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J Biophotonics. 2018 May;11(5):e201700248. doi: 10.1002/jbio.201700248. Epub 2018 Jan 30.

Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs.

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Laboratory of Neurobiology, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Warsaw, Poland.
Department of Immunology, Medical University of Warsaw, Warsaw, Poland.
Laboratory of Biochemistry of Lipids, Department of Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland.


Whole-organ and whole-body optical tissue clearing methods allowing imaging in 3 dimensions are an area of profound research interest. Originally developed to study nervous tissue, they have been successfully applied to all murine organs, yet clearing and imaging of rat peripheral organs is less advanced. Here, a modification of CUBIC clearing protocol is presented. It provides a rapid and simple approach to clear the entire adult rat organism and thus all organs within as little as 4 days. Upgraded perfusion-based rat CUBIC protocol preserves both anatomical structure of organs and signal from proteinaceous fluorophores, and furthermore is compatible with antibody staining. Finally, it enables also volumetric cells analyses and is tailored for staining of calcium deposits within unsectioned soft tissues.


Thy-1 GFP; light-sheet microscope; optical tissue clearing; rat; whole-body clearing


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