A guidebook for DISCO tissue clearing

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature

(2020) Christoph Kirst et al.   CELL

Cellular and Molecular Probing of Intact Human Organs

(2020) Shan Zhao et al.   CELL

Tissue clearing and its applications in neuroscience

(2020) Hiroki R. Ueda et al.   NATURE REVIEWS NEUROSCIENCE

Machine learning analysis of whole mouse brain vasculature

(2020) Mihail Ivilinov Todorov et al.   NATURE METHODS

Tissue clearing technique: Recent progress and biomedical applications

(2020) Ting Tian et al.   JOURNAL OF ANATOMY

FDISCO: Advanced solvent-based clearing method for imaging whole organs

(2019) Yisong Qi et al.   Science Advances

Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging

(2019) Anne C. Rios et al.   CANCER CELL

High‐resolution imaging of fluorescent whole mouse brains using stabilised organic media (sDISCO)

(2019) Christian Hahn et al.   Journal of Biophotonics

Contemporaneous 3D characterization of acute and chronic myocardial I/R injury and response

(2019) Simon F. Merz et al.   Nature Communications

Exploiting Multi-Level Parallelism for Stitching Very Large Microscopy Images

(2019) Alessandro Bria et al.   Frontiers in Neuroinformatics

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

(2019) David Hörl et al.   NATURE METHODS

The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue

(2019) Fabian F. Voigt et al.   NATURE METHODS

Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution

(2019) Tonmoy Chakraborty et al.   NATURE METHODS

Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body

(2019) Chenchen Pan et al.   CELL

Hydrogel-Tissue Chemistry: Principles and Applications

(2018) Viviana Gradinaru et al.   Annual Review of Biophysics

Viral Strategies for Targeting the Central and Peripheral Nervous Systems

(2018) Claire N. Bedbrook et al.   Annual Review of Neuroscience

Tissue clearing of both hard and soft tissue organs with the PEGASOS method

(2018) Dian Jing et al.   CELL RESEARCH

Application of light sheet microscopy for qualitative and quantitative analysis of bronchus-associated lymphoid tissue in mice

(2018) David Twapokera Mzinza et al.   Cellular & Molecular Immunology

An inhibitory antibody targeting Carbonic Anhydrase XII abrogates chemoresistance and significantly reduces lung metastases in an orthotopic breast cancer model in vivo

(2018) Bettina von Neubeck et al.   INTERNATIONAL JOURNAL OF CANCER

A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing

(2018) Tatsuya C. Murakami et al.   NATURE NEUROSCIENCE

Tridimensional visualization reveals direct communication between the embryo and glands critical for implantation

(2018) Jia Yuan et al.   Nature Communications

Light-sheet microscopy: a tutorial

(2018) Omar E. Olarte et al.   Advances in Optics and Photonics

An Overview of the Role of Lipofuscin in Age-Related Neurodegeneration

(2018) Alexandra Moreno-García et al.   Frontiers in Neuroscience

Optimization of GFP Fluorescence Preservation by a Modified uDISCO Clearing Protocol

(2018) Yusha Li et al.   Frontiers in Neuroanatomy

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents

(2018) Kazuki Tainaka et al.   Cell Reports

Protection of tissue physicochemical properties using polyfunctional crosslinkers

(2018) Young-Gyun Park et al.   NATURE BIOTECHNOLOGY

Cell-type-specific and projection-specific brain-wide reconstruction of single neurons

(2018) Rui Lin et al.   NATURE METHODS

Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull–meninges connections

(2018) Ruiyao Cai et al.   NATURE NEUROSCIENCE

EyeCi: Optical clearing and imaging of immunolabeled mouse eyes using light-sheet fluorescence microscopy

(2018) Yoshiyuki Henning et al.   EXPERIMENTAL EYE RESEARCH

3D visualization and quantification of microvessels in the whole ischemic mouse brain using solvent-based clearing and light sheet microscopy

(2017) Erlen Lugo-Hernandez et al.   JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM

Assembly of functionally integrated human forebrain spheroids

(2017) Fikri Birey et al.   NATURE

Developing 3D microscopy with CLARITY on human brain tissue: Towards a tool for informing and validating MRI-based histology

(2017) Markus Morawski et al.   NEUROIMAGE

Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow

(2017) Alon Greenbaum et al.   Science Translational Medicine

Heterogeneity of macrophage infiltration and therapeutic response in lung carcinoma revealed by 3D organ imaging

(2017) Michael F. Cuccarese et al.   Nature Communications

Whole-Body Profiling of Cancer Metastasis with Single-Cell Resolution

(2017) Shimpei I. Kubota et al.   Cell Reports

Light-sheet microscopy for slide-free non-destructive pathology of large clinical specimens

(2017) Adam K. Glaser et al.   Nature Biomedical Engineering

Whole-tissue biopsy phenotyping of three-dimensional tumours reveals patterns of cancer heterogeneity

(2017) Nobuyuki Tanaka et al.   Nature Biomedical Engineering

Pathways to clinical CLARITY: volumetric analysis of irregular, soft, and heterogeneous tissues in development and disease

