Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain

High-definition imaging using line-illumination modulation microscopy

(2021) Qiuyuan Zhong et al.   NATURE METHODS

Medial preoptic area antagonistically mediates stress-induced anxiety and parental behavior

(2021) Guang-Wei Zhang et al.   NATURE NEUROSCIENCE

A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility

(2021) Mathew Birdsall Abrams et al.   NEUROINFORMATICS

Brain microvasculature has a common topology with local differences in geometry that match metabolic load

(2021) Xiang Ji et al.   NEURON

Cellular correlates of gray matter volume changes in magnetic resonance morphometry identified by two-photon microscopy

(2021) Livia Asan et al.   Scientific Reports

Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning

(2021) Philipp Mergenthaler et al.   PLoS Computational Biology

Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain

(2021) David M Young et al.   eLife

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

(2021) Zizhen Yao et al.   CELL

Optimizing tissue clearing and imaging methods for human brain tissue

(2021) Min Sun Kim et al.   JOURNAL OF INTERNATIONAL MEDICAL RESEARCH

A guidebook for DISCO tissue clearing

(2021) Muge Molbay et al.   Molecular Systems Biology

Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy

(2021) Norio Takata et al.   Scientific Reports

Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

(2021) John K. Mich et al.   Cell Reports

Bundle-specific associations between white matter microstructure and Aβ and tau pathology in preclinical Alzheimer's disease

(2021) Alexa Pichet Binette et al.   eLife

FDRN: A Fast Deformable Registration Network for Medical Images

(2021) Kaicong Sun et al.   MEDICAL PHYSICS

Organizational principles of amygdalar input-output neuronal circuits

(2021) Limeng Huang et al.   MOLECULAR PSYCHIATRY

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

(2021) Fang Xu et al.   NATURE BIOTECHNOLOGY

Tutorial: practical considerations for tissue clearing and imaging

(2021) Kurt R. Weiss et al.   Nature Protocols

Mesoscale microscopy and image analysis tools for understanding the brain

(2021) Adam L. Tyson et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Organization of the inputs and outputs of the mouse superior colliculus

(2021) Nora L. Benavidez et al.   Nature Communications

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

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

Convergence Circuit Mapping: Genetic Approaches From Structure to Function

(2021) Jang Soo Yook et al.   Frontiers in Systems Neuroscience

A multimodal cell census and atlas of the mammalian primary motor cortex

(2021) et al.   NATURE

Neuroanatomical tract-tracing techniques that did go viral

(2020) Jose L. Lanciego et al.   Brain Structure & Function

Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature

(2020) Christoph Kirst et al.   CELL

Tissue clearing and its applications in neuroscience

(2020) Hiroki R. Ueda et al.   NATURE REVIEWS NEUROSCIENCE

Multiplex Neural Circuit Tracing With G-Deleted Rabies Viral Vectors

(2020) Toshiaki Suzuki et al.   Frontiers in Neural Circuits

High-brightness anterograde transneuronal HSV1 H129 tracer modified using a Trojan horse-like strategy

(2020) Peng Su et al.   Molecular Brain

The NanoZoomer artificial intelligence connectomics pipeline for tracer injection studies of the marmoset brain

(2020) Alexander Woodward et al.   Brain Structure & Function

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

(2020) Quanxin Wang et al.   CELL

Multimodal Cross‐registration and Quantification of Metric Distortions in Marmoset Whole Brain Histology using Diffeomorphic Mappings

(2020) Brian C. Lee et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Synaptic Specificity and Application of Anterograde Transsynaptic AAV for Probing Neural Circuitry

(2020) Brian Zingg et al.   JOURNAL OF NEUROSCIENCE

Viral approaches to study the mammalian brain: Lineage tracing, circuit dissection and therapeutic applications

(2020) Wei Cong et al.   JOURNAL OF NEUROSCIENCE METHODS

Machine learning analysis of whole mouse brain vasculature

(2020) Mihail Ivilinov Todorov et al.   NATURE METHODS

Learning deformable registration of medical images with anatomical constraints

(2020) Lucas Mansilla et al.   NEURAL NETWORKS

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

(2020) Hiroki R. Ueda et al.   NEURON

Deep learning in medical image registration: a review

(2020) Yabo Fu et al.   PHYSICS IN MEDICINE AND BIOLOGY

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

Quantitative cellular-resolution map of the oxytocin receptor in postnatally developing mouse brains

