Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping

Clarifying Tissue Clearing

(2015) Douglas S. Richardson et al.   CELL

Saturated Reconstruction of a Volume of Neocortex

(2015) Narayanan Kasthuri et al.   CELL

Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo

(2015) Claire N. Bedbrook et al.   CHEMISTRY & BIOLOGY

Camelid nanobodies: killing two birds with one stone

(2015) Aline Desmyter et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Bacterial induction of Snail1 contributes to blood-brain barrier disruption

(2015) Brandon J. Kim et al.   JOURNAL OF CLINICAL INVESTIGATION

Investigating Influenza A Virus Infection: Tools To Track Infection and Limit Tropism: TABLE 1

(2015) Jessica K. Fiege et al.   JOURNAL OF VIROLOGY

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

(2015) Leonard Kuan et al.   METHODS

Structural and functional features of central nervous system lymphatic vessels

(2015) Antoine Louveau et al.   NATURE

Multispectral labeling technique to map many neighboring axonal projections in the same tissue

(2015) Shlomo Tsuriel et al.   NATURE METHODS

Light-sheet fluorescence microscopy for quantitative biology

(2015) Ernst H K Stelzer   NATURE METHODS

CIDRE: an illumination-correction method for optical microscopy

(2015) Kevin Smith et al.   NATURE METHODS

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

Somatic stem cell heterogeneity: diversity in the blood, skin and intestinal stem cell compartments

(2015) Margaret A. Goodell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Visualizing Whole-Brain Activity and Development at the Single-Cell Level Using Light-Sheet Microscopy

(2015) Philipp J. Keller et al.   NEURON

Neural Regulation of Hematopoiesis, Inflammation, and Cancer

(2015) Maher Hanoun et al.   NEURON

BigNeuron: Large-Scale 3D Neuron Reconstruction from Optical Microscopy Images

(2015) Hanchuan Peng et al.   NEURON

The superresolved brain

(2015) H.-U. Dodt   SCIENCE

Expansion microscopy

(2015) F. Chen et al.   SCIENCE

Brain BLAQ: Post-hoc thick-section histochemistry for localizing optogenetic constructs in neurons and their distal terminals

(2015) David A. Kupferschmidt et al.   Frontiers in Neuroanatomy

A three-dimensional image processing program for accurate, rapid, and semi-automated segmentation of neuronal somata with dense neurite outgrowth

(2015) James D. Ross et al.   Frontiers in Neuroanatomy

Scalable and DiI-compatible optical clearance of the mammalian brain

(2015) Bing Hou et al.   Frontiers in Neuroanatomy

Histological validation of high-resolution DTI in human post mortem tissue

(2015) Arne Seehaus et al.   Frontiers in Neuroanatomy

A Rapid Optical Clearing Protocol Using 2,2′-Thiodiethanol for Microscopic Observation of Fixed Mouse Brain

(2015) Yuka Aoyagi et al.   PLoS One

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

(2014) Harry M. T. Choi et al.   ACS Nano

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

Neural Networks of the Mouse Neocortex

(2014) Brian Zingg et al.   CELL

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

(2014) Kazuki Tainaka et al.   CELL

Non-invasive in vivo measurement of cardiac output in C57BL/6 mice using high frequency transthoracic ultrasound: evaluation of gender and body weight effects

(2014) Elisabet Domínguez et al.   INTERNATIONAL JOURNAL OF CARDIOVASCULAR IMAGING

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

The discovery of Homo floresiensis: Tales of the hobbit

(2014) Ewen Callaway   NATURE

Electroceuticals spark interest

(2014) Sara Reardon   NATURE

Emergence of reproducible spatiotemporal activity during motor learning

(2014) Andrew J. Peters et al.   NATURE

The bone marrow niche for haematopoietic stem cells

(2014) Sean J. Morrison et al.   NATURE

Foxc1 is a critical regulator of haematopoietic stem/progenitor cell niche formation

