Chemical sectioning fluorescence tomography: high-throughput, high-contrast, multicolor, whole-brain imaging at subcellular resolution

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

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

(2020) Hiroki R. Ueda et al.   NEURON

Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution

(2019) Ruixuan Gao et al.   SCIENCE

Genetic Single Neuron Anatomy Reveals Fine Granularity of Cortical Axo-Axonic Cells

(2019) Xiaojun Wang et al.   Cell Reports

DeepBouton: Automated Identification of Single-Neuron Axonal Boutons at the Brain-Wide Scale

(2019) Shenghua Cheng et al.   Frontiers in Neuroinformatics

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain

(2019) Johan Winnubst et al.   CELL

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

(2019) Tonmoy Chakraborty et al.   NATURE METHODS

Advanced CUBIC tissue clearing for whole-organ cell profiling

(2019) Katsuhiko Matsumoto et al.   Nature Protocols

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

(2019) Chenchen Pan et al.   CELL

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

(2018) Bianca Migliori et al.   BMC BIOLOGY

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

Light-sheet microscopy: a tutorial

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

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

(2018) Ruiyao Cai et al.   NATURE NEUROSCIENCE

Simultaneous Acquisition of Multicolor Information From Neural Circuits in Resin-Embedded Samples

(2018) Miao Ren et al.   Frontiers in Neuroscience

A guide to light-sheet fluorescence microscopy for multiscale imaging

(2017) Rory M Power et al.   NATURE METHODS

High-Speed and Scalable Whole-Brain Imaging in Rodents and Primates

(2017) Kaoru Seiriki et al.   NEURON

Embedding and Chemical Reactivation of Green Fluorescent Protein in the Whole Mouse Brain for Optical Micro-Imaging

(2017) Yadong Gang et al.   Frontiers in Neuroscience

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

(2016) Chenchen Pan et al.   NATURE METHODS

Fluorescent indicators for simultaneous reporting of all four cell cycle phases

(2016) Bryce T Bajar et al.   NATURE METHODS

High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level

(2016) Hui Gong et al.   Nature Communications

A platform for brain-wide imaging and reconstruction of individual neurons

(2016) Michael N Economo et al.   eLife

Improving brightness and photostability of green and red fluorescent proteins for live cell imaging and FRET reporting

(2016) Bryce T. Bajar et al.   Scientific Reports

Green Fluorescent Protein with Anionic Tryptophan-Based Chromophore and Long Fluorescence Lifetime

(2015) Karen S. Sarkisyan et al.   BIOPHYSICAL JOURNAL

Rapid imaging of large tissues using high-resolution stage-scanning microscopy

(2015) Tao Yang et al.   Biomedical Optics Express

Survey of Red Fluorescence Proteins as Markers for Secretory Granule Exocytosis

(2015) Nikhil R. Gandasi et al.   PLoS One

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

(2014) Nicolas Renier et al.   CELL

pHuji, a pH-sensitive red fluorescent protein for imaging of exo- and endocytosis

(2014) Yi Shen et al.   JOURNAL OF CELL BIOLOGY

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

(2014) Raju Tomer et al.   Nature Protocols

Chemical reactivation of quenched fluorescent protein molecules enables resin-embedded fluorescence microimaging

(2014) Hanqing Xiong et al.   Nature Communications

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Continuously tracing brain-wide long-distance axonal projections in mice at a one-micron voxel resolution

(2013) Hui Gong et al.   NEUROIMAGE

Development of a Plastic Embedding Method for Large-Volume and Fluorescent-Protein-Expressing Tissues

(2013) Zhongqin Yang et al.   PLoS One

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

(2012) Timothy Ragan et al.   NATURE METHODS

pHTomato, a red, genetically encoded indicator that enables multiplex interrogation of synaptic activity

(2012) Yulong Li et al.   NATURE NEUROSCIENCE

Two-photon absorption properties of fluorescent proteins

(2011) Mikhail Drobizhev et al.   NATURE METHODS

An Improved Cerulean Fluorescent Protein with Enhanced Brightness and Reduced Reversible Photoswitching

(2011) Michele L. Markwardt et al.   PLoS One

The Big and the Small: Challenges of Imaging the Brain's Circuits

(2011) J. W. Lichtman et al.   SCIENCE

Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells

(2010) Bo Huang et al.   CELL

Protein localization in electron micrographs using fluorescence nanoscopy

(2010) Shigeki Watanabe et al.   NATURE METHODS

Fast, high-contrast imaging of animal development with scanned light sheet–based structured-illumination microscopy

(2010) Philipp J Keller et al.   NATURE METHODS

From the Connectome to the Synaptome: An Epic Love Story

(2010) J. DeFelipe   SCIENCE

Micro-Optical Sectioning Tomography to Obtain a High-Resolution Atlas of the Mouse Brain

(2010) A. Li et al.   SCIENCE

Improving the photostability of bright monomeric orange and red fluorescent proteins

(2008) Nathan C Shaner et al.   NATURE METHODS