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Cheng S, Chang S, Li Y, Novoseltseva A, Lin S, Wu Y, Zhu J, McKee AC, Rosene DL, Wang H, Bigio IJ, Boas DA, Tian L. Enhanced Multiscale Human Brain Imaging by Semi-supervised Digital Staining and Serial Sectioning Optical Coherence Tomography. RESEARCH SQUARE 2024:rs.3.rs-4014687. [PMID: 38562721 PMCID: PMC10984089 DOI: 10.21203/rs.3.rs-4014687/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A major challenge in neuroscience is to visualize the structure of the human brain at different scales. Traditional histology reveals micro- and meso-scale brain features, but suffers from staining variability, tissue damage and distortion that impedes accurate 3D reconstructions. Here, we present a new 3D imaging framework that combines serial sectioning optical coherence tomography (S-OCT) with a deep-learning digital staining (DS) model. We develop a novel semi-supervised learning technique to facilitate DS model training on weakly paired images. The DS model performs translation from S-OCT to Gallyas silver staining. We demonstrate DS on various human cerebral cortex samples with consistent staining quality. Additionally, we show that DS enhances contrast across cortical layer boundaries. Furthermore, we showcase geometry-preserving 3D DS on cubic-centimeter tissue blocks and visualization of meso-scale vessel networks in the white matter. We believe that our technique offers the potential for high-throughput, multiscale imaging of brain tissues and may facilitate studies of brain structures.
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Affiliation(s)
- Shiyi Cheng
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
| | - Shuaibin Chang
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
| | - Yunzhe Li
- Department of Electrical Engineering and Computer Sciences, University of California, Cory Hall, Berkeley, California, 94720, USA
| | - Anna Novoseltseva
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
| | - Sunni Lin
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
| | - Yicun Wu
- Department of Computer Science, Boston University, 665 Commonwealth Ave, Boston, MA, 02215, USA
| | - Jiahui Zhu
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
| | - Ann C. McKee
- Boston University Alzheimer’s Disease Research Center and CTE Center, Boston University, Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- Department of Neurology, Boston University, Chobanian and Avedisian School of Medicine, Boston, MA, 02118, USA
- VA Boston Healthcare System, U.S. Department of Veteran Affairs, Jamaica Plain, MA, 02130, USA
- Department of Psychiatry and Ophthalmology, Boston University School of Medicine, Boston, MA, 02118, USA
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Douglas L. Rosene
- Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts, USA
| | - Hui Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA, 02129, USA
| | - Irving J. Bigio
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
- Neurophotonics Center, Boston University, Boston, MA, 02215, USA
| | - David A. Boas
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
- Neurophotonics Center, Boston University, Boston, MA, 02215, USA
| | - Lei Tian
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston, MA, 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA, 02215, USA
- Neurophotonics Center, Boston University, Boston, MA, 02215, USA
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2
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Makris N, Rushmore R, Kaiser J, Albaugh M, Kubicki M, Rathi Y, Zhang F, O’Donnell LJ, Yeterian E, Caviness VS, Kennedy DN. A Proposed Human Structural Brain Connectivity Matrix in the Center for Morphometric Analysis Harvard-Oxford Atlas Framework: A Historical Perspective and Future Direction for Enhancing the Precision of Human Structural Connectivity with a Novel Neuroanatomical Typology. Dev Neurosci 2023; 45:161-180. [PMID: 36977393 PMCID: PMC10526721 DOI: 10.1159/000530358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
A complete structural definition of the human nervous system must include delineation of its wiring diagram (e.g., Swanson LW. Brain architecture: understanding the basic plan, 2012). The complete formulation of the human brain circuit diagram (BCD [Front Neuroanat. 2020;14:18]) has been hampered by an inability to determine connections in their entirety (i.e., not only pathway stems but also origins and terminations). From a structural point of view, a neuroanatomic formulation of the BCD should include the origins and terminations of each fiber tract as well as the topographic course of the fiber tract in three dimensions. Classic neuroanatomical studies have provided trajectory information for pathway stems and their speculative origins and terminations [Dejerine J and Dejerine-Klumpke A. Anatomie des Centres Nerveux, 1901; Dejerine J and Dejerine-Klumpke A. Anatomie des Centres Nerveux: Méthodes générales d'étude-embryologie-histogénèse et histologie. Anatomie du cerveau, 1895; Ludwig E and Klingler J. Atlas cerebri humani, 1956; Makris N. Delineation of human association fiber pathways using histologic and magnetic resonance methodologies; 1999; Neuroimage. 1999 Jan;9(1):18-45]. We have summarized these studies previously [Neuroimage. 1999 Jan;9(1):18-45] and present them here in a macroscale-level human cerebral structural connectivity matrix. A matrix in the present context is an organizational construct that embodies anatomical knowledge about cortical areas and their connections. This is represented in relation to parcellation units according to the Harvard-Oxford Atlas neuroanatomical framework established by the Center for Morphometric Analysis at Massachusetts General Hospital in the early 2000s, which is based on the MRI volumetrics paradigm of Dr. Verne Caviness and colleagues [Brain Dev. 1999 Jul;21(5):289-95]. This is a classic connectional matrix based mainly on data predating the advent of DTI tractography, which we refer to as the "pre-DTI era" human structural connectivity matrix. In addition, we present representative examples that incorporate validated structural connectivity information from nonhuman primates and more recent information on human structural connectivity emerging from DTI tractography studies. We refer to this as the "DTI era" human structural connectivity matrix. This newer matrix represents a work in progress and is necessarily incomplete due to the lack of validated human connectivity findings on origins and terminations as well as pathway stems. Importantly, we use a neuroanatomical typology to characterize different types of connections in the human brain, which is critical for organizing the matrices and the prospective database. Although substantial in detail, the present matrices may be assumed to be only partially complete because the sources of data relating to human fiber system organization are limited largely to inferences from gross dissections of anatomic specimens or extrapolations of pathway tracing information from nonhuman primate experiments [Front Neuroanat. 2020;14:18, Front Neuroanat. 2022;16:1035420, and Brain Imaging Behav. 2021;15(3):1589-1621]. These matrices, which embody a systematic description of cerebral connectivity, can be used in cognitive and clinical studies in neuroscience and, importantly, to guide research efforts for further elucidating, validating, and completing the human BCD [Front Neuroanat. 2020;14:18].
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Affiliation(s)
- Nikos Makris
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Psychiatry Neuroimaging Laboratory, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Richard Rushmore
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Psychiatry Neuroimaging Laboratory, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, USA
| | - Jonathan Kaiser
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew Albaugh
- Department of Psychiatry, University of Vermont Larner College of Medicine, Burlington, VT, USA
| | - Marek Kubicki
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Psychiatry Neuroimaging Laboratory, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Yogesh Rathi
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Psychiatry Neuroimaging Laboratory, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, USA
| | - Fan Zhang
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren J. O’Donnell
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Edward Yeterian
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychology, Colby College, Waterville, ME, USA
| | - Verne S. Caviness
- Center for Morphometric Analysis, Harvard Medical School, Massachusetts General Hospital, Boston, MA, USA
| | - David N. Kennedy
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA, USA
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3
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Yang J, Chang S, Chen IA, Kura S, Rosen GA, Saltiel NA, Huber BR, Varadarajan D, Balbastre Y, Magnain C, Chen SC, Fischl B, McKee AC, Boas DA, Wang H. Volumetric Characterization of Microvasculature in Ex Vivo Human Brain Samples By Serial Sectioning Optical Coherence Tomography. IEEE Trans Biomed Eng 2022; 69:3645-3656. [PMID: 35560084 PMCID: PMC9888394 DOI: 10.1109/tbme.2022.3175072] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Serial sectioning optical coherence tomography (OCT) enables accurate volumetric reconstruction of several cubic centimeters of human brain samples. We aimed to identify anatomical features of the ex vivo human brain, such as intraparenchymal blood vessels and axonal fiber bundles, from the OCT data in 3D, using intrinsic optical contrast. METHODS We developed an automatic processing pipeline to enable characterization of the intraparenchymal microvascular network in human brain samples. RESULTS We demonstrated the automatic extraction of the vessels down to a 20 μm in diameter using a filtering strategy followed by a graphing representation and characterization of the geometrical properties of microvascular network in 3D. We also showed the ability to extend this processing strategy to extract axonal fiber bundles from the volumetric OCT image. CONCLUSION This method provides a viable tool for quantitative characterization of volumetric microvascular network as well as the axonal bundle properties in normal and pathological tissues of the ex vivo human brain.
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Yendiki A, Aggarwal M, Axer M, Howard AF, van Cappellen van Walsum AM, Haber SN. Post mortem mapping of connectional anatomy for the validation of diffusion MRI. Neuroimage 2022; 256:119146. [PMID: 35346838 PMCID: PMC9832921 DOI: 10.1016/j.neuroimage.2022.119146] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 01/13/2023] Open
Abstract
Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both the macroscopic trajectories and the microstructural properties of axon bundles in vivo. The Human Connectome Project ushered in an era of impressive advances in dMRI acquisition and analysis. As a result of these efforts, the quality of dMRI data that could be acquired in vivo improved substantially, and large collections of such data became widely available. Despite this progress, the main limitation of dMRI remains: it does not image axons directly, but only provides indirect measurements based on the diffusion of water molecules. Thus, it must be validated by methods that allow direct visualization of axons but that can only be performed in post mortem brain tissue. In this review, we discuss methods for validating the various features of connectional anatomy that are extracted from dMRI, both at the macro-scale (trajectories of axon bundles), and at micro-scale (axonal orientations and other microstructural properties). We present a range of validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.
