The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue

Voigt, Fabian F.; Kirschenbaum, Daniel S.; Platonova, Evgenia; Pagès, Stéphane; Campbell, Robert A. A.; Kästli, Rahel; Schaettin, Martina; Egolf, Ladan; Bourg, Alexander van der; Bethge, Philipp; Haenraets, Karen; Frezel, Noémie; Topilko, Thomas; Perin, Paola; Hillier, Dániel; Hildebrand, Sven; Schueth, Anna; Roebroeck, Alard; Roska, Botond; Stoeckli, Esther T.; Pizzala, Roberto; Renier, Nicolas; Zeilhofer, Hanns Ulrich; Karayannis, Theofanis; Ziegler, Urs; Batti, Laura; Holtmaat, Anthony; Lüscher, Christian; Aguzzi, Adriano; Helmchen, Fritjof

doi:10.1038/s41592-019-0554-0

Cited by 211 publications

(209 citation statements)

References 75 publications

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“…MesoSPIM 52 has been used to determine the 3D distribution of AOI987 in brains of arcAβ mice and non-transgenic littermates with luminescent conjugated oligothiophene probe. SPIM imaging of the cleared brain of arcAβ mice revealed signals in the cortical, hippocampal and thalamic parenchyma as well as in vascular structures, indicative of aggregated Aβ accumulation.…”

Section: Resultsmentioning

confidence: 99%

“…Two arcAβ mice and two non-transgenic littermates were perfused using hydrogel and cleared using a modified electrophoretic clearing chamber for CLARITY 50, 51 . The detailed procedure for Aβ staining using LCOs (hFTAA and qFTAA) and analysis methods for mesoscopic selective plane illumination microscopy (mesoSPIM) 52 are provided as Suppl materials . Paraffin fixed brains from arcAβ, APP/PS1 and non-transgenic littermate mice were cut horizontally at 5 μm thickness.…”

Section: Methodsmentioning

confidence: 99%

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Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models

Deán‐Ben

Kirschenbaum

et al. 2020

Preprint

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Deposition of beta-amyloid (Aβ) deposits is one major histopathological hallmark of Alzheimer's disease (AD). Here, we introduce volumetric multi-spectral optoacoustic tomography (vMSOT), which covers 10×10×10 mm 3 field-of-view, capable of 3D whole mouse brain imaging. We show for the first time the optoacoustic properties of oxazine-derivative AOI987 probe, which binds to Aβ, and the application of vMSOT for the quantification of brainwide Aβ deposition. Administration of AOI987 to two common transgenic mouse strains of AD amyloidosis led to a retention of the probe in Aβ-laden brain regions. Co-registered of vMSOT data to a brain atlas revealed strain-specific pattern of AOI987 uptake. A comparison with ex vivo light-sheet microscopy in cleared mouse brains showed a good correspondence in Aβ distribution. Lastly, we demonstrate the specificity of the AOI987 probe by immunohistochemistry. vMSOT with AOI987 facilitates preclinical brain region-specific studies of Aβ spread and accumulation, and the monitoring of putative treatments targeting Aβ.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models

Deán‐Ben

Kirschenbaum

et al. 2020

Preprint

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“…However, clearing requires often complex, lengthy and costly tissue preparation, with variable efficacy (9,12), and widely acknowledged morphological changes to the sample (9,13). Additionally, sample size is limited by the working distance of the microscope objective lens (7) and the objective lens must be protected from the often corrosive clearing solutions. Resolution is also limited by the need for broader light sheets to penetrate greater tissue depth (14).…”

Section: Introductionmentioning

confidence: 99%

“…Cleared samples can be imaged using techniques such as light-sheet microscopy (2,4,7) and optical projection tomography (OPT) (10,11). However, clearing requires often complex, lengthy and costly tissue preparation, with variable efficacy (9,12), and widely acknowledged morphological changes to the sample (9,13).…”

Section: Introductionmentioning

confidence: 99%

Multi-Fluorescence High-Resolution Episcopic Microscopy (MF-HREM) for Three-Dimensional Imaging of Adult Murine Organs

Walsh

Holroyd

Finnerty

et al. 2020

Preprint

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10 Three-dimensional microscopy of large biological samples (>0.5 cm 3 ) is transforming 11 biological research. Many existing techniques require trade-offs between image resolution 12 and sample size, require clearing or use optical sectioning. These factors complicate the 13 implementation of large volume 3D imaging. Here we present Multi-fluorescent High 14 Resolution Episcopic Microscopy (MF-HREM) which allows 3D imaging of large samples 15 without the need for clearing or optical sectioning. 16MF-HREM uses serial-sectioning and block-facing wide-field fluorescence, without the need 17 for tissue clearing or optical sectioning. We detail developments in sample processing 18 including stain penetration, resin embedding and imaging. In addition, we describe image 19 post-processing methods needed to segment and further quantify these data. Finally, we 20 demonstrate the wide applicability of MF-HREM by: 1) quantifying adult mouse glomeruli. 2) 21 identifying injected cells and vascular networks in tumour xenograft models; 3) quantifying 22 vascular networks and white matter track orientation in mouse brain.

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“…As a reference, when illuminating a range of 1 mm in length, an optimized Gaussian light-sheet diverges to a full-width at halfmaximum (FWHM) thickness of 12.5 μm at either end, and is hence incapable of resolving fine neuronal fibers across a large volume of brain. Sweeping the light-sheet along the propagation direction can extend the confocal range, but the achieved axial resolution remains inadequate, and tissue scattering effects also limit its propagation range 21,22 . Bessel-type light-sheet microscopy [23][24][25] (LSM) can generate a thin and non-diverging light-sheet that can illuminate samples with a much larger field of view while maintaining high axial resolution.…”

Section: Introductionmentioning

confidence: 99%

Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy

Fang

Chu

et al. 2019

Preprint

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We here report on a compressed sensing-enabled Bessel light-sheet microscopy system able to achieve fast scalable mapping of entire organs at an isotropic subcellular resolution. A dualside confocally-scanned Bessel light-sheet with a millimeter-to-centimeter tunable range was developed to illuminate regions-of-interest from a few cells to entire organs, providing uniform optical sectioning of deep tissues with 1-5 μm ultra-thin axial confinement. We also present a new computation pipeline termed content-aware compressed sensing (CACS), which can further improve the contrast and resolution of a 3D image based on a single input of its own, allowing satisfying spatial resolution with data acquisition shorten by two-orders of magnitude.Using this method, we can image any region-of-interest of a selected mouse brain at submicron isotropic resolution in seconds, after screening multiple whole brains in minutes, and then in toto reconstruct the digital whole brain (~400 mm 3 ) at a teravoxel scale with a short acquisition time of ~15 minutes. We also demonstrate subcellular-resolution minute-timescale dual-color imaging of neuromuscular junctions in thick mouse muscles. Various system-level cellular analyses, such as mapping cell populations at different brain sub-regions, tracing long-distance projection neurons over the entire brain, and calculating neuromuscular junction occupancy across whole tissue, were enabled by our high-throughput high-resolution imaging method. `

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The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue

Cited by 211 publications

References 75 publications

Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models

Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models

Multi-Fluorescence High-Resolution Episcopic Microscopy (MF-HREM) for Three-Dimensional Imaging of Adult Murine Organs

Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy

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