 tables |
| title_full | Imaging cellular and molecular biological functions with 13 tables Spencer L. Shorte ... eds. |
| title_fullStr | Imaging cellular and molecular biological functions with 13 tables Spencer L. Shorte ... eds. |
| title_full_unstemmed | Imaging cellular and molecular biological functions with 13 tables Spencer L. Shorte ... eds. |
| title_short | Imaging cellular and molecular biological functions |
| title_sort | imaging cellular and molecular biological functions with 13 tables |
| title_sub | with 13 tables |
| topic | Molekularbiologie (DE-588)4039983-7 gnd Cytologie (DE-588)4070177-3 gnd Bildgebendes Verfahren (DE-588)4006617-4 gnd |
| topic_facet | Molekularbiologie Cytologie Bildgebendes Verfahren Aufsatzsammlung |
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