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Affiliation(s)
- Anastasia Yendiki
- Department of Radiology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, United States,Corresponding author (A. Yendiki)
| | - Manisha Aggarwal
- Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Markus Axer
- Forschungszentrum Jülich, Institute of Neuroscience and Medicine, Jülich, Germany,Department of Physics, University of Wuppertal Germany
| | - Amy F.D. Howard
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Anne-Marie van Cappellen van Walsum
- Department of Medical Imaging, Anatomy, Radboud University Medical Center, Nijmegen, the Netherland,Cognition and Behaviour, Donders Institute for Brain, Nijmegen, the Netherland
| | - Suzanne N. Haber
- Department of Pharmacology and Physiology, University of Rochester, Rochester, NY, United States,McLean Hospital, Belmont, MA, United States
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5
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OCT-Guided Surgery for Gliomas: Current Concept and Future Perspectives. Diagnostics (Basel) 2022; 12:diagnostics12020335. [PMID: 35204427 PMCID: PMC8871129 DOI: 10.3390/diagnostics12020335] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/19/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Optical coherence tomography (OCT) has been recently suggested as a promising method to obtain in vivo and real-time high-resolution images of tissue structure in brain tumor surgery. This review focuses on the basics of OCT imaging, types of OCT images and currently suggested OCT scanner devices and the results of their application in neurosurgery. OCT can assist in achieving intraoperative precision identification of tumor infiltration within surrounding brain parenchyma by using qualitative or quantitative OCT image analysis of scanned tissue. OCT is able to identify tumorous tissue and blood vessels detection during stereotactic biopsy procedures. The combination of OCT with traditional imaging such as MRI, ultrasound and 5-ALA fluorescence has the potential to increase the safety and accuracy of the resection. OCT can improve the extent of resection by offering the direct visualization of tumor with cellular resolution when using microscopic OCT contact probes. The theranostic implementation of OCT as a part of intelligent optical diagnosis and automated lesion localization and ablation could achieve high precision, automation and intelligence in brain tumor surgery. We present this review for the increase of knowledge and formation of critical opinion in the field of OCT implementation in brain tumor surgery.
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6
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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7
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Etievant A, Monnin J, Lihoreau T, Tamadazte B, Rougeot P, Magnin E, Tavernier L, Pazart L, Haffen E. Comparison of Noninvasive Imagery Methods to Observe Healthy and Degenerated Olfactory Epithelium in Mice for the Early Diagnosis of Neurodegenerative Diseases. Front Neuroanat 2020; 14:34. [PMID: 32760253 PMCID: PMC7371997 DOI: 10.3389/fnana.2020.00034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/28/2020] [Indexed: 11/13/2022] Open
Abstract
Olfactory dysfunction could be an early and reliable indicator for the diagnosis of neurodegenerative disorders such as Alzheimer and Parkinson's diseases. In this paper, we compare the potential of different noninvasive medical imaging modalities (optical coherence tomography, confocal microscopy, and fluorescence endomicroscopy) to distinguish how the olfactory epithelium, both at the cellular and the structural levels, is altered. Investigations were carried out on three experimental groups: two pathological groups (mice models with deliberately altered olfactory epithelium and Alzheimer's disease transgenic mice models) were compared with healthy mice models. As histological staining, the three tested noninvasive imaging tools demonstrated the general tubular organization of the olfactory epithelium on healthy mice. Contrary to OCT, confocal microscopy, and endomicroscopy allowed visualizing the inner structure of olfactory epithelium as well as its morphological or functional changes on pathological models, alterations classically observed with histological assessment. The results could lead to relevant development of imaging tools for noninvasive and early diagnosis of neurodegenerative diseases through the in situ characterization of the olfactory epithelium.
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Affiliation(s)
- Adeline Etievant
- Laboratoire de Neurosciences Intégratives et Cliniques, Université Bourgogne-Franche-Comté, Université de Franche-Comté, Besançon, France
| | - Julie Monnin
- Laboratoire de Neurosciences Intégratives et Cliniques, Université Bourgogne-Franche-Comté, Université de Franche-Comté, Besançon, France.,CHU Besançon, INSERM, CIC 1431, Centre d'Investigation Clinique, Besançon, France
| | - Thomas Lihoreau
- CHU Besançon, INSERM, CIC 1431, Centre d'Investigation Clinique, Besançon, France
| | - Brahim Tamadazte
- FEMTO-ST, Dép. AS2M, CNRS, Université Bourgogne Franche-Comté, 24 rue Savary, Besançon, France.,Institut des Systémes Intelligents et de Robotique, Sorbonne Université, CNRS, UMR 7222, Paris, France
| | - Patrick Rougeot
- FEMTO-ST, Dép. AS2M, CNRS, Université Bourgogne Franche-Comté, 24 rue Savary, Besançon, France
| | - Eloi Magnin
- Laboratoire de Neurosciences Intégratives et Cliniques, Université Bourgogne-Franche-Comté, Université de Franche-Comté, Besançon, France
| | - Laurent Tavernier
- Service d'oto-Rhino-Laryngologie et Chirurgie Cervico-Faciale, CHU Besançon, Université Bourgogne-Franche-Comté, Besançon, France
| | - Lionel Pazart
- Laboratoire de Neurosciences Intégratives et Cliniques, Université Bourgogne-Franche-Comté, Université de Franche-Comté, Besançon, France.,CHU Besançon, INSERM, CIC 1431, Centre d'Investigation Clinique, Besançon, France
| | - Emmanuel Haffen
- Laboratoire de Neurosciences Intégratives et Cliniques, Université Bourgogne-Franche-Comté, Université de Franche-Comté, Besançon, France.,CHU Besançon, INSERM, CIC 1431, Centre d'Investigation Clinique, Besançon, France
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8
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Lichtenegger A, Gesperger J, Niederleithner M, Ginner L, Woehrer A, Drexler W, Baumann B, Leitgeb RA, Salas M. Ex-vivo Alzheimer's disease brain tissue investigation: a multiscale approach using 1060-nm swept source optical coherence tomography for a direct correlation to histology. NEUROPHOTONICS 2020; 7:035004. [PMID: 32855993 PMCID: PMC7441220 DOI: 10.1117/1.nph.7.3.035004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Significance: Amyloid-beta ( A - β ) plaques are pathological protein deposits formed in the brain of Alzheimer's disease (AD) patients upon disease progression. Further research is needed to elucidate the complex underlying mechanisms involved in their formation using label-free, tissue preserving, and volumetric techniques. Aim: The aim is to achieve a one-to-one correlation of optical coherence tomography (OCT) data to histological micrographs of brain tissue using 1060-nm swept source OCT. Approach: A - β plaques were investigated in ex-vivo AD brain tissue using OCT with the capability of switching between two magnifications. For the exact correlation to histology, a 3D-printed tool was designed to generate samples with parallel flat surfaces. Large field-of-view (FoV) and sequentially high-resolution volumes at different locations were acquired. The large FoV served to align the OCT to histology images; the high-resolution images were used to visualize fine details. Results: The instrument and the presented method enabled an accurate correlation of histological micrographs with OCT data. A - β plaques were identified as hyperscattering features in both FoV OCT modalities. The plaques identified in volumetric OCT data were in good agreement with immunohistochemically derived micrographs. Conclusion: OCT combined with the 3D-printed tool is a promising approach for label-free, nondestructive, volumetric, and fast tissue analysis.
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Affiliation(s)
- Antonia Lichtenegger
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Johanna Gesperger
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- Medical University of Vienna, Division of Neuropathology and Neurochemistry, Department of Neurology, Vienna, Austria
| | - Michael Niederleithner
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Laurin Ginner
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Adelheid Woehrer
- Medical University of Vienna, Division of Neuropathology and Neurochemistry, Department of Neurology, Vienna, Austria
| | - Wolfgang Drexler
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Bernhard Baumann
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
| | - Rainer A. Leitgeb
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- Medical University of Vienna, Christian Doppler Laboratory for Innovative Optical Imaging and its Translation to Medicine, Vienna, Austria
| | - Matthias Salas
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, Vienna, Austria
- Medical University of Vienna, Division of Neuropathology and Neurochemistry, Department of Neurology, Vienna, Austria
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9
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Rushmore RJ, Bouix S, Kubicki M, Rathi Y, Yeterian EH, Makris N. How Human Is Human Connectional Neuroanatomy? Front Neuroanat 2020; 14:18. [PMID: 32351367 PMCID: PMC7176274 DOI: 10.3389/fnana.2020.00018] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/23/2020] [Indexed: 01/16/2023] Open
Abstract
The structure of the human brain has been studied extensively. Despite all the knowledge accrued, direct information about connections, from origin to termination, in the human brain is extremely limited. Yet there is a widespread misperception that human connectional neuroanatomy is well-established and validated. In this article, we consider what is known directly about human structural and connectional neuroanatomy. Information on neuroanatomical connections in the human brain is derived largely from studies in non-human experimental models in which the entire connectional pathway, including origins, course, and terminations, is directly visualized. Techniques to examine structural connectivity in the human brain are progressing rapidly; nevertheless, our present understanding of such connectivity is limited largely to data derived from homological comparisons, particularly with non-human primates. We take the position that an in-depth and more precise understanding of human connectional neuroanatomy will be obtained by a systematic application of this homological approach.