(2020) Kyra T. Newmaster et al.   Nature Communications

Deep-learning–based whole-brain imaging atsingle-neuron resolution

(2020) KEFU NING et al.   Biomedical Optics Express

A single‐synapse resolution survey of PSD95‐positive synapses in twenty human brain regions

(2020) Olimpia E. Curran et al.   EUROPEAN JOURNAL OF NEUROSCIENCE

Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy

(2020) Erin E. Diel et al.   Nature Protocols

Brainwide Genetic Sparse Cell Labeling to Illuminate the Morphology of Neurons and Glia with Cre-Dependent MORF Mice

(2020) Matthew B. Veldman et al.   NEURON

A brain-wide atlas of synapses across the mouse lifespan

(2020) Mélissa Cizeron et al.   SCIENCE

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

A community-based transcriptomics classification and nomenclature of neocortical cell types

(2020) Rafael Yuste et al.   NATURE NEUROSCIENCE

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

(2020) Johanna Perens et al.   NEUROINFORMATICS

A multimodal computational pipeline for 3D histology of the human brain

(2020) Matteo Mancini et al.   Scientific Reports

Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

(2020) Jennifer D. Whitesell et al.   NEURON

Common cell type nomenclature for the mammalian brain

(2020) Jeremy A Miller et al.   eLife

Multimodal 3D atlas of the macaque monkey motor and premotor cortex

(2020) Lucija Rapan et al.   NEUROIMAGE

Automatic navigation system for the mouse brain

(2019) Susan J. Tappan et al.   JOURNAL OF COMPARATIVE NEUROLOGY

FDISCO: Advanced solvent-based clearing method for imaging whole organs

(2019) Yisong Qi et al.   Science Advances

Single‐neuron axonal reconstruction: The search for a wiring diagram of the brain

(2019) Michael N. Economo et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Objective Morphological Classification of Neocortical Pyramidal Cells

(2019) Lida Kanari et al.   CEREBRAL CORTEX

A high-throughput neurohistological pipeline for brain-wide mesoscale connectivity mapping of the common marmoset

(2019) Meng Kuan Lin et al.   eLife

Light-Sheet Microscopy in Neuroscience

(2019) Elizabeth M.C. Hillman et al.   Annual Review of Neuroscience

Advances in Ex Situ Tissue Optical Clearing

(2019) Paweł Matryba et al.   Laser & Photonics Reviews

Review of micro-optical sectioning tomography (MOST): technology and applications for whole-brain optical imaging [Invited]

(2019) Ting Zheng et al.   Biomedical Optics Express

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

VoxelMorph: A Learning Framework for Deformable Medical Image Registration

(2019) Guha Balakrishnan et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

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

(2019) David Hörl et al.   NATURE METHODS

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0

(2019) Venkatakaushik Voleti et al.   NATURE METHODS

A Student’s Guide to Neural Circuit Tracing

(2019) Christine Saleeba et al.   Frontiers in Neuroscience

Quantitative whole-brain 3D imaging of tyrosine hydroxylase-labeled neuron architecture in the mouse MPTP model of Parkinson's disease

(2019) Urmas Roostalu et al.   Disease Models & Mechanisms

Cardiorespiratory fitness predicts effective connectivity between the hippocampus and default mode network nodes in young adults

(2019) Corey A. Kronman et al.   HIPPOCAMPUS

Hierarchical organization of cortical and thalamic connectivity

(2019) Julie A. Harris et al.   NATURE

Enhanced and unified anatomical labeling for a common mouse brain atlas

(2019) Uree Chon et al.   Nature Communications

Adeno-Associated Virus Technologies and Methods for Targeted Neuronal Manipulation

