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Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 1

Part I: Ex vivo biological imaging
Andreas Walter, Julia Mannheim, Carmel J Caruana


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.

About Editors

Andreas Walter is Director of Austrian BioImaging/CMI ( His goal is to advance correlated multimodality imaging (CMI) as a valuable tool in biomedical research. He is also the main proposer and Chair of the EU-funded COST Action COMULIS (CA17121) that aims at promoting the benefits of CMI through showcase pipelines and paving the way for its technological advancement and implementation as a versatile tool in biological and preclinical research (

Julia Mannheim is a group leader for PET and Multimodal Imaging Science in the Department of Preclinical Imaging and Radiopharmacy at the Eberhard Karls University Tübingen, Germany, alongside being the Deputy Director of the Department since November 2014. She is an expert in PET quantification and reproducibility/reliability of the acquired data. Her focus is currently on the standardization of preclinical imaging to enhance the scientific integrity and reliability of the acquired data.

Carmel J Caruana is Professor and Head of the Department of Medical Physics of the Faculty of Health Sciences at the University of Malta where he lectures in X-ray imaging, fluoroscopy, magnetic resonance imaging, computed tomography, ultrasound and nuclear medicine imaging including PET/CT and PET/MRI. Carmel has over 30 years experience in the teaching of all imaging modalities to all healthcare professions and at all levels including the specialty level. He is very much involved in curriculum development for Medical Physicists at the European and international levels and was previously the Chair of the Education and Training Committee of the European Federation of Organisations for Medical Physics. In the last few years he has been encouraging Medical Physicists to expand their scope of practice to pre-clinical and biological imaging.

Table of Contents


Part I: Ex-vivo Imaging

I.1 - Light and fluorescence microscopy
I.1.a Transmission light microscopy
I.1.b Fluorescence and confocal microscopy
I.1.c Lensless digital inline holographic microscopy
I.1.d High-content microscopy
I.1.e Calcium imaging
I.1.f Fluorescence cryo-microscopy

I.2 - Light microscopy of tissues and thick samples
I.2.a Light sheet fluorescence microscopy (LSFM)
I.2.b Lattice light sheet microscopy
I.2.c Multiphoton microscopy
I.2.d Second and third harmonic generation imaging
I.2.e Adaptive optics
I.2.f Optical projection tomography
I.2.g High-resolution episcopic microscopy (HREM)
I.2.h Tissue image cytometry
I.2.i Histopathology

I.3 - Super-resolution microscopy
I.3.a Total internal reflection fluorescence microscopy
I.3.b Structured illumination microscopy
I.3.c Single-molecule localization microscopy (SMLM)
I.3.d Stimulated emission depletion (STED) microscopy
I.3.e Expansion microscopy
I.3.f Scattering-type scanning near-field optical microscopy (s-SNOM)

I.4 - X-ray microscopy
I.4.a Hard x-ray tomographic microscopy
I.4.b Soft x-ray tomography

I.5 - Electron microscopy
I.5.a Transmission electron microscopy
I.5.b Cryo-transmission electron microscopy
I.5.c Scanning electron microscopy
I.5.d Volume SEM
I.5.e Nanotomy
I.5.f Electron microscopy—STEM

I.6 - Atomic force microscopy and spectroscopy

I.7 - Helium ion microscopy

I.8 - Dynamic techniques
I.8.a Förster resonance energy transfer (FRET)—fluorescence lifetime imaging microscopy (FLIM)
I.8.b Fluorescence correlation spectroscopy (FCS)
I.8.c Fluorescence recovery after photobleaching (FRAP)
I.8.d Single particle tracking
I.8.e BIOSPECKLE imaging

I.9 - Imaging and spectrometry
I.9.a Raman imaging
I.9.b Coherent Raman imaging (CARS, SRS)
I.9.c Brillouin microscopy
I.9.d Chemical analysis—EELS and EFTEM
I.9.e Chemical analysis—EDX
I.9.f Micro-x-ray fluorescence analysis
I.9.g Mass spectrometry-based imaging
I.9.h Imaging mass cytometry
I.9.i Magnetic resonance microscopy

I.10 - Autoradiography


Hardback ISBN: 9780750330572

Ebook ISBN: 9780750330596

DOI: 10.1088/978-0-7503-3059-6

Publisher: Institute of Physics Publishing

Series: IPEM-IOP Series in Physics and Engineering in Medicine and Biology


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