Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 1 : Part I: Ex Vivo Biological Imaging

The relentless pace of innovation in biomedical imaging has provided modern researchers with an unprecedented number of techniques and tools to choose from. While the development of new imaging techniques is vital for ongoing progress in the life sciences, it is challenging for researchers to keep pace. __Imaging Modalities for Biological and Preclinical Research__ is designed to provide a comprehensive overview of currently available biological and preclinical imaging methods, including their benefits and limitations. Experts in the field guide the reader through both the physical principles and biomedical applications of each imaging modality, including description of typical setups and sample preparation. __Volume 1__ focuses on __ex-vivo__ imaging. It covers all available advanced and basic light and fluorescence microscopy modalities, X-ray, electron, atomic force and helium ion microscopy, dynamic techniques such as fluorescence recovery after photobleaching as well as spectroscopic techniques such as coherent Raman imaging or mass spectrometry imaging. **Key features** * Provides an overview of fast-evolving __ex-vivo__ imaging technologies. * Bridges biological and preclinical imaging. * Written by imaging specialists with extensive expertise in their respective fields. PRELIMS.pdf Preface Acknowledgements Editor biographies Andreas Walter Julia G Mannheim Carmel J Caruana List of contributors CH001.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH002.pdf Chapter I.1.b Fluorescence and confocal microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH003.pdf Chapter I.1.c Lensless holographic microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Light source 4.2 Imaging sensor 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments Acknowledgments References and further reading CH004.pdf Chapter I.1.d High-content microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 3.3 Parameters of image quality 4 Data processing 5 Conclusions 5.1 Strength and limitations 5.2 Future developments Acknowledgments Further reading References CH005.pdf Chapter I.1.e Calcium imaging 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH006.pdf Chapter I.1.f Fluorescence cryo-microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH007.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Optical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Spatial resolution 4.2 Contrast 5 Data-processing 6 Conclusions References and further reading CH008.pdf Chapter I.2.b Lattice light sheet microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Spatial and temporal resolution 4.2 Light sheet focusing 4.3 Imaging depth 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments Movie legends References and further reading CH009.pdf Chapter I.2.c Multiphoton microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance of multiphoton microscopy 3.1 Application range and relevance of multiphoton microscopy (MPM) 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH010.pdf Chapter I.2.d Second and third harmonic generation imaging 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH011.pdf Chapter I.2.e Adaptive optics 1 Introduction 2 Principles and setups 2.1 Aberrations as phase functions in the pupil plane 2.2 Wavefront correctors 2.3 Wavefront measurement 2.4 Typical setups and state-of-the-art 2.5 Computational adaptive optics 3 Biomedical relevance 4 Conclusions 4.1 Strength and limitations 4.2 Future developments References and further reading CH012.pdf Chapter I.2.f Optical projection tomography 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality for OPT ‘raw projection data sets’ 5 Data processing—reconstructing optical slices in OPT 6 Conclusions Acknowledgements References and further reading CH013.pdf Chapter I.2.g High-resolution episcopic microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Resolution, voxel size and field of view 4.2 Dye penetration 4.3 Technical characteristics of HREM apparatus 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH014.pdf Chapter I.2.h Tissue image cytometry 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters influencing image and data quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH015.pdf Chapter I.2.i Histopathology 1 Introduction 2 Principles and setup 2.1 Basic principles of histology and pathology 2.2 Typical setup for histopathology 2.3 State-of-the-art in histopathology 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments Acknowledgments References and further reading CH016.