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.

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The X-CLARITY™ systems and reagents standardize, simplify, and accelerate each step of the tissue clearing process. With the CLARITY method, 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. Native cytoarchitecture remains intact and even endogenous fluorescence proteins are preserved for robust fluorescence imaging downstream.

Hydrogel Solution Kit
Polymerization System
Tissue Clearing System II
Tissue Clearing Solution
01. Hydrogel infusion
X-CLARITY™ Hydrogel Solution Kit  C1310X

The X-CLARITY™ Hydrogel Solution Kit is a pre-tested hydrogel solution for uniform and consistent tissue-hydrogel hybridization. The kit is made up of X-CLARITY™ Hydrogel Solution, an acrylamide-based solution used to create polyacrylamide, and X-CLARITY™ Polymerization Initiator, a thermal free radical initiator also known as VA-044.

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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.

Application Note
High throughput
(up to 768 samples/run)
Compatible with various
Steady vacuum &
temperature control
Rapid and consistent
X-CLARITY™ Heat Block for 6 x 50 mL tubes
Catalog #: C20002
Quantity : 1 unit
Holds six 50 mL conical tubes
X-CLARITY™ Heat Block for flat-bottom plates
Catalog #: C20003
Quantity : 1 unit
Holds one flat-bottom plate
03. Lipid removal
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. Users can set tissue clearing conditions through a simple and intuitive touchscreen interface. In ETC (electrophoretic tissue clearing) mode, platinum-plated electrodes generate an electric field to accelerate the removal of lipids from tissues in a highly efficient manner. A built-in temperature control system actively cools and heats buffer to maintain consistent buffer temperatures during clearing. Buffer is constantly circulated to ensure consistent buffering capacity, temperature control, and elimination of tissue clearing byproducts. This advanced system ensures efficient, rapid, and consistent tissue clearing.

Application Note
Sample Holders
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
Holders of various sizes
User-friendly setup
Simple touchscreen
Ready-to-use clearing
Electrophoretic Tissue Clearing Solution  C13001

Electrophoretic Tissue Clearing Solution is a premixed SDS-based buffer optimized for use with the X-CLARITY™ Tissue Clearing System II.

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Whole Thy1-YFP mouse brain
The Thy1-YFP signal is preserved and vibrant after tissue clearing with the X-CLARITY™ systems and reagents.
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
Labeling and imaging
Accelerate antibody labeling with the ALL-NEW DeepLabel™ Antibody Labeling Kit.
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What Do Our Customers Have To Say?
Gabriel Bidaux

For you if you want to accelerate your research!
Positive facts: X-CLARITY system is easy to use, devoted to aqueous-based method for organ clearing. It helps clearing several organs at once and in a short period of time. Works well on a lot of different mouse organs or even pieces of primates and humans organs. Logos Biosystems after Sales are fast and always find a compromise as a solution to our rare issues. Minus: expensive systems in comparison to passive clearing methods. For you if you want to accelerate your research!


Tori N

Great results, easy to use!
This product was effective at clearing my tissue samples. It cleared whole brains, hearts, stomach, kidneys, livers, etc. The user manual was easy to read and easy to follow. There is little attention and maintenance required while the system in running.

Clemson University

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Where The X-CLARITY™ Has Been Cited

Influenza causes alterations to oligodendrocyte-specific transcripts and the myelin lipidome in the adult mouse central nervous system.

2021. Louie A, Kim J, Soto-Diaz K, Dibaeinia P, Koito H, Sinha S, Nowak R, Das A, Steelman A. Research Squre https://doi.org/10.21203/rs.3.rs-310861/v1.

Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models.

2021. Chourrout M, Rositi H, Ong E, Hubert V, Paccalet A, Foucault L, Autret A, Fayard B, Olivier C, Bolbos R, Peyrin F, Crola-da-Silva C, Meyronet D, Raineteau O, Elleaume H, Brun E, Chauveau F, Wiart M. bioRxiv 2021.03.24.436852.

Novel insights into the electrophysiology of murine cardiac macrophages: relevance of voltage-gated potassium channels.

2021. Simon-Chica A, Fernández MC, Wülfers EM, Lother A, Hilgendorf I, Seemann G, Ravens U, Kohl P, Schneider-Warme F. Cardiovascular Research cvab126.

3D in situ imaging of the female reproductive tract reveals molecular signatures of fertilizing spermatozoa in mice.

2020. Ded L, Hwang JY, Miki K, Shi HF, Chung JJ. Elife 9:e62043.

Maximizing lentiviral vector gene transfer in the CNS.

2020. Humbel M, Ramosaj M, Zimmer V, Regio S, Aeby L, Moser S, Boizot A, Sipion M, Rey M, Déglon N. Gene Therapy 10.1038/s41434-020-0172-6.

