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.
Author(s): Andreas Walter, Julia Mannheim, Carmel J. Caruana
Series: IPEM–IOP Series in Physics and Engineering in Medicine and Biology
Publisher: IOP Publishing
Year: 2021
Language: English
Pages: 700
City: Bristol
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
