Advanced Optical Methods for Brain Imaging PDF
Preview Advanced Optical Methods for Brain Imaging
Progress 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 LibraryofCongressControlNumber:2018937352 ©SpringerNatureSingaporePteLtd.2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfrom therelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authorsortheeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinor for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. Printedonacid-freepaper ThisSpringerimprintispublishedbytheregisteredcompanySpringerNatureSingaporePteLtd. partofSpringerNature Theregisteredcompanyaddressis:152BeachRoad,#21-01/04GatewayEast,Singapore189721, Singapore 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
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