• Tissue Clearing

    X-CLARITY™ Systems & Reagents for Tissue Clearing

    The X-CLARITY™ is a collection of systems and ready-to-use reagents developed by Logos Biosystems to make electrophoretic tissue clearing simple, rapid, and efficient.

TISSUE CLEARING FOR 3D IMAGING

  • 01TISSUE-HYDROGEL HYBRIDIZATION
    X-CLARITY™
    Hydrogel Solution Kit
    C1310X
    X-CLARITY™
    Polymerization System
    C20001
  • 02TISSUE CLEARING
    X-CLARITY™
    Tissue Clearing System II
    C30001
    Electrophoretic
    Tissue Clearing Solution
    C13001
  • 03ANTIBODY LABELING COMING SOON!
    DeepLabel™
    Antibody Staining Kit
    C33001
  • 04IMAGING
    X-CLARITY™
    Mounting Solution
    C13101
01

TISSUE-HYDROGEL HYBRIDIZATION

A fixed tissue sample is incubated in the X-CLARITY™ Hydrogel Solution Kit to allow hydrogel monomers to diffuse uniformly throughout the sample. Once the solution has permeated the tissue, the sample is placed in the X-CLARITY™ Polymerization System. Monomers polymerize in the anaerobic environment, covalently linking the biomolecules to a sturdy hydrogel network, preserving molecular information and structural integrity.
  • X-CLARITY™ Polymerization System C20001
    The X-CLARITY™ Polymerization System is a standalone, automated system developed to simplify tissue-hydrogel hybridization, a crucial step for optimal tissue clearing. Multiple samples can be placed in multi-well plates or conical tubes for rapid and efficient high-throughput sample processing. Users can control polymerization by adjusting vacuum strength, temperature, and a timer through a simple touchscreen interface. A ready-to-use X-CLARITY™ Hydrogel Solution Kit simplifies the process even further.
    App Note
  • High throughput
    (up to 768 samples/run)
  • Compatible with various
    vessels
  • Steady vacuum &
    temperature control
  • Rapid and consistent
    polymerization
HYDROGEL SOLUTION KIT
    Cat # Product Qty MSDS Product Insert
    C1310X X-CLARITY™ Hydrogel Solution Kit

    1 box

    FileAction
    C1310X X-CLARITY™ Hydrogel Solution Kit_MSDS.zipDownload 
    C1310X X-CLARITY™ Hydrogel Solution Kit VX1802-01.pdfDownload 
    C13103 X-CLARITY™ Hydrogel Solution

    1 L

    FileAction
    [C13103] X-CLARITY Polymerization HS_rev2.pdfDownload 
    C13103 X-CLARITY™ Hydrogel Solution VX1802-01.pdfDownload 
    C13104 X-CLARITY™ Polymerization Initiator

    2.5 g

    FileAction
    [C13104] X-CLARITY Polymerization PI_rev3.pdfDownload 
    C13104 X-CLARITY™ Polymerization Initiator VX1802-01.pdfDownload 
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    02

    TISSUE CLEARING

    • X-CLARITY™ Tissue Clearing System II C30001
      The X-CLARITY™ Tissue Clearing System II is an all-in-one, easy-to-use solution for electrophoretic tissue clearing. Its unique design accelerates the removal of lipids from tissues while preserving the structural integrity of the sample. Clear a whole mouse brain in just 6 hours, an astounding 8 times faster than the original technology. Electrophoretic Tissue Clearing Solution is a premixed SDS-based buffer optimized for use with the system. This advanced system ensures that tissue clearing occurs efficiently and rapidly.
      APP NOTE Image Gallery
    • Precise temperature control
      • Active buffer cooling and
        heating capacity
      • Sensitive and accurate
        temperature sensor
    • Uniform electric field
      • Platinum plated electrodes
      • Constant current and
        constant voltage modes
    • Compatible with multiple tissue types and sizes
      • Active and passive clearing
        modes
      • Holders of various sizes
        available
    • User-friendly setup
      • Simple touchscreen
        interface
      • Ready-to- use clearing
        solution
    ELECTROPHORETIC TISSUE CLEARING SOLUTION
      Cat # Product Qty MSDS Product Insert
      C13001 Electrophoretic Tissue Clearing Solution

