Innovations in ex vivo Light Sheet Fluorescence Microscopy

From whole-organ imaging to in-silico blood flow modeling: A new multi-scale network analysis for revisiting tissue functional anatomy

(2020) Pol Kennel et al.   PLoS Computational Biology

Positive epistasis between viral polymerase and the 3′ untranslated region of its genome reveals the epidemiologic fitness of dengue virus

(2020) Ayesa Syenina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biomedical applications of tissue clearing and three-dimensional imaging in health and disease

(2020) Maria Victoria Gómez-Gaviro et al.   iScience

iDISCO+ for the Study of Neuroimmune Architecture of the Rat Auditory Brainstem

(2019) Paola Perin et al.   Frontiers in Neuroanatomy

Tissue Clearing and Light Sheet Microscopy: Imaging the Unsectioned Adult Zebra Finch Brain at Cellular Resolution

(2019) Mariana Diales Rocha et al.   Frontiers in Neuroanatomy

Applications of Light-Sheet Microscopy in Microdevices

(2019) Ignacio Albert-Smet et al.   Frontiers in Neuroanatomy

High-throughput, high-resolution deep learning microscopy based on registration-free generative adversarial network

(2019) Hao Zhang et al.   Biomedical Optics Express

Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy

(2019) Ye Chen et al.   Biomedical Optics Express

Open-Top Light-Sheet Microscopy Image Atlas of Prostate Core Needle Biopsies

(2019) Nicholas P. Reder et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0

(2019) Venkatakaushik Voleti et al.   NATURE METHODS

Three-dimensional visualization of cleared human pancreas cancer reveals that sustained epithelial-to-mesenchymal transition is not required for venous invasion

(2019) Seung-Mo Hong et al.   MODERN PATHOLOGY

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

Immunolabeling of Cleared Human Pancreata Provides Insights into Three-Dimensional Pancreatic Anatomy and Pathology

(2018) Michaël Noë et al.   AMERICAN JOURNAL OF PATHOLOGY

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples

(2018) Bianca Migliori et al.   BMC BIOLOGY

Mapping of the three-dimensional lymphatic microvasculature in bladder tumours using light-sheet microscopy

(2018) Nobuyuki Tanaka et al.   BRITISH JOURNAL OF CANCER

Lightsheet fluorescence microscopy of branching human fetal kidney

(2018) Dylan Isaacson et al.   KIDNEY INTERNATIONAL

3D imaging of cleared human skin biopsies using light-sheet microscopy: A new way to visualize in-depth skin structure

(2018) S. Abadie et al.   SKIN RESEARCH AND TECHNOLOGY

3D single-molecule super-resolution microscopy with a tilted light sheet

(2018) Anna-Karin Gustavsson et al.   Nature Communications

Whole-body clearing, staining and screening of calcium deposits in the mdx mouse model of Duchenne muscular dystrophy

(2018) Lukasz Bozycki et al.   Skeletal Muscle

Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy

(2018) Pol Kennel et al.   JOURNAL OF BIOMEDICAL OPTICS

Whole-Brain Vasculature Reconstruction at the Single Capillary Level

(2018) Antonino Paolo Di Giovanna et al.   Scientific Reports

Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging

(2018) Adam K. Glaser et al.   Scientific Reports

Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy

(2018) Tomoyuki Mano et al.   JOURNAL OF NEUROSCIENCE

Optical Clearing in the Kidney Reveals Potassium-Mediated Tubule Remodeling

(2018) Turgay Saritas et al.   Cell Reports

Computational fluid dynamics with imaging of cleared tissue and of in vivo perfusion predicts drug uptake and treatment responses in tumours

(2018) Angela d’Esposito et al.   Nature Biomedical Engineering

Three-Dimensional Cross-Sectional Light-Sheet Microscopy Imaging of the Inflamed Mouse Gut

(2017) Sebastian Zundler et al.   GASTROENTEROLOGY

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

Microfabricated devices for single objective single plane illumination microscopy (SoSPIM)

(2017) Elisa Zagato et al.   OPTICS EXPRESS

Looking inside the heart: a see-through view of the vascular tree

(2017) Imke Nehrhoff et al.   Biomedical Optics Express

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

CUBIC pathology: three-dimensional imaging for pathological diagnosis

(2017) Satoshi Nojima et al.   Scientific Reports

Diagonally Scanned Light-Sheet Microscopy for Fast Volumetric Imaging of Adherent Cells

(2016) Kevin M. Dean et al.   BIOPHYSICAL JOURNAL

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

(2016) Nicolas Renier et al.   CELL

Virtual unfolding of light sheet fluorescence microscopy dataset for quantitative analysis of the mouse intestine

(2016) Alessia Candeo 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

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

(2016) Chenchen Pan et al.   NATURE METHODS

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

SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function

(2015) Raju Tomer et al.   CELL

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

Inverted light-sheet microscope for imaging mouse pre-implantation development

(2015) Petr Strnad et al.   NATURE METHODS

Swept confocally-aligned planar excitation (SCAPE) microscopy for high-speed volumetric imaging of behaving organisms

(2015) Matthew B. Bouchard et al.   Nature Photonics

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

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

(2015) Liang Gao   OPTICS EXPRESS

Confocal multiview light-sheet microscopy

(2015) Gustavo de Medeiros et al.   Nature Communications

Hyperspectral light sheet microscopy

(2015) Wiebke Jahr et al.   Nature Communications

Dual-slit confocal light sheet microscopy for in vivo whole-brain imaging of zebrafish

(2015) Zhe Yang et al.   Biomedical Optics Express

Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis

(2015) Ludovico Silvestri et al.   Frontiers in Neuroanatomy

Light sheet fluorescence microscopy (LSFM): past, present and future

(2014) John Lim et al.   ANALYST

Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images

(2014) Paolo Frasconi et al.   BIOINFORMATICS

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

OPTiSPIM: integrating optical projection tomography in light sheet microscopy extends specimen characterization to nonfluorescent contrasts

(2014) Jürgen Mayer et al.   OPTICS LETTERS

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

Single-molecule imaging of transcription factor binding to DNA in live mammalian cells

(2013) J Christof M Gebhardt et al.   NATURE METHODS

Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain

(2012) L. Silvestri et al.   OPTICS EXPRESS

Light sheet microscopy of living or cleared specimens

(2011) Philipp J Keller et al.   CURRENT OPINION IN NEUROBIOLOGY

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

Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples

(2010) Ulrich Leischner et al.   PLoS One

3D-reconstruction of blood vessels by ultramicroscopy

(2010) Nina Jährling et al.   Organogenesis

Ultramicroscopy: 3D reconstruction of large microscopical specimens

(2008) K. Becker et al.   Journal of Biophotonics

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE