Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy

Tissue libraries enable rapid determination of conditions that preserve antibody labeling in cleared mouse and human tissue

(2023) Theodore J Zwang et al.   eLife

Deep learning-based adaptive optics for light sheet fluorescence microscopy

(2023) Mani Ratnam Rai et al.   Biomedical Optics Express

Volumetric light sheet imaging with adaptive optics correction

(2023) Yang Liu et al.   Biomedical Optics Express

Tissue clearing and immunostaining to visualize the spatial organization of vasculature and tumor cells in mouse liver

(2023) Nicola Frenkel et al.   Frontiers in Oncology

Light-sheets and smart microscopy, an exciting future is dawning

(2023) Stephan Daetwyler et al.   Communications Biology

Whole-body cellular mapping in mouse using standard IgG antibodies

(2023) Hongcheng Mai et al.   NATURE BIOTECHNOLOGY

Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

(2022) Kyra T. Newmaster et al.   Frontiers in Neuroanatomy

Comparative Analyses of Clearing Efficacies of Tissue Clearing Protocols by Using a Punching Assisted Clarity Analysis

(2022) Jiwon Woo et al.   Frontiers in Bioengineering and Biotechnology

Scalable tissue labeling and clearing of intact human organs

(2022) Hongcheng Mai et al.   Nature Protocols

Quality assessment in light microscopy for routine use through simple tools and robust metrics

(2022) Orestis Faklaris et al.   JOURNAL OF CELL BIOLOGY

Practical considerations for quantitative light sheet fluorescence microscopy

(2022) Chad M. Hobson et al.   NATURE METHODS

An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis

(2022) Kei Takahashi et al.   Nature Communications

Immunostaining of Whole-Mount Retinas with the CLARITY Tissue Clearing Method

(2021) Elizabeth J. Alessio et al.   Jove-Journal of Visualized Experiments

Navigating across multi-dimensional space of tissue clearing parameters

(2021) Sergiy V Avilov   Methods and Applications in Fluorescence

A guidebook for DISCO tissue clearing

(2021) Muge Molbay et al.   Molecular Systems Biology

Tissue clearing and imaging methods for cardiovascular development

(2021) Hana Kolesová et al.   iScience

QUAREP‐LiMi: A community‐driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy

(2021) Glyn Nelson et al.   JOURNAL OF MICROSCOPY

QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy

(2021) Ulrike Boehm et al.   NATURE METHODS

Tutorial: practical considerations for tissue clearing and imaging

(2021) Kurt R. Weiss et al.   Nature Protocols

Innovations in ex vivo Light Sheet Fluorescence Microscopy

(2021) Pablo Delgado-Rodriguez et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Whole-Mount Kidney Clearing and Visualization Reveal Renal Sympathetic Hyperinnervation in Heart Failure Mice

(2021) Chao Wu et al.   Frontiers in Physiology

Tissue clearing and 3D imaging in developmental biology

(2021) Alba Vieites-Prado et al.   DEVELOPMENT

Light-sheet microscopy at high resolution

(2021) Reto Fiolka   NATURE BIOTECHNOLOGY

Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis

(2021) Holly C. Gibbs et al.   Frontiers in Cell and Developmental Biology

Tissue clearing and its applications in neuroscience

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

Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy

(2020) Hiroki R. Ueda et al.   NEURON

Live-cell imaging in the era of too many microscopes

(2020) William C. Lemon et al.   CURRENT OPINION IN CELL BIOLOGY

Tissue Clearing and Expansion Methods for Imaging Brain Pathology in Neurodegeneration: From Circuits to Synapses and Beyond

(2020) Arnaldo Parra-Damas et al.   Frontiers in Neuroscience

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

(2019) Yisong Qi et al.   Science Advances

Designing a rigorous microscopy experiment: Validating methods and avoiding bias

(2019) Anna Payne-Tobin Jost et al.   JOURNAL OF CELL BIOLOGY

Light-Sheet Microscopy and Its Potential for Understanding Developmental Processes

