Table Of ContentProgress in Optical Science and Photonics
Fu-Jen Kao
Gerd Keiser
Ankur Gogoi Editors
Advanced Optical
Methods for
Brain Imaging
Progress in Optical Science and Photonics
Volume 5
Series editors
Javid Atai
Rongguang Liang
U. S. Dinish
ThepurposeoftheseriesProgressinOpticalScienceandPhotonicsistoprovidea
forum to disseminate the latest research findings in various areas of Optics and its
applications. The intended audience is physicists, electrical and electronic
engineers, applied mathematicians, and advanced graduate students.
More information about this series at http://www.springer.com/series/10091
Fu-Jen Kao Gerd Keiser
(cid:129)
Ankur Gogoi
Editors
Advanced Optical Methods
for Brain Imaging
123
Editors
Fu-JenKao Ankur Gogoi
Institute of Biophotonics Institute of Biophotonics
National Yang-Ming University National Yang-Ming University
Taipei Taipei
Taiwan Taiwan
Gerd Keiser and
Department ofElectrical andComputer
Engineering Department ofPhysics
BostonUniversity JagannathBarooah College
Boston, MA Jorhat,Assam
USA India
ISSN 2363-5096 ISSN 2363-510X (electronic)
Progressin Optical Science andPhotonics
ISBN978-981-10-9019-6 ISBN978-981-10-9020-2 (eBook)
https://doi.org/10.1007/978-981-10-9020-2
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Preface
Solving the mystery of the brain, in particular the complex interplay between the
nervoussystem’sstructureandfunction,isoneofthemostexcitingfrontiersinthe
contemporary science. Enormous researches have been conducted for better
understanding of brain’s functions (or dysfunctions), with the ultimate aim to
translatethefindingsintothebenefitsofsocietyintermsofbasicscience,improved
diagnosis, and treatment for brain diseases. Approximately 4000 research works,
registeredinPubMed,relatedtobrainsciencehavebeenpublishedeveryyearsince
2013,withanever-increasingrate.Inlightofboostingthispaceandunderstanding
the brain at the level of synapse, a number of large-scale projects, e.g., US Brain
Research through Advancing Innovative Neurotechnologies (BRAIN), Human
Brain Project (EU), Brain/MINDS (Brain Mapping by Innovative
Neurotechnologies for Disease Studies of Japan), The Blue Brain (Switzerland),
havealreadybeeninitiatedglobally.Notably,manyrecentnovelinnovationsinthe
fields of genetic and chemical labeling, biological tissue clearing, cell typing,
microscopy and tomography techniques, image processing, network analysis, etc.,
have been triggered by such initiatives toward revealing newer secrets of thebrain
connectome.
In this context, it is critical to note that recent years have witnessed rapid
progresses in the development of optical methods for brain imaging. Advanced
microscopy methods, like super-resolution microscopy, multiphoton microscopy,
light-sheet microscopy, have laid the foundation for further advancement in brain
science by shedding light on neuronal circuit functions and mapping large brain
volumeswithunprecedenteddetails.Thisbookhighlightsthespectacularadvances
in brain imaging over the past few years. Starting from the fundamentals of con-
nectome and an overview of the imaging tools for connectomics, the book
encompassesastreamlinedandfocusedcoverageofthecoreprinciples,theoretical
and experimental approaches, and state-of-the-art applications of most of the cur-
rentlyusedimagingmethodsinbrainresearch,thathaveallowednovelinsightsinto
the structural and functional details of neuronal circuits.
v
vi Preface
The book is organized as follows: the first part of this book (Part I: Overview)
contains one chapter (Chap. 1) which is focused on the introduction to the brain
connectome and the optical tools for structural and functional brain imaging. The
key considerations for high-speed, high-resolution brain imaging at deeper brain
tissue are also addressed in this chapter.