      12 x 1 L

      FileAction
      [C13001] Electrophoretic Tissue Clearing Solution.pdfDownload 
      C13001 Electrophoretic Tissue Clearing Solution VX1802-01.pdfDownload 
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      03

      ANTIBODY LABELING

      • COMING SOON!
        DeepLabel™ Antibody Staining Kit
        C33001
        The DeepLabel™ Antibody Staining Kit enhances antibody penetration into large clarified tissues for vibrant fluorescence 3D imaging. DeepLabel facilitates the diffusion of molecular probes deep into thick, protein-dense tissues for robust and efficient antibody labeling. DeepLabel has been optimized for the antibody labeling of clarified tissues.
        • Efficient antibody penetration
        • Site-specific labeling
        • Deep permeation into thick tissues
        • Simple protocol with ready-to-use reagents
        • Vibrant imaging at subcellular resolution
      • DeepLabel™ enhances anti-Collagen Ⅳ penetration into clarified mouse brain tissues.

      • Adult mouse brain stained using DeepLabel with anti-β-Amyloid (yellow), anti-Iba1 (red), and anti-SMA (purple).

      • Whole adult mouse brain stained using DeepLabel with anti-TH (red).

      • Whole adult Drosophila brain stained using DeepLabel with anti-GFP (green) and anti-TH (red).

      04

      IMAGING

      • X-CLARITY™ Mounting Solution C13101 C13102 C13107
        X-CLARITY™ Mounting Solution is a high quality, cost-efficient refractive index matching solution (RIMS) modified from the recipe developed by Yang et al. The refractive index (RI) of the solution is 1.460 at 25°C and is stable over a wide temperature range. The X-CLARITY™ Mounting Solution minimizes photobleaching and preserves fluorescence signals, making it an ideal solution for clarified and labeled tissue samples.
        •   ·  RI = 1.460 at 25°C
        •   ·  Minimizes photobleaching
        •   ·  Preserves fluorescence signals
        App Note
      Human cerebral cortex (1 mm)
      • Before ETC
        PFA-fixed (1 week)
      • After ETC
      • After RI matching
      Courtesy of Hyung Jin Choi, PhD
      Seoul National University College of Medicine
      MOUNTING SOLUTION
        Cat # Product Qty MSDS Product Insert
        C13101 X-CLARITY™ Mounting Solution

        1 x 25 mL

        FileAction
        [C13101,2,7] X-CLARITY™ Mounting Solution.pdfDownload 
        C13101,2,7 X-CLARITY™ Mounting Solution VX1802-01.pdfDownload 
        C13102 X-CLARITY™ Mounting Solution Value Pack

        10 x 25 mL

        FileAction
        [C13101] X-CLARITY™ Mounting Solution.pdfDownload 
        C13101,2,7 X-CLARITY™ Mounting Solution VX1802-01.pdfDownload 
        C13107 X-CLARITY™ Mounting Solution Bulk Pack

        20 x 25 mL

        FileAction
        [C13101] X-CLARITY™ Mounting Solution.pdfDownload 
        C13101,2,7 X-CLARITY™ Mounting Solution VX1802-01.pdfDownload 
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        WHAT DO OUR CUSTOMERS HAVE TO SAY?

        Testimonials
        • Doug Richardson, PhD

          Harvard Center for Biological Imaging

          We purchased the X-CLARITY Tissue Clearing System for our facility and have been very satisfied with its easy-to-use design and consistent results. The X-CLARITY Tissue Clearing System has now allowed many more researchers to enter the field of tissue clearing. In my opinion, the X-CLARITY Tissue Clearing System along with the recently introduced X-CLARITY Polymerization System will help expand the availability of this technique to all scientists who hope to add it to their laboratory’s repertoire.