(2014) Yoshiki Omatsu et al.   NATURE

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Label-free in vivo imaging of myelinated axons in health and disease with spectral confocal reflectance microscopy

(2014) Aaron J Schain et al.   NATURE MEDICINE

A robust pipeline for rapid production of versatile nanobody repertoires

(2014) Peter C Fridy et al.   NATURE METHODS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Extensible visualization and analysis for multidimensional images using Vaa3D

(2014) Hanchuan Peng et al.   Nature Protocols

A general protocol for the generation of Nanobodies for structural biology

(2014) Els Pardon et al.   Nature Protocols

Advanced CLARITY for rapid and high-resolution imaging of intact tissues

(2014) Raju Tomer et al.   Nature Protocols

Perfusion decellularization of whole organs

(2014) Jacques P Guyette et al.   Nature Protocols

Bioelectronic medicines: a research roadmap

(2014) Karen Birmingham et al.   NATURE REVIEWS DRUG DISCOVERY

Rapid Reconstruction of 3D Neuronal Morphology from Light Microscopy Images with Augmented Rayburst Sampling

(2014) Xing Ming et al.   PLoS One

Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury

(2014) M.-D. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast tissue staining with chemical tags

(2014) J. Kohl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuronal Activity Promotes Oligodendrogenesis and Adaptive Myelination in the Mammalian Brain

(2014) E. M. Gibson et al.   SCIENCE

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

(2013) Alessandro Bria et al.   BMC BIOINFORMATICS

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Emerging frontiers in detection and control of bacterial biofilms

(2013) Seth Yang-En Tan et al.   CURRENT OPINION IN BIOTECHNOLOGY

ClearT: a detergent- and solvent-free clearing method for neuronal and non-neuronal tissue

(2013) T. Kuwajima et al.   DEVELOPMENT

A multispectral LED array for the reduction of background autofluorescence in brain tissue

(2013) Haison Duong et al.   JOURNAL OF NEUROSCIENCE METHODS

CXCL12 in early mesenchymal progenitors is required for haematopoietic stem-cell maintenance

(2013) Adam Greenbaum et al.   NATURE

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Ultrasensitive fluorescent proteins for imaging neuronal activity

(2013) Tsai-Wen Chen et al.   NATURE

Imaging human connectomes at the macroscale

(2013) R Cameron Craddock et al.   NATURE METHODS

CLARITY for mapping the nervous system

(2013) Kwanghun Chung et al.   NATURE METHODS

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

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

The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology

(2013) Vincent J. Dercksen et al.   NEUROINFORMATICS

Neuronal Morphology Goes Digital: A Research Hub for Cellular and System Neuroscience

(2013) Ruchi Parekh et al.   NEURON

Automated Transmission-Mode Scanning Electron Microscopy (tSEM) for Large Volume Analysis at Nanoscale Resolution

(2013) Masaaki Kuwajima et al.   PLoS One

Autonomic Nerve Development Contributes to Prostate Cancer Progression

(2013) C. Magnon et al.   SCIENCE

Light microscopy mapping of connections in the intact brain

(2013) Sung-Yon Kim et al.   TRENDS IN COGNITIVE SCIENCES

Thalamocortical input onto layer 5 pyramidal neurons measured using quantitative large-scale array tomography

(2013) Jong-Cheol Rah et al.   Frontiers in Neural Circuits

Extended Stokes Shift in Fluorescent Proteins: Chromophore–Protein Interactions in a Near-Infrared TagRFP675 Variant

(2013) Kiryl D. Piatkevich et al.   Scientific Reports

Human Immunodeficiency Virus and Heparan Sulfate: From Attachment to Entry Inhibition

(2013) Bridgette J. Connell et al.   Frontiers in Immunology

Temperature Effect on the Nanostructureof SDS Micelles in Water

(2013) Boualem Hammouda   JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY

Multimodal Magnetic Resonance Imaging Assessment of White Matter Aging Trajectories Over the Lifespan of Healthy Individuals