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Acquisition setup 4.2 Choice of camera 4.3 Environmental controls 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH017.pdf Chapter I.3.b Structured illumination microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH018.pdf Chapter I.3.c Single-molecule localisation microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups 3 Biomedical relevance 3.1 Application range 3.2 Sample preparation 4 Parameters of image quality 4.1 Spatial resolution 4.2 Localisation precision 4.3 Localisation accuracy 4.4 Sample background 4.5 Sample motion 4.6 On-off switching and blinking 4.7 Temporal resolution 4.8 Multi-colour imaging 4.9 Reference structures 5 Data processing and visualisation 5.1 Localisation 5.2 Filtering and corrections 5.3 Visualisation 5.4 Advanced analysis 6 Conclusions 6.1 Strengths and limitations 6.2 Future developments Acknowledgements References and further reading CH019.pdf Chapter I.3.d Stimulated emission depletion microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Molecular events hunting by live STED 3.2 Correlative STED—HIM/SEM microscopy 3.3 STED—Lithography 3.4 STED-controlled photoisomerisation 4 Conclusion References and further reading CH020.pdf Chapter I.3.e Expansion microscopy 1 Introduction 2 Principles and setups 2.1 Labelling strategies for expansion microscopy 2.2 Typical combination with advanced optical microscopy methods 3 Biomedical relevance 3.1 Clinical applications 3.2 Sample preparation 4 Parameters of image quality: S/N and expansion factor 5 Data processing: distortion analysis 6 Conclusions 6.1 Perspectives: multimodal and correlative approaches References and further reading CH021.pdf Chapter I.3.f Scattering-type scanning near-field optical microscopy 1 Introduction 2 Principles and setups 2.1 Physical principle of ASNOM 2.2 Scattering-type scanning near-field optical microscopy 2.3 Typical set-ups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH022.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Practical considerations for tomography acquisitions 4.2 Quality of the images 4.3 Typical tomographic artefacts 5 Data processing 6 Conclusions 6.1 Strengths and limitations 6.2 Future developments References and further reading CH023.pdf Chapter I.4.b Soft X-ray tomography 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH024.pdf Chapter 1 Introduction 1.1 Principles and setups 2 Physical principles 2.1 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 4 Sample preparation 5 Parameters of image quality 6 Data processing 7 Conclusions 7.1 Strength and limitations 7.2 Future developments Acknowledgements References and further reading CH025.pdf Chapter I.5.b Cryo-transmission electron microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation challenges 4 Parameters of image quality 5 Data processing 5.1 SPA data processing 5.2 Cryo-ET data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH026.pdf Chapter I.5.c Scanning electron microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Conclusions References and further reading CH027.pdf Chapter I.5.d Volume scanning electron microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH028.pdf Chapter I.5.e Nanotomy 1 Introduction 2 Principles and setups 3 Biomedical relevance 3.1 Sample preparation 3.2 Application range and relevance 4 Data processing 4.1 Post-acquisition processing 4.2 Data sharing 4.3 Data analysis 5 Conclusions 5.1 Strength and limitations 5.2 Future developments References and further reading CH029.pdf Chapter I.5.f Scanning transmission electron microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 4 Sample preparation 5 Parameters of image quality 5.1 C1 lens, spot size 5.2 Condenser aperture 5.3 Condenser stigmators 5.4 Camera length 6 Data processing 7 Conclusions 7.1 Strength and limitations 8 Future developments References and further reading CH030.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Surface topography 4.2 Mechanical properties of biological samples 4.3 Interaction forces 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH031.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 4 Sample preparation 5 Parameters of image quality 6 Data processing 7 Conclusions 7.1 Strength and limitations 7.2 Future developments References and further reading CH032.