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DeepLabel™ Antibody Staining Kit

2022-04-07 | 458.10 KB

X-CLARITY™ Systems and Reagents for Tissue Clearing

2022-04-07 | 962KB

Logos Biosystems Products

2022-04-07 | 2.14 MB

The effects of DeepLabel Antibody Staining Kit on antibody penetration in diverse organs after tissue clearing with the X-CLARITY

2018-11-26 | 1.25 MB

X-CLARITY™ Systems and Reagents for Tissue Clearing

2018-05-08 | 553 KB

X-CLARITY™ Tissue Clearing System
Quick Start Guide

2018-05-08 | 668.54 KB

X-CLARITY™ Tissue Clearing System II
Installation Guide

2018-05-08 | 841.04 KB

ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging
Product literature

2018-04-17 | 2.6 MB

An automated and high-throughput polymerization solution for downstream tissue clearing: the X-CLARITY™ Polymerization System
Product literature

2018-04-17 | 1.4 MB


2022-04-21 | 548.40 KB

Image gallery
Mouse brain | X-CLARITY™
Mouse brain | X-CLARITY™
Mouse brain hemisphere | X-CLARITY™
Mouse brain - 2 mm slices | X-CLARITY™
Mouse brain - 1,2,3 mm slices | X-CLARITY™
Mouse brain slice | X-CLARITY™
Courtesy of Youngshik Choe, PhD | Korea Brain Research Institute
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Ordering Information
Cat #ProductQty
C20001X-CLARITY™ Polymerization System1 unit
C20002X-CLARITY™ Heat Block for 6 x 50 mL tubes1 unit
C20003X-CLARITY™ Heat Block for flat-bottom plates1 unit
C1310XX-CLARITY™ Hydrogel Solution Kit
– X-CLARITY™ Hydrogel Solution (1 x 1 L)
– X-CLARITY™ Polymerization Initiator (1 x 2.5 g)
1 kit
C30001X-CLARITY™ Tissue Clearing System II1 unit
C12010Holder for 36 Mouse Brain Slices, 1.5 Φ1 set
C12020Holder for 36 Mouse Brain Slices, 0.6 Φ1 set
C12011Holder for 6 Slices, 1.5 Φ1 set
C12021Holder for 6 Slices, 0.6 Φ1 set
C12012Holder for 1 Sample, 1.5 Φ1 set
C12022Holder for 1 Sample, 0.6 Φ1 set
C12013Holder for 6 Mouse Brains, 1.5 Φ1 set
C12023Holder for 6 Mouse Brains, 0.6 Φ1 set
C12014Holder for 48 Samples, 1.5 Φ1 set
C12024Holder for 48 Samples, 0.6 Φ1 set
C12015Holder for 192 Samples, 1.5 Φ1 set
C12025Holder for 192 Samples, 0.6 Φ1 set
C12001Tissue Container (Whole Mouse Brain), 20 units1 box
C12002Container Holder for 1 Tissue Container1 unit
C12004Mouse Brain Slice Holder (Chamber Height: 4 mm)1 unit
C12007Whole Rat Brain Holder1 unit
C13001Electrophoretic Tissue Clearing Solution12 x 1 L
C13101X-CLARITY™ Mounting Solution1 x 25 mL
C13102X-CLARITY™ Mounting Solution Value Pack10 x 25 mL
C13107X-CLARITY™ Mounting Solution Bulk Pack20 x 25 mL
C33001DeepLabel™ Antibody Staining Kit
– DeepLabel™ Solution A (1 x 25 mL)
– DeepLabel™ Solution B (2 x 25 mL)
– DeepLabel™ Washing Buffer (1 x 250 mL)
1 kit


X-CLARITY™ Polymerization System
Display5”  TFT LCD
Temperature RangeRT – 60 °C
Temperature Accuracy±0.3 °C
Vacuum Range-90 – 0 kPa
Power Consumption312 W
Applicable PowerAC 100-240 V, 50/60 Hz
Dimensions (W x D x H)Exterior: 332 x 430 x 222 mm
Interior: 307 x 137 x 140 mm
Weight28 kg



Instrument typeElectrophoretic chamber
External dimensions (W x D x H)176 mm x 128 mm x 154 mm
Internal dimensions (W x D x H)57 mm x 30 mm x 93 mm
Weight2.8 kg


X-CLARITY™ ETC Control Tower

Instrument typePower supply, temperature control,
and buffer circulation device
User interface5 “ TFT LCD touchscreen
Power supply modesConstant current or constant voltage
Current & voltage range0.2-1.5 A, 5-70 V
Temperature range30-60 ° C
Pump speed range50-200 rpm
Electrical requirementsAC 100-240 V, 50/60 Hz
Power consumption500 W (including the X-CLARITY™ ETC Chamber)
Dimensions (W x D x H)205 mm x 430 mm x 370 mm
Weight20 kg