(2017) Brian Hsueh et al.   Scientific Reports

CUBIC pathology: three-dimensional imaging for pathological diagnosis

(2017) Satoshi Nojima et al.   Scientific Reports

Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes

(2016) Nicolas Renier et al.   CELL

Neuro-immune Interactions Drive Tissue Programming in Intestinal Macrophages

(2016) Ilana Gabanyi et al.   CELL

Three-dimensional microscopic analysis of clinical prostate specimens

(2016) Martin E van Royen et al.   HISTOPATHOLOGY

Clearing of fixed tissue: a review from a microscopist’s perspective

(2016) Ludovico Silvestri et al.   JOURNAL OF BIOMEDICAL OPTICS

Fully Automated Evaluation of Total Glomerular Number and Capillary Tuft Size in Nephritic Kidneys Using Lightsheet Microscopy

(2016) Anika Klingberg et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Clearing and Labeling Techniques for Large-Scale Biological Tissues

(2016) Jinyoung Seo et al.   MOLECULES AND CELLS

Hoxb5 marks long-term haematopoietic stem cells and reveals a homogenous perivascular niche

(2016) James Y. Chen et al.   NATURE

Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain

(2016) Benjamin E Deverman et al.   NATURE BIOTECHNOLOGY

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

(2016) Chenchen Pan et al.   NATURE METHODS

Involvement of Ca 2+ -Dependent Hyperpolarization in Sleep Duration in Mammals

(2016) Fumiya Tatsuki et al.   NEURON

Single-cell lineage tracing in the mammary gland reveals stochastic clonal dispersion of stem/progenitor cell progeny

(2016) Felicity M. Davis et al.   Nature Communications

Development of passive CLARITY and immunofluorescent labelling of multiple proteins in human cerebellum: understanding mechanisms of neurodegeneration in mitochondrial disease

(2016) Jonathan Phillips et al.   Scientific Reports

Three-Dimensional Study of Alzheimer’s Disease Hallmarks Using the iDISCO Clearing Method

(2016) Thomas Liebmann et al.   Cell Reports

Super-Resolution Mapping of Neuronal Circuitry With an Index-Optimized Clearing Agent

(2016) Meng-Tsen Ke et al.   Cell Reports

Single-Cell Lineage Tracing Reveals that Oriented Cell Division Contributes to Trabecular Morphogenesis and Regional Specification

(2016) Jingjing Li et al.   Cell Reports

Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene

(2016) Marzena Stefaniuk et al.   Scientific Reports

Deconvolution-free Subcellular Imaging with Axially Swept Light Sheet Microscopy

(2015) Kevin M. Dean et al.   BIOPHYSICAL JOURNAL

Tissue clearing for confocal imaging of native and bio-artificial skeletal muscle

(2015) L Decroix et al.   BIOTECHNIC & HISTOCHEMISTRY

Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems

(2015) Evan Murray et al.   CELL

Clarifying Tissue Clearing

(2015) Douglas S. Richardson et al.   CELL

The ImageJ ecosystem: An open platform for biomedical image analysis

(2015) Johannes Schindelin et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Deep imaging of bone marrow shows non-dividing stem cells are mainly perisinusoidal

(2015) Melih Acar et al.   NATURE

NeuroGPS-Tree: automatic reconstruction of large-scale neuronal populations with dense neurites

(2015) Tingwei Quan et al.   NATURE METHODS

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

ScaleS: an optical clearing palette for biological imaging

(2015) Hiroshi Hama et al.   NATURE NEUROSCIENCE

Efficient processing and analysis of large-scale light-sheet microscopy data

(2015) Fernando Amat et al.   Nature Protocols

Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging

(2015) Etsuo A Susaki et al.   Nature Protocols

Hematogenous macrophage depletion reduces the fibrotic scar and increases axonal growth after spinal cord injury

(2015) Y. Zhu et al.   NEUROBIOLOGY OF DISEASE

Bringing CLARITY to the human brain: visualization of Lewy pathology in three dimensions

(2015) A. K. L. Liu et al.   NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY

Stochastic electrotransport selectively enhances the transport of highly electromobile molecules

(2015) Sung-Yon Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enriched environment reduces glioma growth through immune and non-immune mechanisms in mice

(2015) Stefano Garofalo et al.   Nature Communications

Fluorescent-Protein Stabilization and High-Resolution Imaging of Cleared, Intact Mouse Brains

(2015) Martin K. Schwarz et al.   PLoS One

Inside Alzheimer brain with CLARITY: senile plaques, neurofibrillary tangles and axons in 3-D

(2014) Kunie Ando et al.   ACTA NEUROPATHOLOGICA

Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis

(2014) Etsuo A. Susaki et al.   CELL

Single-Cell Phenotyping within Transparent Intact Tissue through Whole-Body Clearing

(2014) Bin Yang et al.   CELL

iDISCO: A Simple, Rapid Method to Immunolabel Large Tissue Samples for Volume Imaging

(2014) Nicolas Renier et al.   CELL

Whole-Body Imaging with Single-Cell Resolution by Tissue Decolorization

(2014) Kazuki Tainaka et al.   CELL

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

(2013) Alessandro Bria et al.   BMC BIOINFORMATICS

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction

(2013) Meng-Tsen Ke et al.   NATURE NEUROSCIENCE

Three-dimensional imaging of solvent-cleared organs using 3DISCO

(2012) Ali Ertürk et al.   Nature Protocols

Chemical Clearing and Dehydration of GFP Expressing Mouse Brains

(2012) Klaus Becker et al.   PLoS One

New developments in fluorescence diagnostics

(2011) Juraj Hegyi et al.   JOURNAL DER DEUTSCHEN DERMATOLOGISCHEN GESELLSCHAFT

Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury

(2011) Ali Ertürk et al.   NATURE MEDICINE

Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain

(2011) Hiroshi Hama et al.   NATURE NEUROSCIENCE

V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY