Table Of ContentImaging Modalities for Biological
and Preclinical Research:
A Compendium, Volume 1
Part I: Ex vivo biological imaging
IPEM–IOP Series in Physics and Engineering in Medicine and Biology
Editorial Advisory Board Members
Frank Verhaegen Kwan Hoong Ng
Maastro Clinic, the Netherlands University of Malaya, Malaysia
Carmel Caruana John Hossack
University of Malta, Malta University of Virginia, USA
Penelope Allisy-Roberts Tingting Zhu
formerly of BIPM, Sèvres, France University of Oxford, UK
Rory Cooper Dennis Schaart
University of Pittsburgh, USA TU Delft, the Netherlands
Alicia El Haj Indra J Das
University of Birmingham, UK NorthwesternUniversityFeinbergSchool
of Medicine, USA
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Imaging Modalities for Biological
and Preclinical Research:
A Compendium, Volume 1
Part I: Ex vivo biological imaging
Edited by
Andreas Walter
Chair of COMULIS, Austrian BioImaging/CMI, Vienna BioCenter Core Facilities,
Vienna, Austria
Julia G Mannheim
WernerSiemensImagingCenter,DepartmentofPreclinicalImagingandRadiopharmacy,
Eberhard Karls University Tübingen, Tübingen, Germany
Carmel J Caruana
Department of Medical Physics, Faculty of Health Sciences, University of Malta,
Msida, Malta
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ISBN 978-0-7503-3059-6(ebook)
ISBN 978-0-7503-3057-2(print)
ISBN 978-0-7503-3060-2(myPrint)
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DOI 10.1088/978-0-7503-3059-6
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Contents
Preface xxvii
Acknowledgements xxix
Editor biographies xxx
List of contributors xxxii
Part I Ex vivo Imaging
Section 1 Light and fluorescence microscopy
I.1.a Transmission light microscopy I.1.a-1
Andreas Stylianou, Vasiliki Gkretsi, Paula Sampaio, Martin Glo¨smann
and Andreas Walter
1 Introduction I.1.a-1
2 Principles and setups I.1.a-2
2.1 Physical principles I.1.a-2
2.2 Typical setups and state-of-the-art I.1.a-4
3 Biomedical relevance I.1.a-9
3.1 Application range and relevance I.1.a-9
3.2 Sample preparation I.1.a-12
4 Parameters of image quality I.1.a-12
5 Data processing I.1.a-13
6 Conclusions I.1.a-14
6.1 Strength and limitations I.1.a-14
6.2 Future developments I.1.a-14
References and further reading I.1.a-15
I.1.b Fluorescence and confocal microscopy I.1.b-1
Ivana Vrhovac Madunic, Masa Skelin Klemen, Josip Madunic,
Natalie Kah Yun Wee and Paula Sampaio
1 Introduction I.1.b-1
2 Principles and setups I.1.b-2
2.1 Physical principles I.1.b-2
2.2 Typical setups and state-of-the-art I.1.b-4
3 Biomedical relevance I.1.b-5
3.1 Application range and relevance I.1.b-6
3.2 Sample preparation I.1.b-6
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ImagingModalitiesforBiologicalandPreclinicalResearch:ACompendium,Volume1
4 Parameters of image quality I.1.b-7
5 Data processing I.1.b-8
6 Conclusions I.1.b-9
6.1 Strength and limitations I.1.b-9
6.2 Future developments I.1.b-9
References and further reading I.1.b-10
I.1.c Lensless holographic microscopy I.1.c-1
Kerem Delikoyun, Ali Aslan Demir, Engin Ozcivici and Huseyin C Tekin
1 Introduction I.1.c-1
2 Principles and setups I.1.c-2
2.1 Physical principles I.1.c-2
2.2 Typical setups and state-of-the-art I.1.c-3
3 Biomedical relevance I.1.c-4
3.1 Application range and relevance I.1.c-4
3.2 Sample preparation I.1.c-6
4 Parameters of image quality I.1.c-6
4.1 Light source I.1.c-6
4.2 Imaging sensor I.1.c-7
5 Data processing I.1.c-7
6 Conclusions I.1.c-8
6.1 Strength and limitations I.1.c-8
6.2 Future developments I.1.c-9
References and further reading I.1.c-9
I.1.d High-content microscopy I.1.d-1
Andre´ Maia and Maria Gomez-Lazaro
1 Introduction I.1.d-1
2 Principles and setups I.1.d-2
2.1 Physical principles I.1.d-2
2.2 Typical setups and state-of-the-art I.1.d-6
3 Biomedical relevance I.1.d-9
3.1 Application range and relevance I.1.d-9
3.2 Sample preparation I.1.d-10
3.3 Parameters of image quality I.1.d-10
4 Data processing I.1.d-11