(2019) Yinan Wan et al.   Annual Review of Cell and Developmental Biology

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

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

Monitoring microbial communities using light sheet fluorescence microscopy

(2018) Raghuveer Parthasarathy   CURRENT OPINION IN MICROBIOLOGY

Light sheet imaging comes of age

(2018) Simon C. Watkins et al.   JOURNAL OF CELL BIOLOGY

Light-sheet microscopy: a tutorial

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

Optimizing tissue-clearing conditions based on analysis of the critical factors affecting tissue-clearing procedures

(2018) June Hoan Kim et al.   Scientific Reports

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents

(2018) Kazuki Tainaka et al.   Cell Reports

Evaluation of seven optical clearing methods in mouse brain

(2018) Peng Wan et al.   Neurophotonics

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

(2018) Ruiyao Cai et al.   NATURE NEUROSCIENCE

A practical guide to adaptive light-sheet microscopy

(2018) Loïc A. Royer et al.   Nature Protocols

A beginner’s guide to tissue clearing

(2017) Pablo Ariel   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

A guide to light-sheet fluorescence microscopy for multiscale imaging

(2017) Rory M Power et al.   NATURE METHODS

Adaptive optical fluorescence microscopy

(2017) Na Ji   NATURE METHODS

Imaging tissue-mimic with light sheet microscopy: A comparative guideline

(2017) Jordi Andilla et al.   Scientific Reports

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

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

Fast Inertia-Free Volumetric Light-Sheet Microscope

(2017) Martí Duocastella et al.   ACS Photonics

Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development

(2016) Johannes Girstmair et al.   BMC DEVELOPMENTAL BIOLOGY

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

(2016) Nicolas Renier et al.   CELL

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

Selective plane illumination microscopy with a light sheet of uniform thickness formed by an electrically tunable lens

(2016) Per Niklas Hedde et al.   MICROSCOPY RESEARCH AND TECHNIQUE

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

(2016) Chenchen Pan et al.   NATURE METHODS

eduSPIM: Light Sheet Microscopy in the Museum

(2016) Wiebke Jahr et al.   PLoS One

3D imaging in CUBIC-cleared mouse heart tissue: going deeper

(2016) Imke Nehrhoff et al.   Biomedical Optics Express

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

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

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

(2016) Jaroslav Icha et al.   Jove-Journal of Visualized Experiments

Three Dimensional Human Neuro-Spheroid Model of Alzheimer’s Disease Based on Differentiated Induced Pluripotent Stem Cells

(2016) Han-Kyu Lee et al.   PLoS One

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

Guide to light-sheet microscopy for adventurous biologists

(2015) Emmanuel G Reynaud et al.   NATURE METHODS

Extend the field of view of selective plan illumination microscopy by tiling the excitation light sheet

(2015) Liang Gao   OPTICS EXPRESS

Optimization of the excitation light sheet in selective plane illumination microscopy

(2015) Liang Gao   Biomedical Optics Express

Scalable and DiI-compatible optical clearance of the mammalian brain

(2015) Bing Hou et al.   Frontiers in Neuroanatomy

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

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

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

(2014) Etsuo A. Susaki 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

A Simple Method for 3D Analysis of Immunolabeled Axonal Tracts in a Transparent Nervous System

(2014) Morgane Belle et al.   Cell Reports

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

OpenSPIM: an open-access light-sheet microscopy platform

(2013) Peter G Pitrone et al.   NATURE METHODS

Quality Assurance Testing for Modern Optical Imaging Systems

(2011) Robert F. Stack et al.   MICROSCOPY AND MICROANALYSIS

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

(2011) Hiroshi Hama et al.   NATURE NEUROSCIENCE

Software for bead-based registration of selective plane illumination microscopy data

(2010) Stephan Preibisch et al.   NATURE METHODS

Light sheet‐based fluorescence microscopy: More dimensions, more photons, and less photodamage

(2008) Emmanuel G. Reynaud et al.   HFSP Journal