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Affiliation(s)
- R Jarrett Rushmore
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, United States.,Psychiatric Neuroimaging Laboratory, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Center for Morphometric Analysis, Department of Psychiatry and Neurology, A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Sylvain Bouix
- Psychiatric Neuroimaging Laboratory, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States
| | - Marek Kubicki
- Psychiatric Neuroimaging Laboratory, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Center for Morphometric Analysis, Department of Psychiatry and Neurology, A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Yogesh Rathi
- Psychiatric Neuroimaging Laboratory, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Center for Morphometric Analysis, Department of Psychiatry and Neurology, A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Edward H Yeterian
- Psychiatric Neuroimaging Laboratory, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Center for Morphometric Analysis, Department of Psychiatry and Neurology, A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Department of Psychology, Colby College, Waterville, ME, United States
| | - Nikos Makris
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, United States.,Psychiatric Neuroimaging Laboratory, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, United States.,Center for Morphometric Analysis, Department of Psychiatry and Neurology, A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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10
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Speckle modulation enables high-resolution wide-field human brain tumor margin detection and in vivo murine neuroimaging. Sci Rep 2019; 9:10388. [PMID: 31316099 PMCID: PMC6637128 DOI: 10.1038/s41598-019-45902-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
Current in vivo neuroimaging techniques provide limited field of view or spatial resolution and often require exogenous contrast. These limitations prohibit detailed structural imaging across wide fields of view and hinder intraoperative tumor margin detection. Here we present a novel neuroimaging technique, speckle-modulating optical coherence tomography (SM-OCT), which allows us to image the brains of live mice and ex vivo human samples with unprecedented resolution and wide field of view using only endogenous contrast. The increased visibility provided by speckle elimination reveals white matter fascicles and cortical layer architecture in brains of live mice. To our knowledge, the data reported herein represents the highest resolution imaging of murine white matter structure achieved in vivo across a wide field of view of several millimeters. When applied to an orthotopic murine glioblastoma xenograft model, SM-OCT readily identifies brain tumor margins with resolution of approximately 10 μm. SM-OCT of ex vivo human temporal lobe tissue reveals fine structures including cortical layers and myelinated axons. Finally, when applied to an ex vivo sample of a low-grade glioma resection margin, SM-OCT is able to resolve the brain tumor margin. Based on these findings, SM-OCT represents a novel approach for intraoperative tumor margin detection and in vivo neuroimaging.
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11
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Li T, Liu CJ, Akkin T. Contrast-enhanced serial optical coherence scanner with deep learning network reveals vasculature and white matter organization of mouse brain. NEUROPHOTONICS 2019; 6:035004. [PMID: 31338386 PMCID: PMC6646884 DOI: 10.1117/1.nph.6.3.035004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/02/2019] [Indexed: 06/01/2023]
Abstract
Optical coherence tomography provides volumetric reconstruction of brain structure with micrometer resolution. Gray matter and white matter can be highlighted using conventional and polarization-based contrasts; however, vasculature in ex-vivo fixed brain has not been investigated at large scale due to lack of intrinsic contrast. We present contrast enhancement to visualize the vasculature by perfusing titanium dioxide particles transcardially into the mouse vascular system. The brain, after dissection and fixation, is imaged by a serial optical coherence scanner. Accumulation of particles in blood vessels generates distinguishable optical signals. Among these, the cross-polarization images reveal the vasculature organization remarkably well. The conventional and polarization-based contrasts are still available for probing the gray matter and white matter structures. The segmentation and reconstruction of the vasculature are presented by using a deep learning algorithm. Axonal fiber pathways in the mouse brain are delineated by utilizing the retardance and optic axis orientation contrasts. This is a low-cost method that can be further developed to study neurovascular diseases and brain injury in animal models.
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Affiliation(s)
- Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Chao J. Liu
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
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12
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Yashin KS, Kiseleva EB, Gubarkova EV, Moiseev AA, Kuznetsov SS, Shilyagin PA, Gelikonov GV, Medyanik IA, Kravets LY, Potapov AA, Zagaynova EV, Gladkova ND. Cross-Polarization Optical Coherence Tomography for Brain Tumor Imaging. Front Oncol 2019; 9:201. [PMID: 31001471 PMCID: PMC6455095 DOI: 10.3389/fonc.2019.00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/11/2019] [Indexed: 12/23/2022] Open
Abstract
This paper considers valuable visual assessment criteria for distinguishing between tumorous and non-tumorous tissues, intraoperatively, using cross-polarization OCT (CP OCT)—OCT with a functional extension, that enables detection of the polarization properties of the tissues in addition to their conventional light scattering. Materials and Methods: The study was performed on 176 ex vivo human specimens obtained from 30 glioma patients. To measure the degree to which the typical parameters of CP OCT images can be matched to the actual histology, 100 images of tumors and white matter were selected for visual analysis to be undertaken by three “single-blinded” investigators. An evaluation of the inter-rater reliability between the investigators was performed. Application of the identified visual CP OCT criteria for intraoperative use was performed during brain tumor resection in 17 patients. Results: The CP OCT image parameters that can typically be used for visual assessment were separated: (1) signal intensity; (2) homogeneity of intensity; (3) attenuation rate; (4) uniformity of attenuation. The degree of match between the CP OCT images and the histology of the specimens was significant for the parameters “signal intensity” in both polarizations, and “homogeneity of intensity” as well as the “uniformity of attenuation” in co-polarization. A test based on the identified criteria showed a diagnostic accuracy of 87–88%. Intraoperative in vivo CP OCT images of white matter and tumors have similar signals to ex vivo ones, whereas the cortex in vivo is characterized by indicative vertical striations arising from the “shadows” of the blood vessels; these are not seen in ex vivo images or in the case of tumor invasion. Conclusion: Visual assessment of CP OCT images enables tumorous and non-tumorous tissues to be distinguished. The most powerful aspect of CP OCT images that can be used as a criterion for differentiation between tumorous tissue and white matter is the signal intensity. In distinguishing white matter from tumors the diagnostic accuracy using the identified visual CP OCT criteria was 87–88%. As the CP OCT data is easily associated with intraoperative neurophysiological and neuronavigation findings this can provide valuable complementary information for the neurosurgeon tumor resection.
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Affiliation(s)
- Konstantin S Yashin
- Microneurosurgery Group, University Clinic, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Elena B Kiseleva
- Laboratory of Optical Coherence Tomography, Research Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Ekaterina V Gubarkova
- Laboratory of Optical Coherence Tomography, Research Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Alexander A Moiseev
- Laboratory of High-Sensitivity Optical Measurements, Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod, Russia
| | - Sergey S Kuznetsov
- Department of Anatomical Pathology, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Pavel A Shilyagin
- Laboratory of High-Sensitivity Optical Measurements, Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod, Russia
| | - Grigory V Gelikonov
- Laboratory of High-Sensitivity Optical Measurements, Institute of Applied Physics, Russian Academy of Sciences, Nizhny Novgorod, Russia
| | - Igor A Medyanik
- Microneurosurgery Group, University Clinic, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Leonid Ya Kravets
- Microneurosurgery Group, University Clinic, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Alexander A Potapov
- Federal State Autonomous Institution "N.N. Burdenko National Scientific and Practical Center for Neurosurgery" of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Elena V Zagaynova
- Research Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Natalia D Gladkova
- Laboratory of Optical Coherence Tomography, Research Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
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13
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Caspers S, Axer M. Decoding the microstructural correlate of diffusion MRI. NMR IN BIOMEDICINE 2019; 32:e3779. [PMID: 28858413 DOI: 10.1002/nbm.3779] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 06/28/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Diffusion imaging has evolved considerably over the past decade. While it provides valuable information about the structural connectivity at the macro- and mesoscopic scale, bridging the gap to the microstructure at the level of single nerve fibers poses an enormous challenge. This is particularly true for the human brain with its large size, its large white-matter volume and availability of histological techniques for studying human whole-brain sections and subsequent 3D reconstruction. Classic post-mortem techniques for studying the fiber architecture of the brain, such as myeloarchitectonic staining or dye tracing, are complemented by novel histological approaches, such as 3D polarized light imaging or optical coherence tomography, enabling unique insight into the fiber architecture from large fiber bundles within deep white matter to single nerve fibers in the cortex. The present review discusses the benefits and challenges of these latest developments in comparison with the classic techniques, with particular focus on the mutual exchange between in vivo and post-mortem diffusion imaging and post-mortem microstructural approaches for understanding the wiring of the brain across different scales.
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Affiliation(s)
- Svenja Caspers
- C. and O. Vogt Institute for Brain Research, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- JARA-BRAIN, Jülich-Aachen Research Alliance, Jülich, Germany
| | - Markus Axer
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
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14
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Vandenberghe ME, Souedet N, Hérard AS, Ayral AM, Letronne F, Balbastre Y, Sadouni E, Hantraye P, Dhenain M, Frouin F, Lambert JC, Delzescaux T. Voxel-Based Statistical Analysis of 3D Immunostained Tissue Imaging. Front Neurosci 2018; 12:754. [PMID: 30498427 PMCID: PMC6250035 DOI: 10.3389/fnins.2018.00754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 10/01/2018] [Indexed: 12/23/2022] Open
Abstract
Recently developed techniques to visualize immunostained tissues in 3D and in large samples have expanded the scope of microscopic investigations at the level of the whole brain. Here, we propose to adapt voxel-based statistical analysis to 3D high-resolution images of the immunostained rodent brain. The proposed approach was first validated with a simulation dataset with known cluster locations. Then, it was applied to characterize the effect of ADAM30, a gene involved in the metabolism of the amyloid precursor protein, in a mouse model of Alzheimer's disease. This work introduces voxel-based analysis of 3D immunostained microscopic brain images and, therefore, opens the door to localized whole-brain exploratory investigation of pathological markers and cellular alterations.
