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Tissue Clearing at the University Imaging Centers

The University Imaging Centers integrates the most recent tissue clearing and imaging technologies in order to image and analyze intact tissues and organs in three dimensions.

Tissue clearing has been developed in multiple laboratories to make tissues optically transparent to optimize whole-mount imaging. It also enables internal structure preservation and permeability to macromolecules like stains and antibodies. The UIC employs multiple clearing and labeling approaches with X-CLARITY being the most widely useful. With the X-CLARITY method, tissue is immobilized in a hydrogel to study fluorescent labels in biological systems in 3D. This approach brings a new dimension to histology services. This step can process samples of various sizes (the smaller the better with < 8 cubic mm optimal, although larger may be possible and is limited by the imaging modality you require). We have sample holders for 6 mouse brain-sized samples, 2 rat brain-sized samples, tissue slices (<1.5mm each), and 48 tissue samples (< 3 cubic mm each), with many other options.

Cleared Brain XCLARITY

This approach preserves stability while conserving proteins and nucleic acids throughout intact tissue. It offers the opportunity to show the relationship between structure and function of a molecule of interest in an intact organ for imaging. The UIC is equipped with a 3i Cleared Tissue LightSheet, Caliber RS-G4 ribbon scanning, confocal microscopy, multiphoton microscopy, and light sheet fluorescence microscopy. We can work with you to determine which system and which probes are right for you.

The UIC will continue to expand tissue clearing and 3D imaging service to multiple fields of research in samples ranging from plants to animals.

Tissue Preparation

  1. Perfusion d1X PBS and then 4% PFA, followed by brain extraction and immersion in 4% PFA for 24h at 4C.
  2. Brains should then be washed with 1X PBS and stored in PBS at 4C.

After this you may drop off the samples for clearing.

xclarity tissue clearing system


The X-CLARITY is a collection of systems and ready-to-use reagents to standardize, simplify, and accelerate each step of the tissue clearing process. X-CLARITY is based on CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging / Immunostaining / in situ-hybridization-compatible tissue hydrogel) method. With CLARITY, preserved tissues are embedded in a hydrogel matrix and lipids are actively extracted through electrophoresis to create a stable and optically transparent tissue-hydrogel hybrid that is chemically accessible for multiple rounds of antibody labeling and imaging.


  • XClarity Brain 10xG Hippocampus
  • XClarity Kidney 10xG
  • XClarity Brain 10xG Hippocampus

  • XClarity Kidney 10xG