(2019) Leila Haery et al.   Frontiers in Neuroanatomy

3D Neuron Reconstruction in Tangled Neuronal Image With Deep Networks

(2019) Qiufu Li et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

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

(2019) Maged Goubran et al.   Nature Communications

Viral Strategies for Targeting the Central and Peripheral Nervous Systems

(2018) Claire N. Bedbrook et al.   Annual Review of Neuroscience

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

(2018) Tanya L. Daigle et al.   CELL

Dissociable Structural and Functional Hippocampal Outputs via Distinct Subiculum Cell Classes

(2018) Mark S. Cembrowski et al.   CELL

Technical implementations of light sheet microscopy

(2018) Zagato Elisa et al.   MICROSCOPY RESEARCH AND TECHNIQUE

A digital 3D atlas of the marmoset brain based on multi-modal MRI

(2018) Cirong Liu et al.   NEUROIMAGE

A Viral Receptor Complementation Strategy to Overcome CAV-2 Tropism for Efficient Retrograde Targeting of Neurons

(2018) Shu-Jing Li et al.   NEURON

Detecting and Avoiding Problems When Using the Cre–lox System

(2018) Allisa J. Song et al.   TRENDS IN GENETICS

Next generation histology methods for three-dimensional imaging of fresh and archival human brain tissues

(2018) Hei Ming Lai et al.   Nature Communications

Accurate and fiducial-marker-free correction for three-dimensional chromatic shift in biological fluorescence microscopy

(2018) Atsushi Matsuda et al.   Scientific Reports

The Brain/MINDS 3D digital marmoset brain atlas

(2018) Alexander Woodward et al.   Scientific Data

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

Input-output organization of the mouse claustrum

(2018) Brian Zingg et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Light sheet fluorescence microscopy for neuroscience

(2018) Stella Corsetti et al.   JOURNAL OF NEUROSCIENCE METHODS

Image Segmentation, Registration and Characterization in R with SimpleITK

(2018) Richard Beare et al.   Journal of Statistical Software

On the Usage of Brain Atlases in Neuroimaging Research

(2018) Andreas Hess et al.   MOLECULAR IMAGING AND BIOLOGY

The logic of single-cell projections from visual cortex

(2018) Yunyun Han et al.   NATURE

Architecture of the Mouse Brain Synaptome

(2018) Fei Zhu et al.   NEURON

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents

(2018) Kazuki Tainaka et al.   Cell Reports

Evaluation of seven optical clearing methods in mouse brain

(2018) Peng Wan et al.   Neurophotonics

Quantitative assessment of optical clearing methods in various intact mouse organs

(2018) Jianyi Xu et al.   Journal of Biophotonics

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Integration of gene expression and brain-wide connectivity reveals the multiscale organization of mouse hippocampal networks

(2018) Michael S. Bienkowski et al.   NATURE NEUROSCIENCE

Development and Functional Diversification of Cortical Interneurons

(2018) Lynette Lim et al.   NEURON

Advances and perspectives in tissue clearing using CLARITY

(2017) Kristian H. Reveles Jensen et al.   JOURNAL OF CHEMICAL NEUROANATOMY

Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry

(2017) Lisa E. Pomeranz et al.   JOURNAL OF NEUROSCIENCE

3D reconstruction of brain section images for creating axonal projection maps in marmosets

(2017) Hiroshi Abe et al.   JOURNAL OF NEUROSCIENCE METHODS

Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems

(2017) Ken Y Chan et al.   NATURE NEUROSCIENCE

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

(2017) Hongkui Zeng et al.   NATURE REVIEWS NEUROSCIENCE

Vascular density and distribution in neocortex

(2017) Franca Schmid et al.   NEUROIMAGE

Quicksilver: Fast predictive image registration – A deep learning approach

(2017) Xiao Yang et al.   NEUROIMAGE

AAV-Mediated Anterograde Transsynaptic Tagging: Mapping Corticocollicular Input-Defined Neural Pathways for Defense Behaviors

