Novel Methods for 3D Imaging and Quenching Tissue Autofluorescence

Cornell University Background
Visualizing cellular structures in the global context of intact organs is critical for deciphering organ function. However, imaging intact organs is impacted by the natural auto‑fluorescence and lack of transparency of biological tissues. These challenges limit the depth of imaging accessible by light microscopy techniques, and make it hard to resolve signal from noise during fluorescent imaging. As such, there is an unmet need for methods to enable improved light penetration and reduced autofluorescence of biological tissues.
Technology Overview
This technology includes two complementary techniques to address current imaging limitations of 3D tissue. Importantly, tissue preparation protocols are easy to follow and do not require the use of toxic solvents.
Atacama Clear makes tissue optically transparent, enabling 3D imaging of whole organs. Atacama Clear delivers 50% greater signal‑to‑noise ratio than CUBIC during imaging of 1mm murine heart sections.
Atacama Quench eliminates tissue autofluorescence to improve signal‑to‑noise ratio. Atacama Quench provides 10 times more blood vessel signal compared to TrueBlack during immunostaining of a murine brain section.

Atacama Clear does not require use of toxic solvents or dehydration with common alcohols
Atacama Clear clears tough fibrous tissue and preserves fluorescent reporter protein signals
Atacama Quench eliminates autofluorescence throughout the fluorescent light spectrum
Atacama Quench preserves tissue integrity and is compatible with follow-up IF studies


Optical clearing of tissues for superior 3D imaging of intact biological tissues
Elimination of autofluorescence to enable visualization of biological markers in basic science and clinical imaging studies

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