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Affiliation(s)
- Michel E. Vandenberghe
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Nicolas Souedet
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Anne-Marie Ayral
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Florent Letronne
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Yaël Balbastre
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Elmahdi Sadouni
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Marc Dhenain
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Frédérique Frouin
- Laboratoire Imagerie Moléculaire in vivo (IMIV UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS)Orsay, France
| | - Jean-Charles Lambert
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Thierry Delzescaux
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
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15
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Lefebvre J, Delafontaine-Martel P, Pouliot P, Girouard H, Descoteaux M, Lesage F. Fully automated dual-resolution serial optical coherence tomography aimed at diffusion MRI validation in whole mouse brains. NEUROPHOTONICS 2018; 5:045004. [PMID: 30681668 PMCID: PMC6215086 DOI: 10.1117/1.nph.5.4.045004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
An automated dual-resolution serial optical coherence tomography (2R-SOCT) scanner is developed. The serial histology system combines a low-resolution ( 25 μ m / voxel ) 3 × OCT with a high-resolution ( 1.5 μ m / voxel ) 40 × OCT to acquire whole mouse brains at low resolution and to target specific regions of interest (ROIs) at high resolution. The 40 × ROIs positions are selected either manually by the microscope operator or using an automated ROI positioning selection algorithm. Additionally, a multimodal and multiresolution registration pipeline is developed in order to align the 2R-SOCT data onto diffusion MRI (dMRI) data acquired in the same ex vivo mouse brains prior to automated histology. Using this imaging system, 3 whole mouse brains are imaged, and 250 high-resolution 40 × three-dimensional ROIs are acquired. The capability of this system to perform multimodal imaging studies is demonstrated by labeling the ROIs using a mouse brain atlas and by categorizing the ROIs based on their associated dMRI measures. This reveals a good correspondence of the tissue microstructure imaged by the high-resolution OCT with various dMRI measures such as fractional anisotropy, number of fiber orientations, apparent fiber density, orientation dispersion, and intracellular volume fraction.
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Affiliation(s)
- Joël Lefebvre
- École Polytechnique de Montréal, Laboratoire d’imagerie optique et moléculaire, Montreal, Canada
| | | | - Philippe Pouliot
- École Polytechnique de Montréal, Laboratoire d’imagerie optique et moléculaire, Montreal, Canada
- Université de Montréal, Research Centre, Montréal Heart Institute, Montreal, Canada
| | - Hélène Girouard
- Université de Montréal, Institut universitaire de gériatrie de Montréal, Montreal, Canada
| | - Maxime Descoteaux
- Université de Sherbrooke, Sherbrooke Connectivity Imaging Laboratory, Sherbrooke, Canada
| | - Frédéric Lesage
- École Polytechnique de Montréal, Laboratoire d’imagerie optique et moléculaire, Montreal, Canada
- Université de Montréal, Research Centre, Montréal Heart Institute, Montreal, Canada
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16
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Schmitz D, Muenzing SEA, Schober M, Schubert N, Minnerop M, Lippert T, Amunts K, Axer M. Derivation of Fiber Orientations From Oblique Views Through Human Brain Sections in 3D-Polarized Light Imaging. Front Neuroanat 2018; 12:75. [PMID: 30323745 PMCID: PMC6173061 DOI: 10.3389/fnana.2018.00075] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Abstract
3D-Polarized Light Imaging (3D-PLI) enables high-resolution three-dimensional mapping of the nerve fiber architecture in unstained histological brain sections based on the intrinsic birefringence of myelinated nerve fibers. The interpretation of the measured birefringent signals comes with conjointly measured information about the local fiber birefringence strength and the fiber orientation. In this study, we present a novel approach to disentangle both parameters from each other based on a weighted least squares routine (ROFL) applied to oblique polarimetric 3D-PLI measurements. This approach was compared to a previously described analytical method on simulated and experimental data obtained from a post mortem human brain. Analysis of the simulations revealed in case of ROFL a distinctly increased level of confidence to determine steep and flat fiber orientations with respect to the brain sectioning plane. Based on analysis of histological sections of a human brain dataset, it was demonstrated that ROFL provides a coherent characterization of cortical, subcortical, and white matter regions in terms of fiber orientation and birefringence strength, within and across sections. Oblique measurements combined with ROFL analysis opens up new ways to determine physical brain tissue properties by means of 3D-PLI microscopy.
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Affiliation(s)
- Daniel Schmitz
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Sascha E A Muenzing
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Martin Schober
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Nicole Schubert
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Martina Minnerop
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany.,>Center for Movement Disorders and Neuromodulation, Department of Neurology and Institute of Clinical Neuroscience and Medical Psychology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Thomas Lippert
- Jülich Supercomputing Center, Forschungszentrum Jülich, Jülich, Germany.,Bergische Universität Wuppertal, Wuppertal, Germany
| | - Katrin Amunts
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany.,C. and O. Vogt Institute for Brain Research, Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Markus Axer
- Institute of Neuroscience and Medicine-1 (INM-1), Forschungszentrum Jülich, Jülich, Germany
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17
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Delafontaine-Martel P, Lefebvre J, Tardif PL, Lévy BI, Pouliot P, Lesage F. Whole brain vascular imaging in a mouse model of Alzheimer's disease with two-photon microscopy. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-10. [PMID: 29998647 DOI: 10.1117/1.jbo.23.7.076501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/21/2018] [Indexed: 06/08/2023]
Abstract
Given known correlations between vascular health and cognitive impairment, the development of tools to image microvasculature in the whole brain could help investigate these correlations. We explore the feasibility of using an automated serial two-photon microscope to image fluorescent gelatin-filled whole rodent brains in three-dimensions (3-D) with the goal of carrying group studies. Vascular density (VD) was computed using automatic segmentation combined with coregistration techniques to build a group-level vascular metric in the whole brain. Focusing on the medial prefrontal cortex, cerebral cortex, the olfactory bulb, and the hippocampal formation, we compared the VD of three age groups (2-, 4.5-, and 8-months-old), for both wild type mice and a transgenic model (APP/PS1) with pathology resembling Alzheimer's disease (AD). We report a general loss of VD caused by the aging process with a small VD increase in the diseased animals in the somatomotor and somatosensory cortical regions and the olfactory bulb, partly supported by MRI perfusion data. This study supports previous observations that AD transgenic mice show a higher VD in specific regions compared with WT mice during the early and late stages of the disease (4.5 to 8 months), extending results to whole brain mapping.
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Affiliation(s)
| | - Joel Lefebvre
- Ecole Polytechnique Montréal, Department of Electrical Engineering, Quebec, Canada
| | - Pier-Luc Tardif
- Ecole Polytechnique Montréal, Department of Electrical Engineering, Quebec, Canada
| | - Bernard I Lévy
- Vessels and Blood Institute, Inserm U970 and Hôpital Lariboisière, Paris, France
| | - Philippe Pouliot
- Ecole Polytechnique Montréal, Department of Electrical Engineering, Quebec, Canada
- Montreal Heart Institute, Research Centre, Montreal, Quebec, Canada
| | - Frédéric Lesage
- Ecole Polytechnique Montréal, Department of Electrical Engineering, Quebec, Canada
- Montreal Heart Institute, Research Centre, Montreal, Quebec, Canada
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18
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Liu CJ, Rainwater O, Clark HB, Orr HT, Akkin T. Polarization-sensitive optical coherence tomography reveals gray matter and white matter atrophy in SCA1 mouse models. Neurobiol Dis 2018; 116:69-77. [PMID: 29753755 DOI: 10.1016/j.nbd.2018.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/09/2018] [Indexed: 11/25/2022] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is a fatal inherited neurodegenerative disease. In this study, we demonstrate the label-free optical imaging methodology that can detect, with a high degree of sensitivity, discrete areas of degeneration in the cerebellum of the SCA1 mouse models. We used ATXN1[82Q] and ATXN1[30Q]-D776 mice in which the transgene is directed only to Purkinje cells. Molecular layer, granular layer, and white matter regions are analyzed using the intrinsic contrasts provided by polarization-sensitive optical coherence tomography. Cerebellar atrophy in SCA1 mice occurred both in gray matter and white matter. While gray matter atrophy is obvious, indications of white matter atrophy including different birefringence characteristics, and shortened and contorted branches are observed. Imaging results clearly show the loss or atrophy of myelinated axons in ATXN1[82Q] mice. The method provides unbiased contrasts that can facilitate the understanding of the pathological progression in neurodegenerative diseases and other neural disorders.
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Affiliation(s)
- Chao J Liu
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Orion Rainwater
- Institute of Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - H Brent Clark
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Harry T Orr
- Institute of Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Taner Akkin
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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19
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Fan Y, Xia Y, Zhang X, Sun Y, Tang J, Zhang L, Liao H. Optical coherence tomography for precision brain imaging, neurosurgical guidance and minimally invasive theranostics. Biosci Trends 2018; 12:12-23. [PMID: 29332928 DOI: 10.5582/bst.2017.01258] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This review focuses on optical coherence tomography (OCT)-based neurosurgical application for imaging and treatment of brain tumors. OCT has emerged as one of the most innovative and successful translational biomedical-diagnostic techniques. It is a useful imaging tool for noninvasive, in vivo, in situ and real-time imaging in soft biological tissues, such as brain tumor imaging. OCT can detect the structure of biological tissue in a micrometer scale, and functional OCT has some clinical researches and applications, such as nerve fiber tracts and neurovascular imaging. OCT is able to identify tumor margins, and it gives intraoperative precision identification and resection guidance. OCT-based theranostics is introduced into preclinical neurosurgical resection, such as the integration of OCT and laser ablation. We discuss the challenges and opportunities of OCT-based system in the field of combination of intraoperative structural and functional imaging, neurosurgical guidance and minimally invasive theranostics. We point out that OCT and laser ablation-based theranostics can give more precision and intelligence for intraoperative diagnosis and therapeutics in clinical applications. The theranostics can precisely locate, or specifically target cancerous tissues, and then as much as possiblly eliminate them.