PartIIofthebookcontainsfourchapters(Chaps.2–5)anddealswithadvanced
optical microscopy modalities that have generated profound revelations about
structuralandfunctionalconnectomics.Chapter2isdedicatedtoopticalcoherence
tomography (OCT) for whole brain imaging. This chapter describes the basic
principle of OCT and its applications for in vivo and in vitro imaging of brain
tissue. Light-sheet fluorescence microscopy (LSFM), its application in the
whole-brainimaging,aswellasthetechnicalchallengesspecifictothisymodality
are described in Chap. 3. Chapter 4 gives a comprehensive description of the
Airyscan technique and its advantages over traditional laser scanning microscopy.
Notably, while retaining all the benefits of confocal microscopy, in Airyscan the
resolution increases by 1.7X in all three spatial dimensions and the signal-to-noise
ratioincreasesby4–8Xovertraditionallaserscanningmicroscopy(LSM)acquired
with a 1 AU pinhole. Note that Airy scan can be considered as one form of
structured illumination, under Fourier optics. On the other hand, unlike traditional
fluorescence intensity-based imaging methods, fluorescence lifetime imaging
microscopy (FLIM) is a novel spectroscopic technique capable of providing
quantitative spatial and temporal information of the fluorescence lifetime of fluo-
phores. In connection to this exciting imaging modality, Chap. 5 presents the
multi-dimensional time-correlated single photon counting (TCSPC) technique for
the recording of Ca++ transients in live neurons via the fluorescence lifetime
changes of a Ca++-sensitive dye.
Part III of this book is devoted to the microscopy modalities that are based on
nonlinearmultiphotonexcitationandcontainsfivechapters(Chaps.6–10).Chapter
6 elucidates the recent advances in the in vivo multi-photon microscopy for less
invasive visualization of deeper and live brain tissues. The next chapter (Chap. 7)
focusesonthenon-scanhigh-speedfunctionalimagingdeepinsidetherodentbrain
using patterned two-photon illumination. In addition to discussing the advantages
and limitations of this technique, the authors specifically emphasized the combi-
nation of a non-scan technique with optogenetic manipulation and microscopic
imaging.Chapter8describesamultiphotonholographicimagingmodalitycapable
offunctional calcium imaging of neuronal activity. Using this modality multi-site
Ca2+imagingwasachievedbyholographicallyprojectedmulti-foci excitationand
subsequent fluorescence collection by a camera. Chapter 9 presents the detailed
description of the design and construction of a high-resolution, miniaturized
two-photon microscope and its application in the recording of neuronal activities
in vivo with high spatiotemporal resolution. Chapter 10 deals with the stimulated
Raman scattering (SRS) microscopy, which is capable of providing molecular
fingerprints of the target specimen. Also included in this chapter is a description
of the techniques and recent advances in SRS instrumentation for brain imaging.
Preface vii
The next section (Part IV) is devoted to the microscopy techniques capable of
acquiring super-resolved images of the neuronal structures (Chap. 11–13). The
section starts with Chap. 11 that briefly summarizes the optical super-resolving
approaches suitable for brain imaging applications. Chapter 12 is specifically
dedicated to the stimulated emission depletion (STED) microscopy, stochastic
optical reconstruction microscopy (STORM) and photoactivated localization
microscopy (PALM) modalities and their applications in the super-resolved
imaging of neuronal structures and processes. Expansion microscopy (ExM) is
another clever method to obtain super-resolution in ordinary microscopes by
physically expanding the size of the biological tissue in a uniform manner. The
detailed working principles of ExM, its different variants, and their brain imaging
applications are illustrated in Chap. 13.
Thelastpartofthebook(PartV),containingChaps.14and15,isdevotedtothe
recentdevelopmentsonthesupportingtechnologiesusedinopticalmicroscopyfor
efficientimagingofthestructureandfunctionofthebrain.Chapter14isfocusedon
the basic concepts, procedures, and implementations of adaptive optics (AO) in
optical microscopy. Notably, AO is a branch of applied optics that deals with the
aberrations caused due to the refractive index variation inside the biological tissue
to improve the aberration-induced degradation of resolution, contrast, and pene-
trationdepth.TheconcludingChap.15presentscomprehensivedescriptionsofthe
underlying principles of different biological tissue clearing techniques that mini-
mize light scattering to enable deep tissue imaging without physical sectioning.
