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An MR-based brain template and atlas for optical projection tomography and light sheet fluorescence microscopy in neuroscience
Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Department of Medical and Translational Biology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).ORCID iD: 0000-0003-3445-7829
Umeå University, Faculty of Medicine, Department of Medical and Translational Biology.
Umeå University, Faculty of Medicine, Department of Medical and Translational Biology.ORCID iD: 0000-0002-5589-9864
Umeå University, Faculty of Medicine, Department of Clinical Microbiology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).ORCID iD: 0000-0001-8123-3292
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2024 (English)In: Frontiers in Neuroscience, ISSN 1662-4548, E-ISSN 1662-453X, Vol. 18, article id 1328815Article in journal (Refereed) Published
Abstract [en]

Introduction: Optical Projection Tomography (OPT) and light sheet fluorescence microscopy (LSFM) are high resolution optical imaging techniques, ideally suited for ex vivo 3D whole mouse brain imaging. Although they exhibit high specificity for their targets, the anatomical detail provided by tissue autofluorescence remains limited.

Methods: T1-weighted images were acquired from 19 BABB or DBE cleared brains to create an MR template using serial longitudinal registration. Afterwards, fluorescent OPT and LSFM images were coregistered/normalized to the MR template to create fusion images.

Results: Volumetric calculations revealed a significant difference between BABB and DBE cleared brains, leading to develop two optimized templates, with associated tissue priors and brain atlas, for BABB (OCUM) and DBE (iOCUM). By creating fusion images, we identified virus infected brain regions, mapped dopamine transporter and translocator protein expression, and traced innervation from the eye along the optic tract to the thalamus and superior colliculus using cholera toxin B. Fusion images allowed for precise anatomical identification of fluorescent signal in the detailed anatomical context provided by MR.

Discussion: The possibility to anatomically map fluorescent signals on magnetic resonance (MR) images, widely used in clinical and preclinical neuroscience, would greatly benefit applications of optical imaging of mouse brain. These specific MR templates for cleared brains enable a broad range of neuroscientific applications integrating 3D optical brain imaging.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2024. Vol. 18, article id 1328815
Keywords [en]
brain template, LSFM, mesoscopic imaging, MRI, neuroimaging, OPT
National Category
Neurosciences Radiology, Nuclear Medicine and Medical Imaging
Identifiers
URN: urn:nbn:se:umu:diva-223641DOI: 10.3389/fnins.2024.1328815ISI: 001198866200001PubMedID: 38601090Scopus ID: 2-s2.0-85189910322OAI: oai:DiVA.org:umu-223641DiVA, id: diva2:1853999
Funder
The Kempe FoundationsSwedish Research Council, 2020-06224Swedish Research Council, 2018-05851Swedish Research Council, 2020-02300Novo Nordisk FoundationFamiljen Erling-Perssons StiftelseAvailable from: 2024-04-24 Created: 2024-04-24 Last updated: 2024-04-24Bibliographically approved

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Willekens, Stefanie M. A.Morini, FedericoMediavilla, TomásNilsson, EmmaOrädd, GregerHahn, MaxChotiwan, NunyaÖverby, Anna K.Ahlgren, UlfMarcellino, Daniel

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Willekens, Stefanie M. A.Morini, FedericoMediavilla, TomásNilsson, EmmaOrädd, GregerHahn, MaxChotiwan, NunyaÖverby, Anna K.Ahlgren, UlfMarcellino, Daniel
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Department of Clinical MicrobiologyDepartment of Medical and Translational BiologyMolecular Infection Medicine Sweden (MIMS)
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Frontiers in Neuroscience
NeurosciencesRadiology, Nuclear Medicine and Medical Imaging

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