Tissue Clearing System
X-CLARITY tissue clearing system for optically transparent 3D organ imaging
X-CLARITY from Logos Biosystems uses the CLARITY method with dedicated instruments and ready-to-use reagents to process your whole organs and thick tissue blocks. Fixed tissue is embedded in a hydrogel matrix, and lipids are then actively removed by electrophoresis, leaving a stable, transparent tissue-hydrogel hybrid.
Native architecture stays intact, and endogenous fluorescent proteins are preserved for fluorescence imaging. The workflow runs in three parts, moving your sample from fixed tissue to a clear, imaging-ready hybrid. The Hydrogel Solution Kit infuses monomers through your sample. The Polymerization System links biomolecules into your hydrogel network in an anaerobic environment. The Tissue Clearing System II then clears the hybrid, using the ready-to-use Electrophoretic Tissue Clearing Solution, either actively through electrophoresis or passively.
The result is a sample that stays chemically accessible for your repeated rounds of antibody labelling and imaging. The approach is non-destructive and works across a range of your tissue types. Logos Biosystems supplies the X-CLARITY systems and reagents.
Matching the component to the clearing step
1) Hydrogel infusion. The X-CLARITY Hydrogel Solution Kit diffuses monomers evenly through your fixed tissue.
2) Polymerisation. The X-CLARITY Polymerization System links biomolecules into the hydrogel network in an anaerobic environment.
3) Clearing. The X-CLARITY Tissue Clearing System II, with the ready-to-use Electrophoretic Tissue Clearing Solution, removes lipids from your sample, either actively or passively.
4) Imaging readiness. The cleared tissue-hydrogel hybrid keeps endogenous fluorescent proteins intact and accepts repeated antibody labelling for high-resolution 3D imaging.
Applications
- Neuroscience and connectomics. Cleared brain hemispheres reveal axonal projections and cell-type distributions, mapped using your fluorescent protein reporters or antibody staining.
- Tumour microenvironment imaging. Cleared biopsy cores or whole organs let you image tumour vasculature, immune cell infiltration and metastatic foci in three dimensions.
- Developmental biology. Cleared embryos show the spatial organisation of signalling gradients and cell lineages across the whole embryo, without physical sectioning.
- Whole-organ 3D reconstruction. Intact organs and thick tissue blocks turn optically transparent, letting your 3D imaging systems capture architecture without errors from serial sectioning.
- Multiplexed antibody labelling. Hydrogel-tissue chemistry keeps the sample chemically accessible for repeated rounds of antibody labelling, increasing the information you gain per specimen.
- Endogenous fluorescent protein imaging. Hydrogel-tissue chemistry preserves native GFP, tdTomato and other reporters together with RNA, supporting direct imaging of your sample without extra staining.
Frequently asked questions
What does tissue clearing achieve and why is it used?
Tissue clearing removes the lipids that scatter light in biological tissue, making it optically transparent. This lets fluorescence microscopy image through millimetres to centimetres of intact tissue without cutting sections. The result is an uninterrupted 3D view of cellular architecture, connectivity and protein distribution. Physical sectioning cannot match this, because registration errors build up across hundreds of serial sections.
What is the difference between passive and active tissue clearing?
Passive clearing uses detergent solutions to diffuse lipids out of tissue by concentration gradient over days to weeks. Active clearing applies an electric field to drive charged lipid micelles out of the tissue more quickly. This reduces clearing time for thick or dense samples such as brain or liver. Active methods need specialised electrophoresis hardware, but they produce more even clearing in a shorter time.
Does tissue clearing destroy antigenicity?
Hydrogel-based clearing methods preserve protein epitopes. They crosslink biomolecules into the polymer network before lipids are removed. Most antibodies used in standard immunofluorescence work on hydrogel-cleared tissue, after appropriate blocking and incubation steps. Endogenous fluorescent proteins such as GFP and tdTomato also survive the process. Some harsh detergent or solvent-based clearing protocols reduce antigenicity and work less well with antibody labelling.
Which microscope is needed to image cleared tissue?
Confocal microscopy is standard for samples up to a few hundred micrometres thick, or for high-resolution imaging of specific regions. Two-photon microscopy penetrates deeper but is slower and needs specialised lasers. Light-sheet fluorescence microscopy illuminates a thin plane and detects at 90 degrees. This allows rapid whole-organ imaging with low photobleaching. The right choice depends on sample size, required resolution, speed and available instrumentation.