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Affiliation(s)
- Yingwei Fan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University
| | - Yan Xia
- Department of Biomedical Engineering, School of Medicine, Tsinghua University
| | - Xinran Zhang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University
| | - Yu Sun
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University
| | - Jie Tang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University
| | - Hongen Liao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University
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20
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Wang H, Magnain C, Wang R, Dubb J, Varjabedian A, Tirrell LS, Stevens A, Augustinack JC, Konukoglu E, Aganj I, Frosch MP, Schmahmann JD, Fischl B, Boas DA. as-PSOCT: Volumetric microscopic imaging of human brain architecture and connectivity. Neuroimage 2018; 165:56-68. [PMID: 29017866 PMCID: PMC5732037 DOI: 10.1016/j.neuroimage.2017.10.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 01/21/2023] Open
Abstract
Polarization sensitive optical coherence tomography (PSOCT) with serial sectioning has enabled the investigation of 3D structures in mouse and human brain tissue samples. By using intrinsic optical properties of back-scattering and birefringence, PSOCT reliably images cytoarchitecture, myeloarchitecture and fiber orientations. In this study, we developed a fully automatic serial sectioning polarization sensitive optical coherence tomography (as-PSOCT) system to enable volumetric reconstruction of human brain samples with unprecedented sample size and resolution. The 3.5 μm in-plane resolution and 50 μm through-plane voxel size allow inspection of cortical layers that are a single-cell in width, as well as small crossing fibers. We show the abilities of as-PSOCT in quantifying layer thicknesses of the cerebellar cortex and creating microscopic tractography of intricate fiber networks in the subcortical nuclei and internal capsule regions, all based on volumetric reconstructions. as-PSOCT provides a viable tool for studying quantitative cytoarchitecture and myeloarchitecture and mapping connectivity with microscopic resolution in the human brain.
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Affiliation(s)
- Hui Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA.
| | - Caroline Magnain
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Ruopeng Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Jay Dubb
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Ani Varjabedian
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee S Tirrell
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Allison Stevens
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Jean C Augustinack
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Ender Konukoglu
- Computer Vision Laboratory, ETH Zurich, 8092 Zurich, Switzerland
| | - Iman Aganj
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
| | - Matthew P Frosch
- C.S. Kubik Laboratory for Neuropathology, Pathology Service, Massachusetts General Hospital, Boston, MA 02115, USA
| | - Jeremy D Schmahmann
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02114, USA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA; MIT Computer Science and AI Lab, Cambridge, MA 02139, USA
| | - David A Boas
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129, USA
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21
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Castonguay A, Lefebvre J, Lesage F, Pouliot P. Comparing three-dimensional serial optical coherence tomography histology to MRI imaging in the entire mouse brain. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-9. [PMID: 29313322 DOI: 10.1117/1.jbo.23.1.016008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/12/2017] [Indexed: 06/07/2023]
Abstract
An automated serial histology setup combining optical coherence tomography (OCT) imaging with vibratome sectioning was used to image eight wild type mouse brains. The datasets resulted in thousands of volumetric tiles resolved at a voxel size of (4.9×4.9×6.5) μm3 stitched back together to give a three-dimensional map of the brain from which a template OCT brain was obtained. To assess deformation caused by tissue sectioning, reconstruction algorithms, and fixation, OCT datasets were compared to both in vivo and ex vivo magnetic resonance imaging (MRI) imaging. The OCT brain template yielded a highly detailed map of the brain structure, with a high contrast in white matter fiber bundles and was highly resemblant to the in vivo MRI template. Brain labeling using the Allen brain framework showed little variation in regional brain volume among imaging modalities with no statistical differences. The high correspondence between the OCT template brain and its in vivo counterpart demonstrates the potential of whole brain histology to validate in vivo imaging.
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Affiliation(s)
| | - Joël Lefebvre
- École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Frédéric Lesage
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
| | - Philippe Pouliot
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
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22
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Wang H, Magnain C, Sakadžić S, Fischl B, Boas DA. Characterizing the optical properties of human brain tissue with high numerical aperture optical coherence tomography. BIOMEDICAL OPTICS EXPRESS 2017; 8:5617-5636. [PMID: 29296492 PMCID: PMC5745107 DOI: 10.1364/boe.8.005617] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/06/2017] [Accepted: 11/08/2017] [Indexed: 05/22/2023]
Abstract
Quantification of tissue optical properties with optical coherence tomography (OCT) has proven to be useful in evaluating structural characteristics and pathological changes. Previous studies primarily used an exponential model to analyze low numerical aperture (NA) OCT measurements and obtain the total attenuation coefficient for biological tissue. In this study, we develop a systematic method that includes the confocal parameter for modeling the depth profiles of high NA OCT, when the confocal parameter cannot be ignored. This approach enables us to quantify tissue optical properties with higher lateral resolution. The model parameter predictions for the scattering coefficients were tested with calibrated microsphere phantoms. The application of the model to human brain tissue demonstrates that the scattering and back-scattering coefficients each provide unique information, allowing us to differentially identify laminar structures in primary visual cortex and distinguish various nuclei in the midbrain. The combination of the two optical properties greatly enhances the power of OCT to distinguish intricate structures in the human brain beyond what is achievable with measured OCT intensity information alone, and therefore has the potential to enable objective evaluation of normal brain structure as well as pathological conditions in brain diseases. These results represent a promising step for enabling the quantification of tissue optical properties from high NA OCT.
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23
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Jelescu IO, Budde MD. Design and validation of diffusion MRI models of white matter. FRONTIERS IN PHYSICS 2017; 28:61. [PMID: 29755979 PMCID: PMC5947881 DOI: 10.3389/fphy.2017.00061] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Diffusion MRI is arguably the method of choice for characterizing white matter microstructure in vivo. Over the typical duration of diffusion encoding, the displacement of water molecules is conveniently on a length scale similar to that of the underlying cellular structures. Moreover, water molecules in white matter are largely compartmentalized which enables biologically-inspired compartmental diffusion models to characterize and quantify the true biological microstructure. A plethora of white matter models have been proposed. However, overparameterization and mathematical fitting complications encourage the introduction of simplifying assumptions that vary between different approaches. These choices impact the quantitative estimation of model parameters with potential detriments to their biological accuracy and promised specificity. First, we review biophysical white matter models in use and recapitulate their underlying assumptions and realms of applicability. Second, we present up-to-date efforts to validate parameters estimated from biophysical models. Simulations and dedicated phantoms are useful in assessing the performance of models when the ground truth is known. However, the biggest challenge remains the validation of the "biological accuracy" of estimated parameters. Complementary techniques such as microscopy of fixed tissue specimens have facilitated direct comparisons of estimates of white matter fiber orientation and densities. However, validation of compartmental diffusivities remains challenging, and complementary MRI-based techniques such as alternative diffusion encodings, compartment-specific contrast agents and metabolites have been used to validate diffusion models. Finally, white matter injury and disease pose additional challenges to modeling, which are also discussed. This review aims to provide an overview of the current state of models and their validation and to stimulate further research in the field to solve the remaining open questions and converge towards consensus.
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Affiliation(s)
- Ileana O Jelescu
- Centre d'Imagerie Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Matthew D Budde
- Zablocki VA Medical Center, Dept. of Neurosurgery, Medical College Wisconsin, Milwaukee, WI, USA
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24
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Castonguay A, Lefebvre J, Pouliot P, Avti P, Moeini M, Lesage F. Serial optical coherence scanning reveals an association between cardiac function and the heart architecture in the aging rodent heart. BIOMEDICAL OPTICS EXPRESS 2017; 8:5027-5038. [PMID: 29188099 PMCID: PMC5695949 DOI: 10.1364/boe.8.005027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 05/10/2023]
Abstract
Normal aging is accompanied by structural changes in the heart architecture. To explore this remodeling, we used a serial optical coherence tomography scanner to image entire mouse hearts at micron scale resolution. Ex vivo hearts of 7 young (4 months) and 5 old (24 months) C57BL/6 mice were acquired with the imaging platform. OCT of the myocardium revealed myofiber orientation changing linearly from the endocardium to the epicardium. In old mice, this rate of change was lower when compared to young mice while the average volume of old mice hearts was significantly larger (p<0.05). Myocardial wall thickening was also accompanied by extracellular spacing in the endocardium, resulting in a lower OCT attenuation coefficient in old mice endocardium (p<0.05). Prior to serial sectioning, cardiac function of the same hearts was imaged in vivo using MRI and revealed a reduced ejection fraction with aging. The use of a serial optical coherence tomography scanner allows new insight into fine age-related changes of the heart associated with changes in heart function.
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Affiliation(s)
- Alexandre Castonguay
- École Polytechnique de Montréal, C.P. 6079, Succ. Centre-Ville, Montréal QC, H3C3A7, Canada
| | - Joël Lefebvre
- École Polytechnique de Montréal, C.P. 6079, Succ. Centre-Ville, Montréal QC, H3C3A7, Canada
| | - Philippe Pouliot
- École Polytechnique de Montréal, C.P. 6079, Succ. Centre-Ville, Montréal QC, H3C3A7, Canada
- Institut de Cardiologie de Montréal, 5000 rue Bélanger Est, Montréal, QC, H1T1C8, Canada
| | - Pramod Avti
- Department of Biophysics, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Mohammad Moeini
- École Polytechnique de Montréal, C.P. 6079, Succ. Centre-Ville, Montréal QC, H3C3A7, Canada
- Institut de Cardiologie de Montréal, 5000 rue Bélanger Est, Montréal, QC, H1T1C8, Canada
| | - Frédéric Lesage
- École Polytechnique de Montréal, C.P. 6079, Succ. Centre-Ville, Montréal QC, H3C3A7, Canada
- Institut de Cardiologie de Montréal, 5000 rue Bélanger Est, Montréal, QC, H1T1C8, Canada
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25
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Mokbul MI. Optical Coherence Tomography: Basic Concepts and Applications in Neuroscience Research. J Med Eng 2017; 2017:3409327. [PMID: 29214158 PMCID: PMC5682075 DOI: 10.1155/2017/3409327] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/22/2017] [Accepted: 09/14/2017] [Indexed: 12/28/2022] Open
Abstract
Optical coherence tomography is a micrometer-scale imaging modality that permits label-free, cross-sectional imaging of biological tissue microstructure using tissue backscattering properties. After its invention in the 1990s, OCT is now being widely used in several branches of neuroscience as well as other fields of biomedical science. This review study reports an overview of OCT's applications in several branches or subbranches of neuroscience such as neuroimaging, neurology, neurosurgery, neuropathology, and neuroembryology. This study has briefly summarized the recent applications of OCT in neuroscience research, including a comparison, and provides a discussion of the remaining challenges and opportunities in addition to future directions. The chief aim of the review study is to draw the attention of a broad neuroscience community in order to maximize the applications of OCT in other branches of neuroscience too, and the study may also serve as a benchmark for future OCT-based neuroscience research. Despite some limitations, OCT proves to be a useful imaging tool in both basic and clinical neuroscience research.