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ImagingModalitiesforBiologicalandPreclinicalResearch:ACompendium,Volume1
5 Conclusions I.1.d-12
5.1 Strength and limitations I.1.d-12
5.2 Future developments I.1.d-12
References and further reading I.1.d-14
I.1.e Calcium imaging I.1.e-1
Andrazˇ Stozˇer, Jurij Dolensˇek, Lidija Krizˇancˇic´ Bombek,
Marko Gosak and Masˇa Skelin Klemen
1 Introduction I.1.e-1
2 Principles and setups I.1.e-2
2.1 Physical principles I.1.e-2
2.2 Typical setups and state-of-the-art I.1.e-4
3 Biomedical relevance I.1.e-5
3.1 Application range and relevance I.1.e-6
3.2 Sample preparation I.1.e-6
4 Parameters of image quality I.1.e-8
5 Data processing I.1.e-9
6 Conclusions I.1.e-11
6.1 Strength and limitations I.1.e-11
6.2 Future developments I.1.e-12
References and further reading I.1.e-12
I.1.f Fluorescence cryo-microscopy I.1.f-1
Rainer Kaufmann, Vi Quint Duong and Julian Falckenhayn
1 Introduction I.1.f-1
2 Principles and setups I.1.f-2
2.1 Physical principles I.1.f-2
2.2 Typical setups and state-of-the-art I.1.f-3
3 Biomedical relevance I.1.f-5
3.1 Application range and relevance I.1.f-5
3.2 Sample preparation I.1.f-6
4 Parameters of image quality I.1.f-8
5 Data processing I.1.f-8
6 Conclusions I.1.f-9
6.1 Strength and limitations I.1.f-9
6.2 Future developments I.1.f-9
References and further reading I.1.f-9
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ImagingModalitiesforBiologicalandPreclinicalResearch:ACompendium,Volume1
Section 2 Light microscopy of tissues and thick samples
I.2.a Light sheet fluorescence microscopy I.2.a-1
Adam Glaser and Emmanuel G Reynaud
1 Introduction I.2.a-1
2 Principles and setups I.2.a-1
2.1 Optical principles I.2.a-1
2.2 Typical setups and state-of-the-art I.2.a-3
3 Biomedical relevance I.2.a-3
3.1 Application range and relevance I.2.a-3
3.2 Sample preparation I.2.a-4
4 Parameters of image quality I.2.a-4
4.1 Spatial resolution I.2.a-4
4.2 Contrast I.2.a-5
5 Data-processing I.2.a-5
6 Conclusions I.2.a-6
References and further reading I.2.a-6
I.2.b Lattice light sheet microscopy I.2.b-1
Mo´nica Ferna´ndez-Monreal and Mathieu Ducros
1 Introduction I.2.b-1
2 Principles and setups I.2.b-2
2.1 Physical principles I.2.b-2
2.2 Typical setups and state-of-the-art I.2.b-3
3 Biomedical relevance I.2.b-4
3.1 Application range and relevance I.2.b-4
3.2 Sample preparation I.2.b-6
4 Parameters of image quality I.2.b-6
4.1 Spatial and temporal resolution I.2.b-6
4.2 Light sheet focusing I.2.b-7
4.3 Imaging depth I.2.b-7
5 Data processing I.2.b-7
6 Conclusions I.2.b-7
6.1 Strength and limitations I.2.b-7
6.2 Future developments I.2.b-8
Movie legends I.2.b-8
References and further reading I.2.b-8
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ImagingModalitiesforBiologicalandPreclinicalResearch:ACompendium,Volume1
I.2.c Multiphoton microscopy I.2.c-1
Claire Lefort
1 Introduction I.2.c-1
2 Principles and setups I.2.c-2
2.1 Physical principles I.2.c-2
2.2 Typical setups and state-of-the-art I.2.c-3
3 Biomedical relevance of multiphoton microscopy I.2.c-4
3.1 Application range and relevance of multiphoton microscopy I.2.c-4
(MPM)
3.2 Sample preparation I.2.c-5
4 Parameters of image quality I.2.c-6
5 Data processing I.2.c-6
6 Conclusions I.2.c-7
6.1 Strength and limitations I.2.c-7
6.2 Future developments I.2.c-7
References and further reading I.2.c-8
I.2.d Second and third harmonic generation imaging I.2.d-1
Marco Andreana and Angelika Unterhuber
1 Introduction I.2.d-1
2 Principles and setups I.2.d-2
2.1 Physical principles I.2.d-2
2.2 Typical setups and state-of-the-art I.2.d-3
3 Biomedical relevance I.2.d-5
3.1 Application range and relevance I.2.d-6
3.2 Sample preparation I.2.d-6
4 Parameters of image quality I.2.d-7
5 Data processing I.2.d-7
6 Conclusions I.2.d-8
6.1 Strength and limitations I.2.d-8
6.2 Future developments I.2.d-8
References and further reading I.2.d-9
I.2.e Adaptive optics I.2.e-1
Nikita Vladimirov and Xiaodong Tao
1 Introduction I.2.e-1
2 Principles and setups I.2.e-2
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