X-CLARITY tissue clearing system with electrophoretic chamber and cooling unit on lab bench for 3D imaging sample preparation | Logos Biosystems

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.

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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.

01. HYDROGEL INFUSION

X-CLARITY Hydrogel Solution Kit bottle and reagent tube for tissue clearing experiments
X-CLARITY™
Hydrogel Solution Kit
C1310X

02. TISSUE-HYDROGEL HYBRIDIZATION

Diagram showing stabilized hydrogel matrix structure formed inside liver tissue during polymerization
X-CLARITY Polymerization System device with red cover for tissue clearing workflow
X-CLARITY™
Polymerization System
C20001

03. LIPID REMOVAL

Diagram showing electrophoretic tissue clearing process with electric field applied to liver tissue sample
Automated X-CLARITY Tissue Clearing System II for efficient and reproducible tissue clearing experiments
X-CLARITY™
Tissue Clearing System II
C30001
Electrophoretic Tissue Clearing Solution reagent bottle for X-CLARITY tissue clearing system
Electrophoretic
Tissue Clearing Solution
C13001
           

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.

View Hydrogel Solution Kit

02. Tissue-Hydrogel Hybridization

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.

Download Software Update Manual
X-CLARITY Tissue Clearing System device with red lid and front control panel for electrophoretic clearing
Fast tissue clearing icon for accelerated turnaround
High throughput
(up to 768 samples/run)
Reproducibility icon indicating standardized results
Compatible with various
vessels
Easy-to-use icon for simplified operation
Steady vacuum &
temperature control
Safety/quality icon for reliable tissue processing
Rapid and consistent
polymerization
Accessories
X-CLARITY Heat Block accessory designed to hold six 50 mL conical tubes for tissue clearing
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 accessory for flat-bottom plates used in tissue clearing workflows
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.

Read X-CLARITY™ Application Note
Sample Holder Guide
X-CLARITY Tissue Clearing System II electrophoretic device with cooling unit and controller for high-resolution tissue clearing
Precise temperature control
           
X-CLARITY system icon showing active buffer cooling and heating capacity for precise tissue clearing temperature control
Active buffer cooling and
heating capacity
X-CLARITY tissue clearing icon with sensitive accurate temperature sensor for stable clearing process
Sensitive and accurate
temperature sensor
Uniform electric field
X-CLARITY electrophoretic tissue clearing platinum plated electrodes icon ensuring uniform electric field
Platinum plated electrodes
Constant current constant voltage CV CC icon for X-CLARITY tissue clearing stable clearing performance
Constant current and
constant voltage modes
Compatible with multiple tissue types and sizes
X-CLARITY icon for active and passive tissue clearing modes compatible with multiple tissue types
Active and passive clearing
modes
Sample holder icon showing various sizes available for X-CLARITY tissue clearing applications
Holders of various sizes
available
User-friendly setup
Touchscreen interface icon for X-CLARITY tissue clearing system easy operation
Simple touchscreen
interface
Ready-to-use clearing solution reagent bottle icon for X-CLARITY tissue clearing workflow
Ready-to-use clearing
solution
           

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.

View Electrophoretic Clearing Solution
Electrophoretic Tissue Clearing Solution bottles for X-CLARITY tissue clearing system optimized SDS buffer
Whole Thy1-YFP mouse brain
Whole Thy1-YFP mouse brain before and after tissue clearing with X-CLARITY system showing preserved fluorescent signal
The Thy1-YFP signal is preserved and vibrant after tissue clearing with the X-CLARITY™ systems and reagents.
Human cerebral cortex (1 mm)
Human cerebral cortex slice before ETC PFA fixation for tissue clearing
Before ETC PFA-fixed
(1 week)
Human cerebral cortex slice after electrophoretic tissue clearing with X-CLARITY system
After ETC
Human cerebral cortex slice after refractive index RI matching for transparency improvement
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.
Discover DeepLabel™
DeepLabel antibody labeling kit for tissue clearing and imaging, Logos Biosystems solution for fast and efficient immunostaining

Why Scientists Love X-CLARITY™ System

Testimonials

(5.0)
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!

INSERM UMR 1060

(5.0)
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

Citations

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.

View Cited Works

Resources

Downloads

DeepLabel™ Antibody Staining Kit
Flyer

2022-04-07 | 458.10 KB

Download
X-CLARITY™ Systems and Reagents for Tissue Clearing
Brochure

2022-04-07 | 962KB

Download
Logos Biosystems Products
Brochure

2022-04-07 | 2.14 MB

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

2018-11-26 | 1.25 MB

Download
X-CLARITY™ Systems and Reagents for Tissue Clearing
Flyer

2018-05-08 | 553 KB

Download
X-CLARITY™ Tissue Clearing System
Quick Start Guide

2018-05-08 | 668.54 KB

Download
X-CLARITY™ Tissue Clearing System II
Installation Guide

2018-05-08 | 841.04 KB

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

2018-04-17 | 2.6 MB

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

2018-04-17 | 1.4 MB

Download

2022-04-21 | 548.40 KB

Download
Image gallery
X-CLARITY™ cleared whole mouse brain sample on grid background for high-resolution 3D tissue imaging
Mouse brain | X-CLARITY™
X-CLARITY™ tissue clearing of mouse brain showing optical transparency and structural preservation
Mouse brain | X-CLARITY™
X-CLARITY™ cleared mouse brain hemisphere prepared for detailed microscopy and analysis
Mouse brain hemisphere | X-CLARITY™
X-CLARITY™ tissue cleared 2 mm mouse brain slices demonstrating uniform transparency
Mouse brain - 2 mm slices | X-CLARITY™
X-CLARITY™ cleared mouse brain slices (1, 2, 3 mm) comparison before and after tissue clearing
Mouse brain - 1,2,3 mm slices | X-CLARITY™
X-CLARITY™ cleared mouse brain slice with fluorescent labeling from Korea Brain Research Institute
Mouse brain slice | X-CLARITY™
Courtesy of Youngshik Choe, PhD | Korea Brain Research Institute
Explore Entire Cell Image
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
– X-CLARITY™ Hydrogel Solution (1 x 1 L)
– X-CLARITY™ Polymerization Initiator (1 x 2.5 g)
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 (Whole Mouse Brain), 20 units 1 box
C12002 Container Holder for 1 Tissue Container 1 unit
C12004 Mouse Brain Slice Holder (Chamber Height: 4 mm) 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
C33001 DeepLabel™ 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
Specifications

 

X-CLARITY™ Polymerization System

 

Display 5”  TFT LCD
Temperature Range RT – 60 °C
Temperature Accuracy ±0.3 °C
Vacuum Range -90 – 0 kPa
Power Consumption 312 W
Applicable Power AC 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
Weight 28 kg

 

X-CLARITY™ ETC Chamber

 

Instrument type Electrophoretic 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
Weight 2.8 kg

 

X-CLARITY™ ETC Control Tower

 

Instrument type Power supply, temperature control,
and buffer circulation device
User interface 5 “ TFT LCD touchscreen
Power supply modes Constant current or constant voltage
Current & voltage range 0.2-1.5 A, 5-70 V
Temperature range 30-60 ° C
Pump speed range 50-200 rpm
Electrical requirements AC 100-240 V, 50/60 Hz
Power consumption 500 W (including the X-CLARITY™ ETC Chamber)
Dimensions (W x D x H) 205 mm x 430 mm x 370 mm
Weight 20 kg