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Affiliation(s)
- Mobin Ibne Mokbul
- Notre Dame College, Motijheel Circular Road, Arambagh, Motijheel, Dhaka 1000, Bangladesh
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26
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Lefebvre J, Castonguay A, Pouliot P, Descoteaux M, Lesage F. Whole mouse brain imaging using optical coherence tomography: reconstruction, normalization, segmentation, and comparison with diffusion MRI. NEUROPHOTONICS 2017; 4:041501. [PMID: 28721357 PMCID: PMC5506292 DOI: 10.1117/1.nph.4.4.041501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/19/2017] [Indexed: 05/10/2023]
Abstract
An automated massive histology setup combined with an optical coherence tomography (OCT) microscope was used to image a total of [Formula: see text] whole mouse brains. Each acquisition generated a dataset of thousands of OCT volumetric tiles at a sampling resolution of [Formula: see text]. This paper describes techniques for reconstruction and segmentation of the sliced brains. In addition to the measured OCT optical reflectivity, a single scattering photon model was used to compute the attenuation coefficients within each tissue slice. Average mouse brain templates were generated for both the OCT reflectivity and attenuation contrasts and were used with an [Formula: see text]-tissue segmentation algorithm. To better understand the brain tissue OCT contrast origin, one of the mouse brains was acquired using dMRI and coregistered to its corresponding assembled brain. Our results indicate that the optical reflectivity in a fiber bundle varies with its orientation, its fiber density, and the number of fiber orientations it contains. The OCT mouse brain template generation and coregistration to dMRI data demonstrate the potential of this massive histology technique to pursue cross-sectional, multimodal, and multisubject investigations of small animal brains.
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Affiliation(s)
- Joël Lefebvre
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Address all correspondence to: Joël Lefebvre, E-mail:
| | | | - Philippe Pouliot
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
| | - Maxime Descoteaux
- Université de Sherbrooke, Sherbrooke Connectivity Imaging Laboratory, Sherbrooke, Québec, Canada
| | - Frédéric Lesage
- École Polytechnique de Montréal, Montréal, Québec, Canada
- Institut de Cardiologie de Montréal, Montréal, Québec, Canada
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27
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Lichtenegger A, Harper DJ, Augustin M, Eugui P, Muck M, Gesperger J, Hitzenberger CK, Woehrer A, Baumann B. Spectroscopic imaging with spectral domain visible light optical coherence microscopy in Alzheimer's disease brain samples. BIOMEDICAL OPTICS EXPRESS 2017; 8:4007-4025. [PMID: 28966843 PMCID: PMC5611919 DOI: 10.1364/boe.8.004007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/02/2017] [Accepted: 08/02/2017] [Indexed: 05/18/2023]
Abstract
A visible light spectral domain optical coherence microscopy system was developed. A high axial resolution of 0.88 μm in tissue was achieved using a broad visible light spectrum (425 - 685 nm). Healthy human brain tissue was imaged to quantify the difference between white (WM) and grey matter (GM) in intensity and attenuation. The high axial resolution enables the investigation of amyloid-beta plaques of various sizes in human brain tissue and animal models of Alzheimer's disease (AD). By performing a spectroscopic analysis of the OCM data, differences in the characteristics for WM, GM, and neuritic amyloid-beta plaques were found. To gain additional contrast, Congo red stained AD brain tissue was investigated. A first effort was made to investigate optically cleared mouse brain tissue to increase the penetration depth and visualize hyperscattering structures in deeper cortical regions.
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Affiliation(s)
- Antonia Lichtenegger
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Danielle J. Harper
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Marco Augustin
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Pablo Eugui
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Martina Muck
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
- Institute of Neurology, General Hospital and Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Johanna Gesperger
- Institute of Neurology, General Hospital and Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Christoph K. Hitzenberger
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Adelheid Woehrer
- Institute of Neurology, General Hospital and Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
| | - Bernhard Baumann
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna,
Austria
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28
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Zarei V, Liu CJ, Claeson AA, Akkin T, Barocas VH. Image-based multiscale mechanical modeling shows the importance of structural heterogeneity in the human lumbar facet capsular ligament. Biomech Model Mechanobiol 2017; 16:1425-1438. [PMID: 28361294 PMCID: PMC5704991 DOI: 10.1007/s10237-017-0896-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 03/13/2017] [Indexed: 12/12/2022]
Abstract
The lumbar facet capsular ligament (FCL) primarily consists of aligned type I collagen fibers that are mainly oriented across the joint. The aim of this study was to characterize and incorporate in-plane local fiber structure into a multiscale finite element model to predict the mechanical response of the FCL during in vitro mechanical tests, accounting for the heterogeneity in different scales. Characterization was accomplished by using entire-domain polarization-sensitive optical coherence tomography to measure the fiber structure of cadaveric lumbar FCLs ([Formula: see text]). Our imaging results showed that fibers in the lumbar FCL have a highly heterogeneous distribution and are neither isotropic nor completely aligned. The averaged fiber orientation was [Formula: see text] ([Formula: see text] in the inferior region and [Formula: see text] in the middle and superior regions), with respect to lateral-medial direction (superior-medial to inferior-lateral). These imaging data were used to construct heterogeneous structural models, which were then used to predict experimental gross force-strain behavior and the strain distribution during equibiaxial and strip biaxial tests. For equibiaxial loading, the structural model fit the experimental data well but underestimated the lateral-medial forces by [Formula: see text]16% on average. We also observed pronounced heterogeneity in the strain field, with stretch ratios for different elements along the lateral-medial axis of sample typically ranging from about 0.95 to 1.25 during a 12% strip biaxial stretch in the lateral-medial direction. This work highlights the multiscale structural and mechanical heterogeneity of the lumbar FCL, which is significant both in terms of injury prediction and microstructural constituents' (e.g., neurons) behavior.
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Affiliation(s)
- Vahhab Zarei
- Departments of Mechanical Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Chao J Liu
- Departments of Biomedical Engineering, Universityof Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Amy A Claeson
- Departments of Biomedical Engineering, Universityof Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Taner Akkin
- Departments of Biomedical Engineering, Universityof Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Victor H Barocas
- Departments of Biomedical Engineering, Universityof Minnesota-Twin Cities, Minneapolis, MN, USA.
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29
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Polarization Sensitive Optical Coherence Tomography: A Review of Technology and Applications. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7050474] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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Label-free volumetric optical imaging of intact murine brains. Sci Rep 2017; 7:46306. [PMID: 28401897 PMCID: PMC5388920 DOI: 10.1038/srep46306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/14/2017] [Indexed: 12/02/2022] Open
Abstract
A central effort of today’s neuroscience is to study the brain’s ’wiring diagram’. The nervous system is believed to be a network of neurons interacting with each other through synaptic connection between axons and dendrites, therefore the neuronal connectivity map not only depicts the underlying anatomy, but also has important behavioral implications. Different approaches have been utilized to decipher neuronal circuits, including electron microscopy (EM) and light microscopy (LM). However, these approaches typically demand extensive sectioning and reconstruction for a brain sample. Recently, tissue clearing methods have enabled the investigation of a fully assembled biological system with greatly improved light penetration. Yet, most of these implementations, still require either genetic or exogenous contrast labeling for light microscopy. Here we demonstrate a high-speed approach, termed as Clearing Assisted Scattering Tomography (CAST), where intact brains can be imaged at optical resolution without labeling by leveraging tissue clearing and the scattering contrast of optical frequency domain imaging (OFDI).
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31
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Baumann B, Woehrer A, Ricken G, Augustin M, Mitter C, Pircher M, Kovacs GG, Hitzenberger CK. Visualization of neuritic plaques in Alzheimer's disease by polarization-sensitive optical coherence microscopy. Sci Rep 2017; 7:43477. [PMID: 28262719 PMCID: PMC5337955 DOI: 10.1038/srep43477] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/24/2017] [Indexed: 12/16/2022] Open
Abstract
One major hallmark of Alzheimer's disease (AD) and cerebral amyloid angiopathy (CAA) is the deposition of extracellular senile plaques and vessel wall deposits composed of amyloid-beta (Aβ). In AD, degeneration of neurons is preceded by the formation of Aβ plaques, which show different morphological forms. Most of them are birefringent owing to the parallel arrangement of amyloid fibrils. Here, we present polarization sensitive optical coherence microscopy (PS-OCM) for imaging mature neuritic Aβ plaques based on their birefringent properties. Formalin-fixed, post-mortem brain samples of advanced stage AD patients were investigated. In several cortical brain regions, neuritic Aβ plaques were successfully visualized in tomographic and three-dimensional (3D) images. Cortical grey matter appeared polarization preserving, whereas neuritic plaques caused increased phase retardation. Consistent with the results from PS-OCM imaging, the 3D structure of senile Aβ plaques was computationally modelled for different illumination settings and plaque sizes. Furthermore, the birefringent properties of cortical and meningeal vessel walls in CAA were investigated in selected samples. Significantly increased birefringence was found in smaller vessels. Overall, these results provide evidence that PS-OCM is able to assess amyloidosis based on intrinsic birefringent properties.
