A deep learning algorithm for 3D cell detection in whole mouse brain image datasets

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

(2020) Quanxin Wang et al.   CELL

Mapping mesoscale axonal projections in the mouse brain using a 3D convolutional network

(2020) Drew Friedmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mouse Visual Cortex

(2020) Jun Ho Song et al.   Cell Reports

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

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

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

DeNeRD: high-throughput detection of neurons for brain-wide analysis with deep learning

(2019) Asim Iqbal et al.   Scientific Reports

Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI

(2019) Maged Goubran et al.   Nature Communications

A Circuit for Integration of Head- and Visual-Motion Signals in Layer 6 of Mouse Primary Visual Cortex

(2018) Mateo Vélez-Fort et al.   NEURON

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

DeepLabCut: markerless pose estimation of user-defined body parts with deep learning

(2018) Alexander Mathis et al.   NATURE NEUROSCIENCE

An interactive framework for whole-brain maps at cellular resolution

(2017) Daniel Fürth et al.   NATURE NEUROSCIENCE

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

(2017) Kaoru Seiriki et al.   NEURON

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

(2016) Nicolas Renier et al.   CELL

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

(2016) Christian J. Niedworok et al.   Nature Communications

Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy

(2016) Qinyi Fu et al.   Nature Communications

Deep learning

(2015) Yann LeCun et al.   NATURE

Stochastic electrotransport selectively enhances the transport of highly electromobile molecules

(2015) Sung-Yon Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping Social Behavior-Induced Brain Activation at Cellular Resolution in the Mouse

(2015) Yongsoo Kim et al.   Cell Reports

Dopamine neurons projecting to the posterior striatum form an anatomically distinct subclass

(2015) William Menegas et al.   eLife

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

The Stimulus Selectivity and Connectivity of Layer Six Principal Cells Reveals Cortical Microcircuits Underlying Visual Processing

(2014) Mateo Vélez-Fort et al.   NEURON

Organization of Monosynaptic Inputs to the Serotonin and Dopamine Neuromodulatory Systems

(2014) Sachie K. Ogawa et al.   Cell Reports

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

Mapping brain circuitry with a light microscope

(2013) Pavel Osten et al.   NATURE METHODS

Icy: an open bioimage informatics platform for extended reproducible research

(2012) Fabrice de Chaumont et al.   NATURE METHODS

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

(2012) Timothy Ragan et al.   NATURE METHODS

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

(2012) Johannes Schindelin et al.   NATURE METHODS

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

(2012) Ali Ertürk et al.   Nature Protocols

Whole-Brain Mapping of Direct Inputs to Midbrain Dopamine Neurons

(2012) Mitsuko Watabe-Uchida et al.   NEURON

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

Fast free-form deformation using graphics processing units

(2009) Marc Modat et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE