Cleared Sample Imaging

Modifying the properties of usually opaque samples to render them transparent while keeping their structure intact


Cleared-Sample / Cleared-Tissue Applications

The 3D imaging capabilities of light-sheet microscopes, in combination with optical clearing techniques, enable visualization of very large, cleared specimens in-toto, comprehensive and non-destructive within minutes. It has thus become a valuable tool for 3D microstructure analysis of tissues (e.g. in neuroscience, developmental biology, and connectomics).


Bruker light-sheet microscopes are optimized for 3D imaging of intricate tissue structures and deliver best-in-class 3D imaging of cleared samples. These capabilities are particularly relevant to studying the brain or the central nervous tissue in neuroscience, analyzing organ development, or investigating tumor structure and genesis in oncology.


Cleared Sample Imaging Gallery

For more information about cleared sample imaging with light sheet fluorescence microscopy, visit:

Cleared Mouse Lymph Node

Cleared mouse lymph node. High endothelial venules (642 nm, red) and autofluorescence (488 nm, green) to visualize surrounding tissue. Imaged on the MuVi SPIM.

Courtesy of:
Jens Stein
University of Bern
Bern, Switzerland

Cleared Mouse Lymph Node

BABB-cleared mouse lymph node. High endothelial venules (red) and autofluorescence (green) to visualize surrounding tissue. Imaged on the QuVi SPIM.

Courtesy of:
Jens Stein
University of Bern
Bern, Switzerland

Cleared Mouse Head

Labeled with anti-tuj1 (green) to mark developing nerves and with anti-desmin (red) to mark differentiating muscles. Tiled image (6 × 5).
Imaged on the MuVi SPIM.

Courtesy of:
Glenda Comai
Institut Pasteur
Paris, France

Transgenic Drosophila Line Expressing UAS-mCD8-GFP with the Mef2-GAL4 Driver Line

The fruit fly was optically cleared and RI adjusted using alcohol dilutions and ECI. Size: 1.7 mm length (head to tail).
Imaged on the LCS SPIM.

Courtesy of:
Susanne Önel
Philipps University Marburg
Marburg, Germany

Neuronal Network

Neuronal network (stained with GFP) of a CUBIC-cleared mouse brain

Color-coded depth representation: maximal depth displayed 1.23 mm.
Imaged on the MuVi SPIM.

Courtesy of:
Montserrat Coll Lladó
European Molecular Biology Laboratory (EMBL)
Barcelona, Spain

Developing Nerves in a Whole Mouse Embryo

Developing nerves in a whole mouse embryo.
Sample cleared with DBE. Tiled image (3 x 4) acquisition. Scalebars: 1mm.
Imaged on the LCS SPIM.

Sample courtesy of:
James Muller
New York, USA

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