Imaging Modalities for Biological and Preclinical Research: A Compendium: Part II-IV: inn vivo preclinical imaging: correlated multimodality imaging and outlook

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 2__ focuses on __in vivo__ imaging methods, including intravital microscopy, ultrasound, MRI, CT and PET. Correlative multimodal imaging, (pre)clinical hybrid imaging techniques and multimodal image processing methods are also discussed. The volume concludes with a look ahead to emerging technologies and the future of imaging in biological and preclinical research. **Key Features** * Provides an overview of fast-evolving __in-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 4.1 Scattering 4.2 Spatial and temporal resolution 4.3 Setup: movement artefacts and awake imaging 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH002.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 Conclusions 4.1 Strength and limitations 4.2 Future developments References and further reading CH003.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 Excitation light source 4.2 Ultrasound detectors 4.3 Reconstruction methods 4.4 Detection geometry 5 Conclusions 5.1 Strength and limitations 5.2 Future developments References and further reading CH004.pdf Chapter 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 and temporal resolution 4.2 Tissue penetration depth 4.3 Bleed-through and crosstalk 5 Data processing and visualisation 6 Conclusion 6.1 Strengths and limitations 6.2 Future developments References and further reading CH005.pdf Chapter II.4.b Bioluminescence 1 Introduction 2 Principles and setups 2.1 Chemical and 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 and temporal resolution 4.2 Tissue penetration depth 4.3 Background signal 5 Data processing and visualisation 6 Conclusion 6.1 Strengths and limitations 6.2 Future developments References and further reading CH006.pdf Chapter II.4.c Cerenkov luminescence imaging 1 Introduction to Cerenkov luminescence 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Preclinical application range and relevance 3.2 Clinical application range and relevance 3.3 CL activated agents 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments Acknowledgements References and further reading CH007.pdf Chapter 1 Introduction 2 Principles and setups 2.1 General presentation of an endoscopic exploration 2.2 Physical principles of an endomicroscope 2.3 Technical principles, typical setup and state-of-the-art of endomicroscopy 3 Biomedical relevance 4 Parameters of image quality 4.1 Label-free imaging of biological constituents 4.2 Movements and endomicroscopic examination 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH008.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 3.2 Sample preparation 4 Parameters of image quality 4.1 Resolution of ultrasound scanners 4.2 Artefacts in preclinical ultrasound imaging. 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH009.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 CH010.pdf Chapter II.7.b Functional magnetic resonance imaging 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 Signal-to-noise ratio 4.2 Motion and field distortion 4.3 Spatial/temporal resolution 4.4 fMRI statistical parameters 4.5 Physiological parameters 5 Data processing and visualisation 5.1 Masking 5.2 Global mean removal 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH011.pdf Chapter II.7.c Hyperpolarised 13C magnetic resonance spectroscopic imaging 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Radicals 2.3 Typical setups and state-of-the-art 3 Biomedical relevance 3.1 Application range and relevance 3.2 Hyperpolarised 13C-labelled cell substrates 4 Parameters of image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH012.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Particle properties 2.2 Physical principles 2.3 Instrumentation 3 Data processing 3.1 MPI problem formulation 3.2 System matrix reconstruction 3.3 X-space reconstruction 4 Biomedical relevance 4.1 Diagnostic scenarios 4.2 Therapeutic scenarios 5 Conclusions 5.1 Strength and limitations 5.2 Future developments References and further reading CH013.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 Radiation dose 4.2 Control of artefacts and image quality 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments Acknowledgements References and further reading CH014.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Radiopharmaceuticals/radiotracers 2.2 Physical principles 2.3 PET detectors 2.4 Typical setups and state-of-the-art 2.5 Image reconstruction 3 Biomedical relevance 3.1 Application range and relevance 3.2 Subject preparation 4 Parameters of image quality 4.1 Chemical aspect influencing image quantification 4.2 Technological aspect influencing image quantification 4.3 Methodological aspect influencing image quantification 4.4 Biological aspect influencing image quantification 5 Data processing 5.1 Image data analysis 5.2 Sample analysis 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH015.pdf Chapter II.11 Single photon emission computed tomography 1 Introduction 2 Principles and setups 2.1 Principles of SPECT 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 Sensitivity 4.3 Noise 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future improvements References and further reading CH016.pdf Chapter 1 Introduction 2 Principles and setups 2.1 Principle of CLEM 2.2 Setup of a CLEM experiment 3 Biomedical relevance 3.1 The power of CLEM 3.2 CLEM workflows 3.3 A real CLEM example 4 Conclusions 4.1 Strengths and limitations 4.2 Future developments Acknowledgements References and further reading CH017.pdf Chapter III.1.b Correlative atomic force microscopy 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups and state-of-the-art 3 Conclusions 3.1 Strength and limitations 3.2 Future developments References and further reading CH018.