        • Uri Manor, PhD

          Salk Institute for Biological Studies

          The X-CLARITY system is a delight to use and significantly lowers the barrier to tissue clearing imaging applications. With better clearing, and faster turnaround time, we were able to generate many more samples and images than would otherwise have been possible. Highly recommended!

        • Yoko Yazaki-Sugiyama, PhD

          Okinawa Institute of Science and Technology

          For quite a while we were using passive immersion method to obtain transparent zebra finch brains, but this was time-consuming and always a pain in the neck. With the X-CLARITY Tissue Clearing System, even a whole brain can be cleared within several hours with excellent consistency as well as better signal-to-noise ratio when acquiring fluorescent images from deep tissue. It has made our lives a lot easier. TIME IS MONEY!

        • Robert Hunt, PhD

          University of California, Irvine

          We were not sure what to expect when we tried the X-CLARITY Tissue Clearing System. I've tried other tissue clearing methods with varying levels of success. When Jan, a first-year graduate student, showed me a fully cleared whole mouse brain on his first try, I was really impressed! I think this system will really speed up his work.

        • Annick Prigent & Benoît Delatour, PhD

          ICM Histomics

          The X-CLARITY allows us to perform rapid, efficient, and standardized clearing of mouse and human brain tissues. Access to the X-CLARITY technology will undoubtedly help the ICM research teams to better understand the 3D organization of protein assemblies and organelles in tissues.

        • Woong Sun, PhD

          Korea University Medical School

          I tried to design my own DIY ETC chamber for a long time without any success. I tried the X-CLARITY Tissue Clearing System and got a transparent mouse brain on my first try. It works really well and is easy to use. I’ve successfully imaged tissues that contain GFP or that I’ve labeled with fluorescence-tagged antibodies. It makes tissue clearing a stress free process.

        • Youngshik Choe, PhD

          Korea Brain Research Institute

          I find the X-CLARITY simplifies the CLARITY procedure and gives consistent transparency of tissues by plug and play steps.
          The best of it is the speed that can't be achieved by other methods.

        • Yun Kyoung Kang, PhD

          Baylor College of Medicine

          I have tried various tissues besides the brain with the X-CLARITY Tissue Clearing System from Logos Biosystems. The X-CLARITY™ makes CLARITY simple and easy to apply. The X-CLARITY™ produces consistent clearing results with any tissue, including tumors, within a couple of days rather than weeks. Very impressive!

        + SHOW OUR CUSTOMERS

        WHERE THE X-CLARITY™ HAS BEEN CITED

        Citations
        • BigStitcher: Reconstructing high-resolution image datasets of cleared and expanded samples
          D Hörl, FR Rusak, F Preusser, P Tillberg, N Rande, RK Chhetri, A Cardona, PJ Keller, H Harz, H Leonhardt, M Treier, S Preibisch
          bioRxiv 343954 (2018)

        • SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub
          Piazza R, Magistroni V, Redaelli S, Mauri M, Massimino L, Sessa A, Peronaci M, Lalowski M, Soliymani R, Mezzatesta C, Pirola A, Banfi F, Rubio A, Rea D, Stagno F, Usala E, Martino B, Campiotti L, Merli M, Passamonti F, Onida F, Morotti A, Pavesi F, Bregni M, Broccoli V, Baumann M, Gambacorti-Passerini C
          Nature Communications 9, 2192 (2018)

        • PrismPlus: a mouse line expressing distinct fluorophores in four different brain cell types
          Gaire J, Lee HC, Ward R, Currlin S, Woolley AJ, Coleman JE, Williams JC, Otto KJ
          Scientific Reports 8, 7182 (2018)

        • Subepithelial telocytes are an important source of Wnts that supports intestinal crypts Shoshkes-Carmel M, Wang YJ, Wangensteen KJ, Tóth B, Kondo A, Massassa EE, Itzkovitz S, Kaestner KH Nature 557, 242–246 (2018)

        • Heart clearing opens new insights in the quantification of injured area after ischemia reperfusion Paccalet A, Badawi S, Gouriou Y, Bidaux G, Crola Da Silva C
          Archives of Cardiovascular Diseases Supplements 10(2), 254 (2018)

        • Cortico–reticulo–spinal circuit reorganization enables functional recovery after severe spinal cord contusion Asboth L, Friedli L, Beauparlant J, Martinez-Gonzalez C, Anil S, Rey E, Baud L, Pidpruzhnykova G, Anderson MA, Shkorbatova P,, Batti L, Pagès S, Kreider J, Schneider BL, Barraud Q, Courtine G. Nature Neuroscience 21, 576-588 (2018)

        • 3D imaging in the postmortem human brain with CLARITY and CUBIC Ando K, Laborde Q, Brion JP, Duyckaerts C Handbook of Clinical Neurology 150, 303-317

        • Vascular niche IL-6 induces alternative macrophage activation in glioblastoma through HIF-2α Wang Q, He Z, Huang M, Liu T, Wang Y, Xu H, Duan H, Ma P, Zhang L, Zamvil SS, Hidalgo J, Zhang Z, O'Rourke DM, Dahmane N, Brem S, Mou Y, Gong Y, Fan Y Nature Communications 9, 559 (2018)

        • Pitch-tunable pillar arrays for high-throughput culture and immunohistological analysis of tumor spheroids Lee DW, Kang J, Hwang HJ, Oh MS, Shin BC, Lee MY, Kuh HJ RSC Advances 8, 4494-4502 (2018)

        • Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome Lamm KYB, Johnson ML, Phillips JB, Muntifering MB, James JM, Jones HN, Redline RW, Rokas A, Muglia, LJ eLife 7: e31150 (2018)

        • Rapid spheroid clearing on a microfluidic chip Santisteban TS, Rabajania O, Kalinina I, Robinson S, Meier M Lab on a Chip 18, 153-161 (2018)

        • Optical clearing for multi‐scale biological tissues Yu T, Qi Y, Gong H, Luo Q, Zhu D Journal of Biophotonics 11(2), e201700187 (2018)

        • Organism-Level Analysis of Vaccination Reveals Networks of Protection across Tissues Kadoki M, Patil A, Thaiss CC, Brooks DJ, Pandey S, Deep D, Alvarez D, von Andrian UH, Wagers AJ, Nakai K, Mikkelsen TS, Soumillon M, Chevrier N Cell 171, 398-413 (2017)

        • Effects of neural stem cell media on hypoxic injury in rat hippocampal slice cultures Lee NM, Chae SA, Lee HJ Brain Research 1677, 20-25 (2017)

        • Optogenetic targeting of cardiac myocytes and non-myocytes: Tools, challenges and utility Johnston CM, Rog-Zielinska, EA, Wülfers EM, Houwaart T, Siedlecka U, Naumann A, Nitschke R, Knöpfel T, Kohl P, Shrneider-Warme F Progress in Biophysics & Molecular Biology 130, 140-149 (2017)

        • Interactions between fibroblastic reticular cells and B cells promote mesenteric lymph node lymphangiogenesis Dubey LK, Karempudi P, Luther SA, Ludewig B, Harris NL Nature Communications 8, 367 (2017)

        • Advances and perspectives in tissue clearing using CLARITY Jensen KHR, Berg RW Journal of Chemical Neuroanatomy 86, 19-34 (2017)

        • Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens Glaser AK, Reder NP, Chen Y, McCarty EF, Yin C, Wei L, Wang Y, True LD, Liu JTC Nature Biomedical Engineering 1, 0084 (2017)

        • Graphene Oxide-Quenching-Based Fluorescence In Situ Hybridization (G-FISH) To Detect RNA In Tissue: Simple And Fast Tissue RNA Diagnostics Hwang DW, Choi YR, Kim D, Park HY, Kim KW, Kim MY, Park CK, Lee DS bioRxiv 143628 (2017)

        • ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging Lee E, Choi J, Jo Y, Kim JY, Jang YJ, Lee HM, Kim SY, Lee HJ, Cho K, Jung N, Hur EM, Jeong SJ, Moon C, Choe Y, Rhyu IJ, Kim H, Sun W; Scientific Reports 6, 618631 (2016)

        SHOW MORE  +

        Resources

        Downloads
        • Icon
          X-CLARITY™

          Brochure

          2018-05-18 | 962KB
        • Icon
          X-CLARITY™ Flyer VX1606-01

          Brochure

          2018-05-08 | 553 KB
        • Icon
          C10001 X-CLARITY™ Tissue Clearing System Quick Start Guide

          Quick Start Guide

          2018-05-08 | 668.54 KB
        • Icon
          C30001 X-CLARITY™ Tissue Clearing System II Installation Guide

          Installation Guide

          2018-05-08 | 841.04 KB
        • Icon
          Preserving endogenous fluorescent protein signals for volumetric imaging using the X-CLARITY™ systems and reagents for tissue clearing

          Product literature

          2018-04-17 | 1.6 MB
        • Icon
          ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging

          Product literature

          2018-04-17 | 2.6 MB
        • Icon
          The X-CLARITY™ Mounting Solution: an improved RI matching solution for tissues cleared by the X-CLARITY™ Tissue Clearing System

          Product literature

          2018-04-17 | 1.5 MB
        • Icon
          An automated and high-throughput polymerization solution for downstream tissue clearing: the X-CLARITY™ Polymerization System

          Product literature

          2018-04-17 | 1.4 MB
        • Icon
          Logos Biosystems Products

          Brochure

          2018-04-15 | 2.14 MB
          • Icon
            X-CLARITY Tissue Clearing System II S/W ver 1.1.0

            Software

            2018-06-27 | 504KB
          • Icon
            X-CLARITY Polymerization S/W ver 1.1.0

            Software

            2018-06-26 | 452KB
            Videos

            Single-neuron segmentation of 3D confocal images of clarified tissues

            DataBrain: Using deep imaging techniques to develop a high-fidelity map of the brain

            Multiscale analysis of ischemia-reperfusion syndrome

            Studying molecular mechanisms of ischemia-reperfusion

            Polymerization simplified

            The new X-CLARITY™ sample holders

            Innovations in Spinal Treatment using Electrophoretic Tissue Clearing

            Spinal Treatment Techniques in the Lab

            How the CLARITY Method Supports Spinal Cord Research

            A journey through the brain

            Whole mouse brain cleared

            Biocompare explains CLARITY

            Mouse brain slice cleared

            Accessories
              • X-CLARITY™ Heat Block for 6 x 50 mL tubes

                Catalog #: C20002
                Quantity : 1 unit
                Holds six 50 mL conical tube

              • X-CLARITY™ Heat Block for flat-bottom plates

                Catalog #: C20003
                Quantity : 1 unit
                Holds one flat-bottom plate

              • Tissue Container

                Catalog #: C12001
                Quantity : 20 units
                Holds one adult mouse brain

              • Mouse Brain Slice Holder

                Catalog #: C12004
                Quantity : 1 unit
                Holds up to three mouse brain slices

              • Container Holder for 1 Tissue Container

                Catalog #: C12002
                Quantity : 1 unit
                Holds one tissue container

              • Whole Rat Brain Holder

                Catalog #: C12007
                Quantity : 1 unit
                Holds one adult rat brain or two adult mouse brains

              • Holder for 36 Mouse Brain Slices

                Catalog #: C12010 - 1.5 Φ
                Catalog #: C12020 - 0.6 Φ

                · 7 1.5 Φ or 0.6 Φ Mesh Plates
                · 6 Spacers for 6 Slices
                · 3 silicone rings

