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      High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy

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          Abstract

          Multiphoton microscopy has become a powerful tool with which to visualize the morphology and function of neural cells and circuits in the intact mammalian brain. However, tissue scattering, optical aberrations and motion artifacts degrade the imaging performance at depth. Here we describe a minimally invasive intravital imaging methodology based on three-photon excitation, indirect adaptive optics (AO) and active electrocardiogram gating to advance deep-tissue imaging. Our modal-based, sensorless AO approach is robust to low signal-to-noise ratios as commonly encountered in deep scattering tissues such as the mouse brain, and permits AO correction over large axial fields of view. We demonstrate near-diffraction-limited imaging of deep cortical spines and (sub)cortical dendrites up to a depth of 1.4 mm (the edge of the mouse CA1 hippocampus). In addition, we show applications to deep-layer calcium imaging of astrocytes, including fibrous astrocytes that reside in the highly scattering corpus callosum.

          Abstract

          Three-photon microscopy in combination with adaptive optics-based aberration correction and ECG-triggered gating allows high-resolution imaging of neurons and astrocytes up to a depth of 1.4 mm in the mouse brain.

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          Most cited references55

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          Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo.

          Microglial cells represent the immune system of the mammalian brain and therefore are critically involved in various injuries and diseases. Little is known about their role in the healthy brain and their immediate reaction to brain damage. By using in vivo two-photon imaging in neocortex, we found that microglial cells are highly active in their presumed resting state, continually surveying their microenvironment with extremely motile processes and protrusions. Furthermore, blood-brain barrier disruption provoked immediate and focal activation of microglia, switching their behavior from patroling to shielding of the injured site. Microglia thus are busy and vigilant housekeepers in the adult brain.
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            ilastik: interactive machine learning for (bio)image analysis

            We present ilastik, an easy-to-use interactive tool that brings machine-learning-based (bio)image analysis to end users without substantial computational expertise. It contains pre-defined workflows for image segmentation, object classification, counting and tracking. Users adapt the workflows to the problem at hand by interactively providing sparse training annotations for a nonlinear classifier. ilastik can process data in up to five dimensions (3D, time and number of channels). Its computational back end runs operations on-demand wherever possible, allowing for interactive prediction on data larger than RAM. Once the classifiers are trained, ilastik workflows can be applied to new data from the command line without further user interaction. We describe all ilastik workflows in detail, including three case studies and a discussion on the expected performance.
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              A pyramid approach to subpixel registration based on intensity.

              We present an automatic subpixel registration algorithm that minimizes the mean square intensity difference between a reference and a test data set, which can be either images (two-dimensional) or volumes (three-dimensional). It uses an explicit spline representation of the images in conjunction with spline processing, and is based on a coarse-to-fine iterative strategy (pyramid approach). The minimization is performed according to a new variation (ML*) of the Marquardt-Levenberg algorithm for nonlinear least-square optimization. The geometric deformation model is a global three-dimensional (3-D) affine transformation that can be optionally restricted to rigid-body motion (rotation and translation), combined with isometric scaling. It also includes an optional adjustment of image contrast differences. We obtain excellent results for the registration of intramodality positron emission tomography (PET) and functional magnetic resonance imaging (fMRI) data. We conclude that the multiresolution refinement strategy is more robust than a comparable single-stage method, being less likely to be trapped into a false local optimum. In addition, our improved version of the Marquardt-Levenberg algorithm is faster.
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                Author and article information

                Contributors
                prevedel@embl.de
                Journal
                Nat Methods
                Nat Methods
                Nature Methods
                Nature Publishing Group US (New York )
                1548-7091
                1548-7105
                30 September 2021
                30 September 2021
                2021
                : 18
                : 10
                : 1253-1258
                Affiliations
                [1 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Cell Biology and Biophysics Unit, , European Molecular Biology Laboratory (EMBL), ; Heidelberg, Germany
                [2 ]GRID grid.7700.0, ISNI 0000 0001 2190 4373, Collaboration for joint PhD degree between EMBL and Heidelberg University, , Faculty of Biosciences, Heidelberg University, ; Heidelberg, Germany
                [3 ]GRID grid.7700.0, ISNI 0000 0001 2190 4373, The Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, , Heidelberg University, ; Heidelberg, Germany
                [4 ]GRID grid.418924.2, ISNI 0000 0004 0627 3632, Epigenetics and Neurobiology Unit, , European Molecular Biology Laboratory, ; Monterotondo, Italy
                [5 ]GRID grid.7700.0, ISNI 0000 0001 2190 4373, Interdisciplinary Center for Neurosciences, , Heidelberg University, ; Heidelberg, Germany
                [6 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Developmental Biology Unit, , European Molecular Biology Laboratory, ; Heidelberg, Germany
                [7 ]GRID grid.4709.a, ISNI 0000 0004 0495 846X, Molecular Medicine Partnership Unit (MMPU), , European Molecular Biology Laboratory, ; Heidelberg, Germany
                Author information
                http://orcid.org/0000-0002-7225-2878
                http://orcid.org/0000-0003-3366-4703
                Article
                1257
                10.1038/s41592-021-01257-6
                8490155
                34594033
                239c469e-e98c-4bb7-9b8d-215a8952d7dd
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 12 January 2021
                : 30 July 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/100013060, European Molecular Biology Laboratory (EMBL Heidelberg);
                Funded by: FundRef https://doi.org/10.13039/501100000780, European Commission (EC);
                Award ID: 951991, Brainiaqs
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (German Research Foundation);
                Award ID: P8/FOR2289
                Award ID: A09N/SFB1158
                Award Recipient :
                Funded by: Chica and Heinz Schaller Research Foundation
                Categories
                Article
                Custom metadata
                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2021

                Life sciences
                glial biology,multiphoton microscopy,fluorescence imaging,ca2+ imaging
                Life sciences
                glial biology, multiphoton microscopy, fluorescence imaging, ca2+ imaging

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