(2017) Brian Zingg et al.   NEURON

Precise Cerebral Vascular Atlas in Stereotaxic Coordinates of Whole Mouse Brain

(2017) Benyi Xiong et al.   Frontiers in Neuroanatomy

Multimodal Image Alignment via Linear Mapping between Feature Modalities

(2017) Yanyun Jiang et al.   Journal of Healthcare Engineering

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

(2016) Nicolas Renier et al.   CELL

Cre-dependent DREADD (Designer Receptors Exclusively Activated by Designer Drugs) mice

(2016) Hu Zhu et al.   GENESIS

Comprehensive cellular-resolution atlas of the adult human brain

(2016) Song-Lin Ding et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Long distance projections of cortical pyramidal neurons

(2016) Charles R. Gerfen et al.   JOURNAL OF NEUROSCIENCE RESEARCH

A survey of medical image registration – under review

(2016) Max A. Viergever et al.   MEDICAL IMAGE ANALYSIS

The mouse cortico-striatal projectome

(2016) Houri Hintiryan et al.   NATURE NEUROSCIENCE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

Strategies and Tools for Combinatorial Targeting of GABAergic Neurons in Mouse Cerebral Cortex

(2016) Miao He et al.   NEURON

GABAergic Interneurons in the Neocortex: From Cellular Properties to Circuits

(2016) Robin Tremblay et al.   NEURON

A Designer AAV Variant Permits Efficient Retrograde Access to Projection Neurons

(2016) D. Gowanlock R. Tervo et al.   NEURON

Whole Brain Imaging with Serial Two-Photon Tomography

(2016) Stephen P. Amato et al.   Frontiers in Neuroanatomy

Comparative three-dimensional connectome map of motor cortical projections in the mouse brain

(2016) Minju Jeong et al.   Scientific Reports

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

(2016) Michael N Economo et al.   eLife

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

CAV-2—why a canine virus is a neurobiologist's best friend

(2015) Felix Junyent et al.   CURRENT OPINION IN PHARMACOLOGY

Monosynaptic Circuit Tracing with Glycoprotein-Deleted Rabies Viruses

(2015) E. M. Callaway et al.   JOURNAL OF NEUROSCIENCE

Robust methods to create ex vivo minimum deformation atlases for brain mapping

(2015) Andrew L. Janke et al.   METHODS

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

(2015) Leonard Kuan et al.   METHODS

Viral-genetic tracing of the input–output organization of a central noradrenaline circuit

(2015) Lindsay A. Schwarz et al.   NATURE

Integration of electrophysiological recordings with single-cell RNA-seq data identifies neuronal subtypes

(2015) János Fuzik et al.   NATURE BIOTECHNOLOGY

4D MEMRI atlas of neonatal FVB/N mouse brain development

(2015) Kamila U. Szulc et al.   NEUROIMAGE

Transgenic Mice for Intersectional Targeting of Neural Sensors and Effectors with High Specificity and Performance

(2015) Linda Madisen et al.   NEURON

Brain-mapping projects using the common marmoset

(2015) Hideyuki Okano et al.   NEUROSCIENCE RESEARCH

Multiplex assessment of the positions of odorant receptor-specific glomeruli in the mouse olfactory bulb by serial two-photon tomography

(2015) Bolek Zapiec 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

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

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Oxytocin mediates early experience–dependent cross-modal plasticity in the sensory cortices

(2014) Jing-Jing Zheng et al.   NATURE NEUROSCIENCE

Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements

(2014) Nicholas J. Tustison et al.   NEUROIMAGE

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

(2014) Carol L. Thompson et al.   NEURON

Neurodevelopment and the Origins of Brain Disorders

(2014)   NEUROPSYCHOPHARMACOLOGY

Anatomical characterization of Cre driver mice for neural circuit mapping and manipulation

(2014) Julie A. Harris et al.   Frontiers in Neural Circuits

The Insight ToolKit image registration framework

(2014) Brian B. Avants et al.   Frontiers in Neuroinformatics

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

(2014) Melissa A Haendel et al.   Journal of Biomedical Semantics

Genetic Approaches to Neural Circuits in the Mouse

(2013) Z. Josh Huang et al.   Annual Review of Neuroscience

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

(2013) Alessandro Bria et al.   BMC BIOINFORMATICS

Structural and molecular interrogation of intact biological systems

(2013) Kwanghun Chung et al.   NATURE

CLARITY for mapping the nervous system

(2013) Kwanghun Chung et al.   NATURE METHODS

The cortical angiome: an interconnected vascular network with noncolumnar patterns of blood flow

(2013) Pablo Blinder 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

GENSAT BAC Cre-Recombinase Driver Lines to Study the Functional Organization of Cerebral Cortical and Basal Ganglia Circuits

(2013) Charles R. Gerfen et al.   NEURON

A developmental ontology for the mammalian brain based on the prosomeric model

(2013) Luis Puelles et al.   TRENDS IN NEUROSCIENCES

NeuroGPS: automated localization of neurons for brain circuits using L1 minimization model

(2013) Tingwei Quan et al.   Scientific Reports

Non-uniformity of cell density and networks in the monkey brain

(2013) Masanori Shimono   Scientific Reports

NeuroLex.org: an online framework for neuroscience knowledge

(2013) Stephen D. Larson et al.   Frontiers in Neuroinformatics

Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

(2012) Hongkui Zeng et al.   CELL

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

A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing

(2012) Linda Madisen et al.   NATURE NEUROSCIENCE

Concept of neural genoarchitecture and its genomic fundament

(2012) Luis Puelles et al.   Frontiers in Neuroanatomy

FSL

(2011) Mark Jenkinson et al.   NEUROIMAGE

A Transcriptomic Atlas of Mouse Neocortical Layers

(2011) T. Grant Belgard et al.   NEURON

A Cre-Dependent, Anterograde Transsynaptic Viral Tracer for Mapping Output Pathways of Genetically Marked Neurons

(2011) Liching Lo et al.   NEURON

A Resource of Cre Driver Lines for Genetic Targeting of GABAergic Neurons in Cerebral Cortex

(2011) Hiroki Taniguchi et al.   NEURON

How Inhibition Shapes Cortical Activity

(2011) Jeffry S. Isaacson et al.   NEURON

Genetic Fate Mapping Reveals That the Caudal Ganglionic Eminence Produces a Large and Diverse Population of Superficial Cortical Interneurons

(2010) G. Miyoshi et al.   JOURNAL OF NEUROSCIENCE

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

(2010) Hanchuan Peng et al.   NATURE BIOTECHNOLOGY

Highly accurate inverse consistent registration: A robust approach

(2010) Martin Reuter et al.   NEUROIMAGE

An MRI-based atlas and database of the developing mouse brain

(2010) Nelson Chuang et al.   NEUROIMAGE

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

(2010) Brian B. Avants et al.   NEUROIMAGE

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

(2010) A. Li et al.   SCIENCE

Pattern Recognition Software and Techniques for Biological Image Analysis

(2010) Lior Shamir et al.   PLoS Computational Biology

elastix: A Toolbox for Intensity-Based Medical Image Registration

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

Correlations of Neuronal and Microvascular Densities in Murine Cortex Revealed by Direct Counting and Colocalization of Nuclei and Vessels

(2009) P. S. Tsai et al.   JOURNAL OF NEUROSCIENCE

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

(2009) Linda Madisen et al.   NATURE NEUROSCIENCE

A Review of Geometric Transformations for Nonrigid Body Registration

(2008) M. Holden   IEEE TRANSACTIONS ON MEDICAL IMAGING

Knife-edge scanning microscopy for imaging and reconstruction of three-dimensional anatomical structures of the mouse brain

(2008) D. MAYERICH et al.   JOURNAL OF MICROSCOPY

Effects of spatial transformation on regional brain volume estimates

(2008) John S. Allen et al.   NEUROIMAGE

High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice

(2008) A.E. Dorr et al.   NEUROIMAGE

Genetic Dissection of Neural Circuits

(2008) Liqun Luo et al.   NEURON

Non-rigid registration of multi-modal images using both mutual information and cross-correlation

(2007) A ANDRONACHE et al.   MEDICAL IMAGE ANALYSIS

Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain

(2007) B AVANTS et al.   MEDICAL IMAGE ANALYSIS