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.
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: 550
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
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