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions References and further reading CH033.pdf Chapter I.8.b Fluorescence correlation spectroscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of data quality 4.1 Signal-to-noise ratio (SNR) 4.2 Spatial resolution 4.3 Temporal resolution 4.4 Artefacts 5 Data processing 6 Conclusions 6.1 Strengths and limitations 6.2 Comparison to other techniques 6.3 Future developments References and further reading CH034.pdf Chapter I.8.c Fluorescence recovery after photobleaching 1 Introduction 2 Principles and experimental setups 2.1 Physical principles 2.2 Experimental setups 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of acquisition and measurement quality 5 Data analysis 5.1 Empirical approach 5.2 Analytical approach: theory and limits 6 Conclusions References and further reading CH035.pdf Chapter I.8.d Single-particle tracking 1 Introduction 2 Principles and setups 2.1 FRAP/FLIP 2.2 FCS 2.3 STED—FCS 2.4 MINFLUX 2.5 SPT 3 Conclusions 3.1 Strength and limitations 3.2 Future developments References and further reading CH036.pdf Chapter I.8.e Biospeckle imaging 1 Introduction 2 Principles and setups 2.1 Physical principles of the dynamic biospeckle phenomenon 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing metrics of the biospeckle activity 6 Conclusion 6.1 Strength and limitations 6.2 Future developments References and further reading CH037.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles and state-of-the-art 2.2 Typical setups 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength (↑) and Limitations (↓) 6.2 Future developments References and further reading CH038.pdf Chapter I.9.b Coherent Raman imaging 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 4 Parameters of image quality 5 Conclusions 5.1 Strength and limitations 5.2 Future developments References and further reading CH039.pdf Chapter I.9.c Brillouin microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical BLS-microscopy setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Resolution in Brillouin microscopy 4.2 Multimodal Brillouin microscopy 4.3 Relation to other measured mechanical properties 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH040.pdf Chapter I.9.d Electron energy loss spectroscopy and energy filtered transmission electron microscopy 1 Introduction 2 Principles and setups 2.1 The EELS spectrum 2.2 The energy filter and spectrometer 2.3 Chemical quantification 3 Biomedical relevance 3.1 Zero-loss filtering 3.2 Plasmon loss filtering 3.3 Chemical mapping 4 Parameters of image quality 4.1 Spatial resolution of energy filtered images 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH041.pdf Chapter I.9.e Energy-dispersive X-ray spectroscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 EDX-artefacts 4.1 Sum peaks (pile-up peaks) 4.2 Escape peaks 4.3 Silicon internal fluorescence 4.4 Spurious signals 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH042.pdf Chapter I.9.f Micro-X-ray fluorescence spectroscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 7 Future developments References and further reading CH043.pdf Chapter I.9.g Mass spectrometry-based imaging 1 Introduction 2 Principles and setups 2.1 Physical principles [7] 2.2 Setup and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Spectral quality 4.2 Image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH044.pdf Chapter I.9.h Imaging mass cytometry 1 Introduction 2 Principles and setups 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation: verification testing 4 Parameters of image quality 4.1 Panel design and metal assignment 4.2 IMC versus IF comparison 5 Data processing 5.1 Data on characterisation of immune profiles of normal and cancerous tissues 6 Conclusions References and further reading CH045.pdf Chapter I.9.i Magnetic resonance microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH046.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Sample preparation 4 Parameters of image quality 4.1 Radionuclide 4.2 Tissue condition and section thickness 4.3 Specificity of radioligand 4.4 Exposure time 4.5 Films and phosphor screens 4.6 Light 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading The relentless pace of innovation in biomedical imaging has provided modern researchers with an unprecedented number of techniques and tools to choose from. While the development of new imaging techniques is vital for ongoing progress in the life sciences, it is challenging for researchers to keep pace. Imaging Modalities for Biological and Preclinical Research is designed to provide a comprehensive overview of currently available biological and preclinical imaging methods, including their benefits and limitations. Experts in the field guide the reader through both the physical principles and biomedical applications of each imaging modality, including description of typical setups and sample preparation. Volume 1 focuses on ex vivo imaging. It covers all available advanced and basic light and fluorescence microscopy modalities, X-ray, electron, atomic force and helium ion microscopy, dynamic techniques such as fluorescence recovery after photobleaching as well as spectroscopic techniques such as coherent Raman imaging or mass spectrometry imaging. Part of IPEM-IOP Series in Physics and Engineering in Medicine and Biology