4.8 Article

Cross-modal coherent registration of whole mouse brains

Related references

Note: Only part of the references are listed.
Article Computer Science, Interdisciplinary Applications

GTree: an Open-source Tool for Dense Reconstruction of Brain-wide Neuronal Population

Hang Zhou et al.

Summary: A new open-source software called GTree has been developed to address the time-consuming process of neuron digital reconstruction from large datasets. GTree features an error-screening system for fast error localization in neuron branches and achieves high automation. The study shows that GTree is five times faster than widely used commercial software and applicable to large datasets.

NEUROINFORMATICS (2021)

Article Computer Science, Interdisciplinary Applications

An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO plus and Light Sheet Fluorescence Microscopy

Johanna Perens et al.

Summary: In recent years, advances in whole-brain immunolabelling and LSFM have led to the development of an optimized digital mouse brain atlas for more accurate and efficient registration of neuronal activity patterns. This atlas has shown to be beneficial in mapping changes in c-Fos expression and evaluating drug effects on whole-brain activity, providing a valuable tool for neuroscience research.

NEUROINFORMATICS (2021)

Article Multidisciplinary Sciences

Morphological diversity of single neurons in molecularly defined cell types

Hanchuan Peng et al.

Summary: The study systematically examined the complete single-neuron morphologies on a brain-wide scale and identified 11 major projection neuron types with distinct features. The research found extensive projectional diversity within each major type, following generalizable principles governing long-range axonal projections including molecular correspondence, divergent or convergent projection, axon termination pattern, and regional specificity. This study highlights the crucial need for quantitative description of complete single-cell anatomy in cell-type classification.

NATURE (2021)

Article Multidisciplinary Sciences

Cellular anatomy of the mouse primary motor cortex

Rodrigo Munoz-Castaneda et al.

Summary: The research team provided a comprehensive cell type-based anatomical description of the mouse primary motor cortex, upper limb area using various cutting-edge technologies. They identified different types of projection neurons and derived an input-output wiring diagram, laying a foundation for future analyses of motor control circuitry in the mammalian brain.

NATURE (2021)

Article Biotechnology & Applied Microbiology

High-throughput mapping of a whole rhesus monkey brain at micrometer resolution

Fang Xu et al.

Summary: This study introduces a new method combining primate-optimized tissue sectioning and clearing with high-speed fluorescence microscopy to achieve high-resolution imaging of the entire rhesus monkey brain. Researchers have also developed an efficient method for tracing sparse axonal fibers in large datasets, enabling connectome-scale mapping of large primate brains.

NATURE BIOTECHNOLOGY (2021)

Article Biochemistry & Molecular Biology

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Quanxin Wang et al.

Article Biochemical Research Methods

Real-time 3D movement correction for two-photon imaging in behaving animals

Victoria A. Griffiths et al.

NATURE METHODS (2020)

Article Computer Science, Artificial Intelligence

BIRNet: Brain image registration using dual-supervised fully convolutional networks

Jingfan Fan et al.

MEDICAL IMAGE ANALYSIS (2019)

Article Multidisciplinary Sciences

Scalable volumetric imaging for ultrahigh-speed brain mapping at synaptic resolution

Hao Wang et al.

NATIONAL SCIENCE REVIEW (2019)

Article Multidisciplinary Sciences

Hierarchical organization of cortical and thalamic connectivity

Julie A. Harris et al.

NATURE (2019)

Article Multidisciplinary Sciences

TeraVR empowers precise reconstruction of complete 3-D neuronal morphology in the whole brain

Yimin Wang et al.

NATURE COMMUNICATIONS (2019)

Article Neurosciences

An interactive framework for whole-brain maps at cellular resolution

Daniel Furth et al.

NATURE NEUROSCIENCE (2018)

Article Biochemical Research Methods

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

Rui Lin et al.

NATURE METHODS (2018)

Review Neurosciences

Neuronal cell-type classification: challenges, opportunities and the path forward

Hongkui Zeng et al.

NATURE REVIEWS NEUROSCIENCE (2017)

Article Biochemistry & Molecular Biology

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

Nicolas Renier et al.

Article Biochemical Research Methods

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

Chenchen Pan et al.

NATURE METHODS (2016)

Article Neurosciences

The mouse cortico-striatal projectome

Houri Hintiryan et al.

NATURE NEUROSCIENCE (2016)

Article Multidisciplinary Sciences

aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

Christian J. Niedworok et al.

NATURE COMMUNICATIONS (2016)

Article Biochemistry & Molecular Biology

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

Evan Murray et al.

Review Biochemistry & Molecular Biology

Clarifying Tissue Clearing

Douglas S. Richardson et al.

Article Biochemical Research Methods

LittleQuickWarp: An ultrafast image warping tool

Lei Qu et al.

METHODS (2015)

Article Biochemical Research Methods

Whole-brain activity mapping onto a zebrafish brain atlas

Owen Randlett et al.

NATURE METHODS (2015)

Article Biochemical Research Methods

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

Etsuo A. Susaki et al.

NATURE PROTOCOLS (2015)

Editorial Material Neurosciences

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

Hanchuan Peng et al.

NEURON (2015)

Article Anatomy & Morphology

Long-range projection neurons of the mouse ventral tegmental area: a single-cell axon tracing analysis

Ana Aransay et al.

Frontiers in Neuroanatomy (2015)

Article Biochemistry & Molecular Biology

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

Nicolas Renier et al.

Article Biochemistry & Molecular Biology

Neural Networks of the Mouse Neocortex

Brian Zingg et al.

Article Multidisciplinary Sciences

A mesoscale connectome of the mouse brain

Seung Wook Oh et al.

NATURE (2014)

Article Biochemical Research Methods

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

Raju Tomer et al.

NATURE PROTOCOLS (2014)

Article Multidisciplinary Sciences

Structural and molecular interrogation of intact biological systems

Kwanghun Chung et al.

NATURE (2013)

Review Biochemical Research Methods

Mapping brain circuitry with a light microscope

Pavel Osten et al.

NATURE METHODS (2013)

Article Biochemical Research Methods

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

Timothy Ragan et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

BrainAligner: 3D registration atlases of Drosophila brains

Hanchuan Peng et al.

NATURE METHODS (2011)

Article Computer Science, Interdisciplinary Applications

Fast free-form deformation using graphics processing units

Marc Modat et al.

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2010)

Article Computer Science, Interdisciplinary Applications

elastix: A Toolbox for Intensity-Based Medical Image Registration

Stefan Klein et al.

IEEE TRANSACTIONS ON MEDICAL IMAGING (2010)

Article Biotechnology & Applied Microbiology

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

Hanchuan Peng et al.

NATURE BIOTECHNOLOGY (2010)

Article Biochemical Research Methods

A 3D digital atlas of C. elegans and its application to single-cell analyses

Fuhui Long et al.

NATURE METHODS (2009)

Article Biochemical Research Methods

Ultramicroscopy:: three-dimensional visualization of neuronal networks in the whole mouse brain

Hans-Ulrich Dodt et al.

NATURE METHODS (2007)

Article Computer Science, Artificial Intelligence

A new point matching algorithm for non-rigid registration

HL Chui et al.

COMPUTER VISION AND IMAGE UNDERSTANDING (2003)