(2012) George Bartzokis et al.   BIOLOGICAL PSYCHIATRY

Placental regulation of maternal-fetal interactions and brain development

(2012) Elaine Y. Hsiao et al.   Developmental Neurobiology

High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO)

(2012) Ali Ertürk et al.   EXPERIMENTAL NEUROLOGY

Cell-penetrating anti-GFAP VHH and corresponding fluorescent fusion protein VHH-GFP spontaneously cross the blood-brain barrier and specifically recognize astrocytes: application to brain imaging

(2012) Tengfei Li et al.   FASEB JOURNAL

Live Imaging of Targeted Cell Ablation in Xenopus: A New Model to Study Demyelination and Repair

(2012) F. Kaya et al.   JOURNAL OF NEUROSCIENCE

Optimization of a GCaMP Calcium Indicator for Neural Activity Imaging

(2012) J. Akerboom et al.   JOURNAL OF NEUROSCIENCE

High-resolution gene expression atlases for adult and developing mouse brain and spinal cord

(2012) Alex M. Henry et al.   MAMMALIAN GENOME

Restriction of intestinal stem cell expansion and the regenerative response by YAP

(2012) Evan R. Barry et al.   NATURE

BioImageXD: an open, general-purpose and high-throughput image-processing platform

(2012) Pasi Kankaanpää et al.   NATURE METHODS

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Serial two-photon tomography for automated ex vivo mouse brain imaging

(2012) Timothy Ragan et al.   NATURE METHODS

Computerized video analysis of social interactions in mice

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy

(2012) Juan Carlos Tapia et al.   Nature Protocols

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

(2012) Ali Ertürk et al.   Nature Protocols

Scanned light sheet microscopy with confocal slit detection

(2012) Eugen Baumgart et al.   OPTICS EXPRESS

Chemical Clearing and Dehydration of GFP Expressing Mouse Brains

(2012) Klaus Becker et al.   PLoS One

Modeling an autism risk factor in mice leads to permanent immune dysregulation

(2012) E. Y. Hsiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive connectivity of the mouse main olfactory bulb: analysis and online digital atlas

(2012) Houri Hintiryan et al.   Frontiers in Neuroanatomy

Neuromantic – from Semi-Manual to Semi-Automatic Reconstruction of Neuron Morphology

(2012) Darren R. Myatt et al.   Frontiers in Neuroinformatics

Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes

(2011) M. H. Longair et al.   BIOINFORMATICS

Validation of Noninvasive Measurements of Cardiac Output in Mice Using Echocardiography

(2011) François Tournoux et al.   JOURNAL OF THE AMERICAN SOCIETY OF ECHOCARDIOGRAPHY

Several rAAV Vectors Efficiently Cross the Blood–brain Barrier and Transduce Neurons and Astrocytes in the Neonatal Mouse Central Nervous System

(2011) Hongwei Zhang et al.   MOLECULAR THERAPY

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

The lymphatic vasculature in disease

(2011) Kari Alitalo   NATURE MEDICINE

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

(2011) Hiroshi Hama et al.   NATURE NEUROSCIENCE

The FARSIGHT Trace Editor: An Open Source Tool for 3-D Inspection and Efficient Pattern Analysis Aided Editing of Automated Neuronal Reconstructions

(2011) Jonathan Luisi et al.   NEUROINFORMATICS

Automated Tracing of Neurites from Light Microscopy Stacks of Images

(2011) Paarth Chothani et al.   NEUROINFORMATICS

A high-level 3D visualization API for Java and ImageJ

(2010) Benjamin Schmid et al.   BMC BIOINFORMATICS

Activation of the maternal immune system induces endocrine changes in the placenta via IL-6

(2010) Elaine Y. Hsiao et al.   BRAIN BEHAVIOR AND IMMUNITY

Neuron tracing in perspective

(2010) Erik Meijering   CYTOMETRY PART A

Tubular Structure Segmentation Based on Minimal Path Method and Anisotropic Enhancement