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Affiliation(s)
- Bernhard Baumann
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, A-1090, Vienna, Austria
| | - Adelheid Woehrer
- General Hospital and Medical University of Vienna, Institute of Neurology, A-1090, Vienna, Austria
| | - Gerda Ricken
- General Hospital and Medical University of Vienna, Institute of Neurology, A-1090, Vienna, Austria
| | - Marco Augustin
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, A-1090, Vienna, Austria
| | - Christian Mitter
- General Hospital and Medical University of Vienna, Institute of Neurology, A-1090, Vienna, Austria
- General Hospital and Medical University of Vienna, Department of Biomedical Imaging and Image-guided Therapy, A-1090, Vienna, Austria
| | - Michael Pircher
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, A-1090, Vienna, Austria
| | - Gabor G. Kovacs
- General Hospital and Medical University of Vienna, Institute of Neurology, A-1090, Vienna, Austria
| | - Christoph K. Hitzenberger
- Medical University of Vienna, Center for Medical Physics and Biomedical Engineering, A-1090, Vienna, Austria
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32
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Full-Field Optical Coherence Tomography as a Diagnosis Tool: Recent Progress with Multimodal Imaging. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7030236] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Liu CJ, Williams KE, Orr HT, Akkin T. Visualizing and mapping the cerebellum with serial optical coherence scanner. NEUROPHOTONICS 2017; 4:011006. [PMID: 27725947 PMCID: PMC5048104 DOI: 10.1117/1.nph.4.1.011006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/12/2016] [Indexed: 05/12/2023]
Abstract
We present the visualization of the mouse cerebellum and adjacent brainstem using a serial optical coherence scanner, which integrates a vibratome slicer and polarization-sensitive optical coherence tomography for ex vivo imaging. The scanner provides intrinsic optical contrasts to distinguish the cerebellar cortical layers and white matter. Images from serial scans reveal the large-scale anatomy in detail and map the nerve fiber pathways in the cerebellum and brainstem. By incorporating a water-immersion microscope objective, we also present high-resolution tiled images that delineate fine structures in the cerebellum and brainstem.
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Affiliation(s)
- Chao J. Liu
- University of Minnesota, Department of Biomedical Engineering, 312 Church Street S.E., Minneapolis, Minnesota 55455, United States
| | - Kristen E. Williams
- University of Minnesota, Department of Biomedical Engineering, 312 Church Street S.E., Minneapolis, Minnesota 55455, United States
| | - Harry T. Orr
- University of Minnesota, Institute of Translational Neuroscience, 2101 6th Street S.E., Minneapolis, Minnesota 55455, United States
- University of Minnesota, Department of Laboratory Medicine and Pathology, 420 Delaware Street S.E., Minneapolis, Minnesota 55455, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, 312 Church Street S.E., Minneapolis, Minnesota 55455, United States
- Address all correspondence to: Taner Akkin, E-mail:
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Validating Intravascular Imaging with Serial Optical Coherence Tomography and Confocal Fluorescence Microscopy. Int J Mol Sci 2016; 17:ijms17122110. [PMID: 27983695 PMCID: PMC5187910 DOI: 10.3390/ijms17122110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/25/2016] [Accepted: 12/09/2016] [Indexed: 01/20/2023] Open
Abstract
Atherosclerotic cardiovascular diseases are characterized by the formation of a plaque in the arterial wall. Intravascular ultrasound (IVUS) provides high-resolution images allowing delineation of atherosclerotic plaques. When combined with near infrared fluorescence (NIRF), the plaque can also be studied at a molecular level with a large variety of biomarkers. In this work, we present a system enabling automated volumetric histology imaging of excised aortas that can spatially correlate results with combined IVUS/NIRF imaging of lipid-rich atheroma in cholesterol-fed rabbits. Pullbacks in the rabbit aortas were performed with a dual modality IVUS/NIRF catheter developed by our group. Ex vivo three-dimensional (3D) histology was performed combining optical coherence tomography (OCT) and confocal fluorescence microscopy, providing high-resolution anatomical and molecular information, respectively, to validate in vivo findings. The microscope was combined with a serial slicer allowing for the imaging of the whole vessel automatically. Colocalization of in vivo and ex vivo results is demonstrated. Slices can then be recovered to be tested in conventional histology.
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35
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Hieber SE, Bikis C, Khimchenko A, Schweighauser G, Hench J, Chicherova N, Schulz G, Müller B. Tomographic brain imaging with nucleolar detail and automatic cell counting. Sci Rep 2016; 6:32156. [PMID: 27581254 PMCID: PMC5007499 DOI: 10.1038/srep32156] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/19/2016] [Indexed: 01/27/2023] Open
Abstract
Brain tissue evaluation is essential for gaining in-depth insight into its diseases and disorders. Imaging the human brain in three dimensions has always been a challenge on the cell level. In vivo methods lack spatial resolution, and optical microscopy has a limited penetration depth. Herein, we show that hard X-ray phase tomography can visualise a volume of up to 43 mm3 of human post mortem or biopsy brain samples, by demonstrating the method on the cerebellum. We automatically identified 5,000 Purkinje cells with an error of less than 5% at their layer and determined the local surface density to 165 cells per mm2 on average. Moreover, we highlight that three-dimensional data allows for the segmentation of sub-cellular structures, including dendritic tree and Purkinje cell nucleoli, without dedicated staining. The method suggests that automatic cell feature quantification of human tissues is feasible in phase tomograms obtained with isotropic resolution in a label-free manner.
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Affiliation(s)
- Simone E Hieber
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Anna Khimchenko
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Gabriel Schweighauser
- Institute of Pathology, Department of Neuropathology, University Hospital of Basel, Schönbeinstrasse 40, 4001 Basel, Switzerland
| | - Jürgen Hench
- Institute of Pathology, Department of Neuropathology, University Hospital of Basel, Schönbeinstrasse 40, 4001 Basel, Switzerland
| | - Natalia Chicherova
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland.,Medical Image Analysis Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14, 4123 Allschwil, Switzerland
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36
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Liu CJ, Black AJ, Wang H, Akkin T. Quantifying three-dimensional optic axis using polarization-sensitive optical coherence tomography. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:70501. [PMID: 27387702 DOI: 10.1117/1.jbo.21.7.070501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/16/2016] [Indexed: 05/23/2023]
Abstract
The optic axis of birefringent samples indicates the direction of optical anisotropy, which should be described in three-dimensional (3-D) space. We present a method to quantify the complete 3-D optic axis orientation calculated from in-plane optic axis measurements from a polarization-sensitive optical coherence tomography system. The in-plane axis orientations with different illumination angles allow the calculation of the necessary polar angle. The method then provides the information to produce the actual birefringence. The method and results from a biological sample are presented.
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37
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Khimchenko A, Deyhle H, Schulz G, Schweighauser G, Hench J, Chicherova N, Bikis C, Hieber SE, Müller B. Extending two-dimensional histology into the third dimension through conventional micro computed tomography. Neuroimage 2016; 139:26-36. [PMID: 27321044 DOI: 10.1016/j.neuroimage.2016.06.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 05/11/2016] [Accepted: 06/04/2016] [Indexed: 11/28/2022] Open
Abstract
Histological examination achieves sub-micrometer resolution laterally. In the third dimension, however, resolution is limited to section thickness. In addition, histological sectioning and mounting sections on glass slides introduce tissue-dependent stress and strain. In contrast, state-of-the-art hard X-ray micro computed tomography (μCT) systems provide isotropic sub-micrometer resolution and avoid sectioning artefacts. The drawback of μCT in the absorption contrast mode for visualising physically soft tissue is a low attenuation difference between anatomical features. In this communication, we demonstrate that formalin-fixed paraffin-embedded human cerebellum yields appropriate absorption contrast in laboratory-based μCT data, comparable to conventional histological sections. Purkinje cells, for example, are readily visible. In order to investigate the pros and cons of complementary approaches, two- and three-dimensional data were manually and automatically registered. The joint histogram of histology and the related μCT slice allows for a detailed discussion on how to integrate two-dimensional information from histology into a three-dimensional tomography dataset. This methodology is not only rewarding for the analysis of the human cerebellum, but it also has relevance for investigations of tissue biopsies and post-mortem applications. Our data indicate that laboratory-based μCT as a modality can fill the gap between synchrotron radiation-based μCT and histology for a variety of tissues. As the information from haematoxylin and eosin (H&E) stained sections and μCT data is related, one can colourise local X-ray absorption values according to the H&E stain. Hence, μCT data can correlate and virtually extend two-dimensional (2D) histology data into the third dimension.
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Affiliation(s)
- Anna Khimchenko
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Hans Deyhle
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Gabriel Schweighauser
- Institute of Pathology, Department of Neuropathology, Basel University Hospital, Basel, Switzerland
| | - Jürgen Hench
- Institute of Pathology, Department of Neuropathology, Basel University Hospital, Basel, Switzerland
| | - Natalia Chicherova
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Medical Image Analysis Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Simone E Hieber
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.
