Mesoscale microscopy and image analysis tools for understanding the brain

Deep learning-based point-scanning super-resolution imaging

(2021) Linjing Fang et al.   NATURE METHODS

SNT: a unifying toolbox for quantification of neuronal anatomy

(2021) Cameron Arshadi et al.   NATURE METHODS

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

(2021) Adam L. Tyson et al.   PLoS Computational Biology

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

(2020) Quanxin Wang et al.   CELL

Machine learning analysis of whole mouse brain vasculature

(2020) Mihail Ivilinov Todorov et al.   NATURE METHODS

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

Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues

(2020) Etsuo A. Susaki et al.   Nature Communications

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 natverse, a versatile toolbox for combining and analysing neuroanatomical data

(2020) Alexander Shakeel Bates et al.   eLife

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

(2020) Reka Hollandi et al.   Cell Systems

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

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

(2020) Hang Zhou et al.   NEUROINFORMATICS

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

Histology‐Based Average Template of the Marmoset Cortex With Probabilistic Localization of Cytoarchitectural Areas

(2020) Piotr Majka et al.   NEUROIMAGE

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

(2019) Daniel Sage et al.   NATURE METHODS

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

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

(2019) David Hörl et al.   NATURE METHODS

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 three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing

(2018) Tatsuya C. Murakami et al.   NATURE NEUROSCIENCE

Tau induces blood vessel abnormalities and angiogenesis-related gene expression in P301L transgenic mice and human Alzheimer’s disease

(2018) Rachel E. Bennett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

Dual-color deep-tissue three-photon microscopy with a multiband infrared laser

(2018) Khmaies Guesmi et al.   Light-Science & Applications

The Brain/MINDS 3D digital marmoset brain atlas

(2018) Alexander Woodward et al.   Scientific Data

The logic of single-cell projections from visual cortex

(2018) Yunyun Han et al.   NATURE

Evaluation of seven optical clearing methods in mouse brain

(2018) Peng Wan et al.   Neurophotonics

Content-aware image restoration: pushing the limits of fluorescence microscopy

(2018) Martin Weigert et al.   NATURE METHODS

QuickNAT: A fully convolutional network for quick and accurate segmentation of neuroanatomy

(2018) Abhijit Guha Roy et al.   NEUROIMAGE

Fully integrated silicon probes for high-density recording of neural activity

(2017) James J. Jun et al.   NATURE

An objective comparison of cell-tracking algorithms

(2017) Vladimír Ulman et al.   NATURE METHODS

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

TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images

(2016) Alessandro Bria et al.   NATURE METHODS

The mouse cortico-striatal projectome

(2016) Houri Hintiryan et al.   NATURE NEUROSCIENCE

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

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

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

Three-Dimensional Study of Alzheimer’s Disease Hallmarks Using the iDISCO Clearing Method

(2016) Thomas Liebmann et al.   Cell Reports

A comprehensive excitatory input map of the striatum reveals novel functional organization

(2016) Barbara J Hunnicutt et al.   eLife

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

(2016) Michael N Economo et al.   eLife

Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene

(2016) Marzena Stefaniuk et al.   Scientific Reports

Clarifying Tissue Clearing

(2015) Douglas S. Richardson et al.   CELL

Intact-Brain Analyses Reveal Distinct Information Carried by SNc Dopamine Subcircuits

(2015) Talia N. Lerner et al.   CELL

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

(2015) Leonard Kuan et al.   METHODS

Deep learning

(2015) Yann LeCun et al.   NATURE

BigDataViewer: visualization and processing for large image data sets

(2015) Tobias Pietzsch et al.   NATURE METHODS

ScaleS: an optical clearing palette for biological imaging

(2015) Hiroshi Hama et al.   NATURE NEUROSCIENCE

The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content

(2015) Rembrandt Bakker et al.   NEUROINFORMATICS

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

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

(2014) Paolo Frasconi et al.   BIOINFORMATICS

Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis

(2014) Etsuo A. Susaki et al.   CELL

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

(2014) Nicolas Renier et al.   CELL

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

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

(2014) Raju Tomer et al.   Nature Protocols

Waxholm Space atlas of the Sprague Dawley rat brain

(2014) Eszter A. Papp et al.   NEUROIMAGE

A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

(2014) Carol L. Thompson et al.   NEURON

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

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

(2013) T. Kuwajima et al.   DEVELOPMENT

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

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

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

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

(2013) Hui Gong et al.   NEUROIMAGE

ImgLib2—generic image processing in Java

(2012) Tobias Pietzsch et al.   BIOINFORMATICS

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

High-accuracy neurite reconstruction for high-throughput neuroanatomy

(2011) Moritz Helmstaedter et al.   NATURE NEUROSCIENCE

FSL

(2011) Mark Jenkinson et al.   NEUROIMAGE

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

A reproducible evaluation of ANTs similarity metric performance in brain image registration

(2010) Brian B. Avants et al.   NEUROIMAGE

CATMAID: collaborative annotation toolkit for massive amounts of image data

(2009) S. Saalfeld et al.   BIOINFORMATICS

Fast free-form deformation using graphics processing units

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

elastix: A Toolbox for Intensity-Based Medical Image Registration

(2009) S. Klein et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration

(2009) Arno Klein et al.   NEUROIMAGE