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


Light-sheet microscopy is an ideal technique for imaging large cleared samples; however, the community is still lacking instruments capable of producing volumetric images of centimeter-sized cleared samples with near-isotropic resolution within minutes. Here, we introduce the mesoscale selective plane-illumination microscopy initiative, an open-hardware project for building and operating a light-sheet microscope that addresses these challenges and is compatible with any type of cleared or expanded sample (

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Fig. 1: Example demonstrations of the mesoSPIM light-sheet microscope.
Fig. 2: Large-scale dataset acquired with the mesoSPIM.

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Data availability

Data was deposited to the Image Data Resource ( under accession number idr0066.

Code availability

The mesoSPIM software and documentation are available as Supplementary Software. Updated versions can be found on Github ( mesoSPIM-control is licensed under the GNU General Public License v.3.0 (GPL v.3).


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This work was supported by grants from the Swiss National Science Foundation (grant nos. 31003A-149858, 31003B-170269 to F.H.; no. 31003A_170037 to T.K.; nos. 31003A-153448, 31003A_173125, CRSII3_154453 and NCCR Synapsy no. 51NF40-158776 to A.H.), the European Research Council (ERC Advanced Grant BRAINCOMPATH, project no. 670757 to F.H.), ERC Starting Grants (InterWiring, project no. 679175 to T.K. and MULTICONNECT, project no. 639938 to A.R.), the Dutch science foundation (NWO VIDI Grant, project no. 14637 to A.R.), a PhD fellowship by the Swiss Foundation for Excellence in Biomedical Research (to R.K.), a gift from a private foundation with public interest through the International Foundation for Research in Paraplegia (to A.H. and S.P.), and a Distinguished Scientist Award of the Nomis Foundation (to A.A.). In addition, we would like to thank D. Göckeritz-Dujmovic and S. Bichet for help with sample preparation and M. Wieckhorst for help with custom electronics.

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Authors and Affiliations



F.F.V. and F.H. designed the project. F.F.V designed the microscope, wrote control software and documentation, coordinated the mesoSPIM initiative and analyzed data. F.F.V., E.P. and P.B. imaged samples. D.K., E.P., R.K., M.S., L.E., A.v.d.B., K.H., N.F., T.T., N.R., H.U.Z., T.K., P.P., R.P., D.H., B.R., S.H., A.S. and A.R. prepared samples for imaging. F.F.V., S.P., E.P., D.K., R.A.A.C., F.M., U.Z., L.B. A.H., C.L. and A.A. set up the mesoSPIM instruments. F.F.V. and F.H. wrote the manuscript with input from all coauthors.

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Correspondence to Fabian F. Voigt.

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The authors declare no competing interests.

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Peer review information Rita Strack was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Voigt, F.F., Kirschenbaum, D., Platonova, E. et al. The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nat Methods 16, 1105–1108 (2019).

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