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38
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Wang H, Akkin T, Magnain C, Wang R, Dubb J, Kostis WJ, Yaseen MA, Cramer A, Sakadžić S, Boas D. Polarization sensitive optical coherence microscopy for brain imaging. OPTICS LETTERS 2016; 41:2213-6. [PMID: 27176965 PMCID: PMC5357322 DOI: 10.1364/ol.41.002213] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Optical coherence tomography (OCT) and optical coherence microscopy (OCM) have demonstrated the ability to investigate cyto- and myelo-architecture in the brain. Polarization-sensitive OCT provides sensitivity to additional contrast mechanisms, specifically the birefringence of myelination and, therefore, is advantageous for investigating white matter fiber tracts. In this Letter, we developed a polarization-sensitive optical coherence microscope (PS-OCM) with a 3.5 μm axial and 1.3 μm transverse resolution to investigate fiber organization and orientation at a finer scale than previously demonstrated with PS-OCT. In a reconstructed mouse brain section, we showed that at the focal depths of 20-70 μm, the PS-OCM reliably identifies the neuronal fibers and quantifies the in-plane orientation.
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Affiliation(s)
- Hui Wang
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
- Corresponding author:
| | - Taner Akkin
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455
| | - Caroline Magnain
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - Ruopeng Wang
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - Jay Dubb
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - William J Kostis
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - Mohammad A Yaseen
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - Avilash Cramer
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - Sava Sakadžić
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
| | - David Boas
- Athinoula A. Martinos Martinos Center for Biomedical Imaging, Massachusetts General Hospital/Harvard Medical School, Charlestown, MA 02129
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39
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Mitter C, Jakab A, Brugger PC, Ricken G, Gruber GM, Bettelheim D, Scharrer A, Langs G, Hainfellner JA, Prayer D, Kasprian G. Validation of In utero Tractography of Human Fetal Commissural and Internal Capsule Fibers with Histological Structure Tensor Analysis. Front Neuroanat 2015; 9:164. [PMID: 26732460 PMCID: PMC4689804 DOI: 10.3389/fnana.2015.00164] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/07/2015] [Indexed: 12/20/2022] Open
Abstract
Diffusion tensor imaging (DTI) and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establish in utero DTI as a clinical imaging tool, an independent comparison between macroscopic imaging and microscopic histology data in the same subject is needed. The present study aimed to cross-validate normal as well as abnormal in utero tractography results of commissural and internal capsule fibers in human fetal brains using postmortem histological structure tensor (ST) analysis. In utero tractography findings from two structurally unremarkable and five abnormal fetal brains were compared to the results of postmortem ST analysis applied to digitalized whole hemisphere sections of the same subjects. An approach to perform ST-based deterministic tractography in histological sections was implemented to overcome limitations in correlating in utero tractography to postmortem histology data. ST analysis and histology-based tractography of fetal brain sections enabled the direct assessment of the anisotropic organization and main fiber orientation of fetal telencephalic layers on a micro- and macroscopic scale, and validated in utero tractography results of corpus callosum and internal capsule fiber tracts. Cross-validation of abnormal in utero tractography results could be achieved in four subjects with agenesis of the corpus callosum (ACC) and in two cases with malformations of internal capsule fibers. In addition, potential limitations of current DTI-based in utero tractography could be demonstrated in several brain regions. Combining the three-dimensional nature of DTI-based in utero tractography with the microscopic resolution provided by histological ST analysis may ultimately facilitate a more complete morphologic characterization of axon guidance disorders at prenatal stages of human brain development.
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Affiliation(s)
- Christian Mitter
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging and Image-guided Therapy, Medical University of ViennaVienna, Austria; Institute of Neurology, Medical University of ViennaVienna, Austria
| | - András Jakab
- Computational Imaging Research Lab, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna Vienna, Austria
| | - Peter C Brugger
- Department of Systematic Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna Vienna, Austria
| | - Gerda Ricken
- Institute of Neurology, Medical University of Vienna Vienna, Austria
| | - Gerlinde M Gruber
- Department of Systematic Anatomy, Center for Anatomy and Cell Biology, Medical University of Vienna Vienna, Austria
| | - Dieter Bettelheim
- Division of Obstetrics and Feto-maternal Medicine, Department of Obstetrics and Gynecology, Medical University of Vienna Vienna, Austria
| | - Anke Scharrer
- Clinical Institute for Pathology, Medical University of Vienna Vienna, Austria
| | - Georg Langs
- Computational Imaging Research Lab, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna Vienna, Austria
| | | | - Daniela Prayer
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna Vienna, Austria
| | - Gregor Kasprian
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna Vienna, Austria
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40
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Min E, Lee J, Vavilin A, Jung S, Shin S, Kim J, Jung W. Wide-field optical coherence microscopy of the mouse brain slice. OPTICS LETTERS 2015; 40:4420-3. [PMID: 26421546 DOI: 10.1364/ol.40.004420] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The imaging capability of optical coherence microscopy (OCM) has great potential to be used in neuroscience research because it is able to visualize anatomic features of brain tissue without labeling or external contrast agents. However, the field of view of OCM is still narrow, which dilutes the strength of OCM and limits its application. In this study, we present fully automated wide-field OCM for mosaic imaging of sliced mouse brains. A total of 308 segmented OCM images were acquired, stitched, and reconstructed as an en-face brain image after intensive imaging processing. The overall imaging area was 11.2×7.0 mm (horizontal×vertical), and the corresponding pixel resolution was 1.2×1.2 μm. OCM images were compared to traditional histology stained with Nissl and Luxol fast blue (LFB). In particular, the orientation of the fibers was analyzed and quantified in wide-field OCM.
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41
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Ding Z, Liang CP, Tang Q, Chen Y. Quantitative single-mode fiber based PS-OCT with single input polarization state using Mueller matrix. BIOMEDICAL OPTICS EXPRESS 2015; 6:1828-43. [PMID: 26137383 PMCID: PMC4467718 DOI: 10.1364/boe.6.001828] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/12/2015] [Accepted: 04/14/2015] [Indexed: 05/18/2023]
Abstract
We present a simple but effective method to quantitatively measure the birefringence of tissue by an all single-mode fiber (SMF) based polarization-sensitive optical coherence tomography (PS-OCT) with single input polarization state. We theoretically verify that our SMF based PS-OCT system can quantify the phase retardance and optic axis orientation after a simple calibration process using a quarter wave plate (QWP). Based on the proposed method, the quantification of the phase retardance and optic axis orientation of a Berek polarization compensator and biological tissues were demonstrated.
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Affiliation(s)
- Zhenyang Ding
- College of Precision Instrument and Opto-Electronics Engineering, Tianjin University, Tianjin, 300072,
China
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742
USA
- These authors contributed equally to this work
| | - Chia-Pin Liang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742
USA
- These authors contributed equally to this work
| | - Qinggong Tang
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742
USA
| | - Yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742
USA
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42
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Wang H, Lenglet C, Akkin T. Structure tensor analysis of serial optical coherence scanner images for mapping fiber orientations and tractography in the brain. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:036003. [PMID: 25741662 PMCID: PMC4350401 DOI: 10.1117/1.jbo.20.3.036003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 02/19/2015] [Indexed: 05/05/2023]
Abstract
Quantitative investigations of fiber orientation and structural connectivity at microscopic resolution have led to great challenges for current neuroimaging techniques. Here, we present a structure tensor (ST) analysis of ex vivo rat brain images acquired by a multicontrast (MC) serial optical coherence scanner. The ST considers the gradients of images in local neighbors to generate a matrix whose eigen-decomposition can estimate the local features such as the edges, anisotropy, and orientation of tissue constituents. This computational analysis is applied on the conventional- and polarization-based contrasts of optical coherence tomography. The three-dimensional (3-D) fiber orientation maps are computed from the image stacks of sequential scans both at mesoresolution for a global view and at high-resolution for the details. The computational orientation maps demonstrate a good agreement with the optic axis orientation contrast which measures the in-plane fiber orientation. Moreover, tractography is implemented using the directional information extracted from the 3-D ST. The study provides a unique opportunity to leverage MC high-resolution information to map structural connectivity of the whole brain.
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Affiliation(s)
- Hui Wang
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota 55455, United States
- Address all correspondence to: Hui Wang, E-mail:
| | - Christophe Lenglet
- University of Minnesota, Center for Magnetic Resonance Research, Department of Radiology, Minneapolis, Minnesota 55455, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota 55455, United States
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43
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Wang H, Zhu J, Reuter M, Vinke LN, Yendiki A, Boas DA, Fischl B, Akkin T. Cross-validation of serial optical coherence scanning and diffusion tensor imaging: a study on neural fiber maps in human medulla oblongata. Neuroimage 2014; 100:395-404. [PMID: 24954840 DOI: 10.1016/j.neuroimage.2014.06.032] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 06/04/2014] [Accepted: 06/12/2014] [Indexed: 11/26/2022] Open
Abstract
We established a strategy to perform cross-validation of serial optical coherence scanner imaging (SOCS) and diffusion tensor imaging (DTI) on a postmortem human medulla. Following DTI, the sample was serially scanned by SOCS, which integrates a vibratome slicer and a multi-contrast optical coherence tomography rig for large-scale three-dimensional imaging at microscopic resolution. The DTI dataset was registered to the SOCS space. An average correlation coefficient of 0.9 was found between the co-registered fiber maps constructed by fractional anisotropy and retardance contrasts. Pixelwise comparison of fiber orientations demonstrated good agreement between the DTI and SOCS measures. Details of the comparison were studied in regions exhibiting a variety of fiber organizations. DTI estimated the preferential orientation of small fiber tracts; however, it didn't capture their complex patterns as SOCS did. In terms of resolution and imaging depth, SOCS and DTI complement each other, and open new avenues for cross-modality investigations of the brain.
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Affiliation(s)
- Hui Wang
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Junfeng Zhu
- Department of Industrial and Systems Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martin Reuter
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Louis N Vinke
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Anastasia Yendiki
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - David A Boas
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Taner Akkin
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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