                Well size: 16.8 x 16.8 x 2 mm
                Sample: 36 mouse brain slices

              • Holder for 6 Slices

                Catalog #: C12011 - 1.5 Φ
                Catalog #: C12021 - 0.6 Φ

                · 7 1.5 Φ or 0.6 Φ Mesh Plates
                · 6 Spacers for 1 Slice
                · 3 silicone rings

                Well size: 35 x 53 x 2 mm
                Sample: 6 slices

              • Holder for 1 Sample

                Catalog #: C12012 - 1.5 Φ
                Catalog #: C12022 - 0.6 Φ

                · 7 1.5 Φ or 0.6 Φ Mesh Plates
                · 6 Spacers for 6 Slices
                · 3 silicone rings

                Well size: 35 x 53 x 20 mm
                Sample: 1 sample

              • Holder for 6 Mouse Brains

                Catalog #: C12013 - 1.5 Φ
                Catalog #: C12023 - 0.6 Φ

                · 2 1.5 Φ or 0.6 Φ Mesh Plates
                · 1 Spacer for 6 Mouse Brains
                · 3 silicone rings

                Well size: 16.8 x 16.8 x 20 mm
                Sample: 6 adult mouse brains

              • Holder for 48 Samples

                Catalog #: C12014 - 1.5 Φ
                Catalog #: C12024 - 0.6 Φ

                · 3 1.5 Φ or 0.6 Φ Mesh Plates
                · 2 Spacers for 24 Samples
                · 3 silicone rings

                Well size: 6.5 x 6.5 x 10 mm
                Sample: 48 samples

              • Holder for 192 Samples

                Catalog #: C12015 - 1.5 Φ
                Catalog #: C12025 - 0.6 Φ

                · 3 1.5 Φ or 0.6 Φ Mesh Plates
                · 2 Spacers for 96 Samples
                · 3 silicone rings

                Well size: 3 x 3 x 10 mm
                Sample: 192 samples

            show more  +

            ORDERING INFORMATION

            Cat # Product Qty
            C20001 X-CLARITY™ Polymerization System 1 unit
            C20002 X-CLARITY™ Heat Block for 6 x 50 mL tubes 1 unit
            C20003 X-CLARITY™ Heat Block for flat-bottom plates 1 unit
            C1310X X-CLARITY™ Hydrogel Solution Kit 1 kit
            C30001 X-CLARITY™ Tissue Clearing System II 1 unit
            C12010 Holder for 36 Mouse Brain Slices (1.5 Φ) 1 set
            C12020 Holder for 36 Mouse Brain Slices (0.6 Φ) 1 set
            C12011 Holder for 6 Slices (1.5 Φ) 1 set
            C12021 Holder for 6 Slices (0.6 Φ) 1 set
            C12012 Holder for 1 Sample (1.5 Φ) 1 set
            C12022 Holder for 1 Sample (0.6 Φ) 1 set
            C12013 Holder for 6 Mouse Brains (1.5 Φ) 1 set
            C12023 Holder for 6 Mouse Brains (0.6 Φ) 1 set
            C12014 Holder for 48 Samples (1.5 Φ) 1 set
            C12024 Holder for 48 Samples (0.6 Φ) 1 set
            C12015 Holder for 192 Samples (1.5 Φ) 1 set
            C12025 Holder for 192 Samples (0.6 Φ) 1 set
            C12001 Tissue Container (20 units) 1 box
            C12002 Container Holder for 1 Tissue Container 1 unit
            C12004 Mouse Brain Slice Holder 1 unit
            C12007 Whole Rat Brain Holder 1 unit
            C13001 Electrophoretic Tissue Clearing Solution 12 x 1 L
            C13101 X-CLARITY™ Mounting Solution 1 x 25 mL
            C13102 X-CLARITY™ Mounting Solution Value Pack 10 x 25 mL
            C13107 X-CLARITY™ Mounting Solution Bulk Pack 20 x 25 mL