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 Subject preparation 4 Parameters of image quality 4.1 Factors degrading image quality 4.2 PET/CT artefacts 4.3 PET calibration and quality control 4.4 CT calibration and quality control 4.5 PET/CT annual testing 5 Data processing 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH019.pdf Chapter III.2.b PET/SPECT/CT 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 CH020.pdf Chapter III.2.c PET/MR 1 Introduction 2 Principles and setups 2.1 Physical principles 2.2 Typical setups 3 Biomedical relevance 3.1 Applications in biological/preclinical research 3.2 Sample preparation and requirements 4 Parameters of image quality 5 Data processing and visualisation 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References for further reading References CH021.pdf Chapter III.2.d Fluorescence molecular tomography/CT 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 Factors affecting sensitivity of fluorescence measurement 4.2 Imaging parameters ensuring desirable signal acquisition 4.3 Absolute signal quantification, fluorescence database 5 Data processing and visualisation 6 Conclusions 6.1 Strength and limitations 6.2 Future developments References and further reading CH022.pdf Chapter III.2.e PET/CT/ultrasound 1 Introduction 2 Principles and setups of PETRUS 2.1 Physical principles 2.2 Typical setup 3 Biomedical relevance 3.1 Oncology 3.2 Cardiology 3.3 Sample preparation 4 Parameters of image quality 5 Data processing 6 Conclusion 6.1 Strength and limitations 6.2 Future developments Acknowledgements References and further reading CH023.pdf Chapter 1 Introduction 2 Showcases and setups 2.1 Multimodality microCT-guided correlative microscopy 2.2 X-ray microscopy in CMI approaches for neuroscience 3 Parameters of image quality 4 Data processing 5 Conclusions 5.1 Strength and limitations 5.2 Future developments References and further reading CH024.pdf Chapter Acknowledgements References and further reading CH025.pdf Chapter III.4.b Multimodal image registration 1 Introduction 2 Challenges in a multimodal setting 3 Principles and main approaches 3.1 Similarity criterion 3.2 Deformation model, regularisation, and optimisation 3.3 Dealing with multimodal images 4 Examples of application 4.1 Correlating genotype and phenotype in rat models of hypertension (2-D histological images to 3-D MR scans) 4.2 Characterising the immune response to colorectal cancer (IHC to IHC) 5 Conclusions References and further reading CH026.pdf Chapter III.4.c Learning-based approaches for multimodal imaging 1 Introduction: machine learning in image analysis 1.1 Machine learning basics 1.2 Artificial neural networks and deep learning 2 Use case for state-of-the-art learning models for the analysis of biological images: cell nuclei segmentation using U-Nets and multimodality imaging 3 Machine learning in image registration and image fusion 3.1 Image registration 3.2 Image fusion 4 Conclusion References and further reading CH027.pdf Chapter III.4.d Multimodal image segmentation 1 Introduction 2 Challenges in a multimodal setting 3 Principles and main approaches 3.1 Neural networks 3.2 Data pre-processing 3.3 Ground truth: manual annotation for learning strategies 3.4 Semantic segmentation 3.5 Object detection 3.6 Instance segmentation 3.7 Segmentation quality measures 3.8 GUI-based segmentation tools 4 Examples of application 4.1 T1 and T2-based MRI 4.2 Digital pathology slides 4.3 Multichannel microscopy 4.4 Neural networks-based generally applicable segmentation tools 5 Conclusions References and further reading CH028.pdf Chapter III.4.e Visualisation for correlative multimodal imaging 1 Introduction 2 Challenges in a multimodal setting 2.1 Different sampling grids 2.2 Data size 2.3 Information fusion 2.4 Visualisation design 3 Principles and main approaches 3.1 2D slice-based visualisation 3.2 2D slice-based visualisation 3.3 3D volumetric visualisation 3.4 Spatio-temporal visualisation 3.5 Glyph visualisation 3.6 Visual analytics 3.7 Pixel/voxel level fusion 3.8 Feature level fusion 3.9 Decision level fusion 4 Examples of application 5 Conclusions References and further reading CH029.pdf Chapter III.4.f Data compression algorithms for biomedical images 1 Introduction 2 Challenges in a multimodal setting 3 Principles and main approaches 4 Examples of application 4.1 JPEG-LS 4.2 JPEG 2000 4.3 H.265/HEVC 4.4 CALIC 4.5 MRP 4.6 JPEG-XL 4.7 VVC 5 Comparative overview 6 Conclusions References and further reading CH030.pdf Chapter III.4.g Computer-assisted analysis of multimodal image data—perspectives and conclusion 1 Challenges in a multimodal setting 2 Principles and main approaches 2.1 Model-based versus learning-based approaches 2.2 Moving information between modalities 2.3 Images versus their representations 2.4 Fusion—early, late, or middle 2.5 Registration for segmentation or segmentation for registration 3 Examples of application—available software and how to find the right one 4 Conclusion References and further reading CH031.pdf Chapter IV.1 Emerging technologies and outlook 1 Introduction 2 Emerging technologies 2.1 (In vivo) imaging of thick tissue at high resolution 2.2 Spectroscopic label-free imaging 2.3 Correlated multimodality imaging 2.4 Macroscopic preclinical imaging 2.5 Automation in bioimaging 3 Big data in bioimaging 4 Other trends 4.1 Zooming in 4.2 Zooming out 5 Conclusions References and further reading