(2010) Fethallah Benmansour et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Total-Circumference Intraoperative Frozen Section Analysis Reduces Margin-Positive Rate in Breast-Conservation Surgery

(2010) K. Fukamachi et al.   JAPANESE JOURNAL OF CLINICAL ONCOLOGY

Metadata matters: access to image data in the real world

(2010) Melissa Linkert et al.   JOURNAL OF CELL BIOLOGY

Transgene expression and effective gene silencing in vagal afferent neuronsin vivousing recombinant adeno-associated virus vectors

(2010) M. Kollarik et al.   JOURNAL OF PHYSIOLOGY-LONDON

Mesenchymal and haematopoietic stem cells form a unique bone marrow niche

(2010) Simón Méndez-Ferrer et al.   NATURE

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Real-time imaging of hepatitis C virus infection using a fluorescent cell-based reporter system

(2010) Christopher T Jones et al.   NATURE BIOTECHNOLOGY

NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail

(2010) Padraig Gleeson et al.   PLoS Computational Biology

Llama VHH antibody fragments against GFAP: better diffusion in fixed tissues than classical monoclonal antibodies

(2009) Claire Perruchini et al.   ACTA NEUROPATHOLOGICA

Bisque: a platform for bioimage analysis and management

(2009) Kristian Kvilekval et al.   BIOINFORMATICS

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

Selective plane illumination microscopy techniques in developmental biology

(2009) J. Huisken et al.   DEVELOPMENT

XuvTools: free, fast and reliable stitching of large 3D datasets

(2009) M. EMMENLAUER et al.   JOURNAL OF MICROSCOPY

Neuroscience: Making connections

(2009) Jonah Lehrer   NATURE

Three-dimensional microscopy of the tumor microenvironment in vivo using optical frequency domain imaging

(2009) Benjamin J Vakoc et al.   NATURE MEDICINE

Comparison of landmark-based and automatic methods for cortical surface registration

(2009) Dimitrios Pantazis et al.   NEUROIMAGE

Neurocartography

(2009) Narayanan Kasthuri et al.   NEUROPSYCHOPHARMACOLOGY

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale

(2009) Jason W. Bohland et al.   PLoS Computational Biology

HaloTag: A Novel Protein Labeling Technology for Cell Imaging and Protein Analysis

(2008) Georgyi V. Los et al.   ACS Chemical Biology

Transparent Adult Zebrafish as a Tool for In Vivo Transplantation Analysis

(2008) Richard Mark White et al.   Cell Stem Cell

An Engineered Protein Tag for Multiprotein Labeling in Living Cells

(2008) Arnaud Gautier et al.   CHEMISTRY & BIOLOGY

Ome sweet ome: what can the genome tell us about the connectome?

(2008) Jeff W Lichtman et al.   CURRENT OPINION IN NEUROBIOLOGY

Concentrated dyes as a source of two-dimensional fluorescent field for characterization of a confocal microscope

(2008) M. A. MODEL et al.   JOURNAL OF MICROSCOPY

Intravascular AAV9 preferentially targets neonatal neurons and adult astrocytes

(2008) Kevin D Foust et al.   NATURE BIOTECHNOLOGY

Perfusion-decellularized matrix: using nature's platform to engineer a bioartificial heart

(2008) Harald C Ott et al.   NATURE MEDICINE

L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies

(2008) Ruggero Scorcioni et al.   Nature Protocols

Avoiding the void: cell-to-cell spread of human viruses

(2008) Quentin Sattentau   NATURE REVIEWS MICROBIOLOGY

Validation of a fiducial-based atlas localization method for deep brain stimulation contacts in the area of the subthalamic nucleus

(2007) Tom O. Videen et al.   JOURNAL OF NEUROSCIENCE METHODS

The role of inflammation in CNS injury and disease

(2006) Sian-Marie Lucas et al.   BRITISH JOURNAL OF PHARMACOLOGY