We are extremely pleased that we have contributions in this book from the
international leaders of different photonics-based brain imaging modalities and
techniques.Ithasbeenourprivilegetoworkwiththeseauthors,andwewouldlike
to take this opportunity to thank them all.
Itnowremainstoacknowledgethosewhosecontributionsmadethepublication
of this book possible. First and foremost, we wish to thank Loyola D’Silva and
Prasanna Kumar Narayanasamy of Springer Nature Singapore for their superb
professional support. We are also grateful to the National Yang-Ming University
(NYMU), Taiwan; Boston University (BU), US; and Jagannath Barooah College
(JBC), Jorhat, India, for their institutional support. We would like to acknowledge
the Ministry of Science and Technology (MOST), Taiwan, and University Grants
Commission(UGC),India,fortheirsupporttothebiophotonicsresearchprojectsat
NYMU and JBC. Last but not least, we are most grateful to our families for their
understanding, support, and encouragement during the entire period of editing this
book.
TheEditorshopethatthereaderswillderiveasmuchjoyfromthecontributions
in this book as we did while working on it.
Taipei, Taiwan Fu-Jen Kao
Boston, USA Gerd Keiser
Taipei, Taiwan Ankur Gogoi
January 2018
Contents
Part I Overview
1 Multiscale and Multimodal Imaging for Connectomics. . . . . . . . . . 3
Ankur Gogoi, Gerd Keiser, Fu-Jen Kao and Ann-Shyn Chiang
Part II Advanced Optical Microscopy Methods
2 Optical Coherence Tomography for Brain Imaging . . . . . . . . . . . . 49
Bernhard Baumann
3 Light-Sheet Microscopy for Whole-Brain Imaging . . . . . . . . . . . . . 69
Monika Pawłowska, Marzena Stefaniuk, Diana Legutko
and Leszek Kaczmarek
4 The Airyscan Detector: Confocal Microscopy Evolution
for the Neurosciences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Joseph Huff
5 Recording Ca++ Transients in Neurons by TCSPC FLIM. . . . . . . . 103
Wolfgang Becker, Samuel Frere and Inna Slutsky
Part III Multiphoton Microscopy
6 In Vivo Imaging of All Cortical Layers and Hippocampal CA1
Pyramidal Cells by Two-Photon Excitation Microscopy . . . . . . . . . 113
Ryosuke Kawakami and Tomomi Nemoto
7 Patterned Two-Photon Illumination for High-Speed Functional
Imaging of Brain Networks In Vivo . . . . . . . . . . . . . . . . . . . . . . . . 123
Serena Bovetti, Claudio Moretti and Tommaso Fellin
8 Holographic Functional Calcium Imaging of Neuronal
Circuit Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
Michael Castanares, Greg J. Stuart and Vincent Daria
ix
x Contents
9 Advanced Miniature Microscopy for Brain Imaging. . . . . . . . . . . . 167
Weijian Zong and Liangyi Chen
10 Stimulated Raman Scattering Microscopy for Brain Imaging:
Basic Principle, Measurements, and Applications . . . . . . . . . . . . . . 189
Ankur Gogoi, Yi-Chih Liang, Gerd Keiser and Fu-Jen Kao
Part IV Super-Resolution Microscopy
11 Super-Resolving Approaches Suitable for Brain Imaging
Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Omer Wagner and Zeev Zalevsky
12 Super-Resolution STED and STORM/PALM Microscopy for
Brain Imaging. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Boris Egger and Simon G. Sprecher
13 Expansion Microscopy for Brain Imaging. . . . . . . . . . . . . . . . . . . . 259
Jae-Byum Chang
Part V Supporting Technologies in Brain Imaging
14 Adaptive Optics in Multiphoton Microscopy. . . . . . . . . . . . . . . . . . 277
Juan M. Bueno
15 Chemical Processing of Brain Tissues for Large-Volume,
High-Resolution Optical Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Jinyoung Seo, Dong-Jun Koo and Sung-Yon Kim
