Watch your brains quickly disappear — accelerate your research with X-CLARITY

ATA Scientific Pty Ltd

Tuesday, 11 February, 2020


Techniques that can render tissues clearer than glass allow scientists to reveal the inner workings of biological systems. Clearing tissue helps to drive deeper explorations of structures to expand our understanding of internal functions buried within cells and how these are associated with disease.

Traditional analysis of large-scale tissues has mostly depended on microtomes to cut thin sections, but this process can lead to loss of information. Reconstructing 3D images from thin tissue slices by aligning hundreds or even thousands of snapshots to map long-range projections of cells is laborious and error-prone, and can render fine-grain analysis of whole tissue practically impossible. Recent innovations have led to new tissue-clearing techniques that can be used to acquire high-resolution 3D images without the need to reduce samples to thin serial sections.

The X-CLARITY (Logos Biosystems) is an all-in-one, easy-to-use solution for electrophoretic tissue clearing. Based on the pioneering work of the Deisseroth lab in Stanford, it enables biological tissue to be transformed into a transparent state for single-cell resolution imaging. Its unique design accelerates the efficient removal of lipids, the main component of light scattering in biological tissues from the tissue hydrogel hybrid. The cleared tissue can then be labelled with appropriate probes such as fluorescent-labelled antibodies and mounted in a refractive index (RI) matching medium to enhance optical clarity for 3D imaging. This provides an optimal environment for 3D imaging with fluorescent microscopy and for prolonged preservation of fluorescence signals in the labelled tissue.

The X-CLARITY tissue clearing system is capable of clearing tissue in half the time of the original method and has become the system of choice for leading research institutes and pharma globally. Using easy-to-follow workflows, efficient control of temperature and a uniform electric current, even the most challenging samples such as bone, spinal cord and plants can be cleared rapidly and reproducibly. By simply pushing a few buttons and applying ready-to-use reagents, a whole mouse brain can be cleared in just six hours.

Whole Thy1-YFP mouse brain. The Thy1-YFP signal is preserved and vibrant after tissue clearing with the X-CLARITY™ systems and reagents.

Optical clarity for 3D imaging is enhanced using specifically designed consumables that help make the process even more convenient. Transparent samples can be labelled with antibodies using the DeepLabelTM Antibody Staining Kit, which can rapidly and efficiently penetrate thick, protein-dense tissues for site-specific binding at lower antibody concentrations. DeepLabel facilitates homogenous antibody staining with 2.6x greater signal-to-background than conventional staining methods. It allows for vibrant fluorescence imaging at subcellular resolution and is compatible with virtually all antibodies and all cleared tissues.

Finally, the labelled tissue is infused and mounted in a refractive index (RI) matching medium to enhance optical clarity for 3D imaging. X-CLARITY Mounting Solution is a newly developed optical clearing agent specifically formulated to overcome known challenges of similar products, mainly lack of availability and high cost. X-CLARITY Mounting Solution is a high-quality refractive index matching solution that minimises photobleaching and preserves fluorescence signals for vibrant fluorescence imaging, making it an ideal solution for clarified and labelled tissue samples.

For more information, please contact Peter Davis at

Top image caption: Thy1-YFP mouse brain slices cleared with the X-CLARITY systems and reagents: Thy1-YFP (green), Anti-Collagen IV (red), TO-PRO-3 (blue).

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