Localization and Registration of 2D Histological Mouse Brain Images in 3D Atlas Space

Method for counting labeled neurons in mouse brain regions based on image representation and registration

(2022) Songwei Wang et al.   MEDICAL & BIOLOGICAL ENGINEERING & COMPUTING

Brain-wide mapping reveals that engrams for a single memory are distributed across multiple brain regions

(2022) Dheeraj S. Roy et al.   Nature Communications

VIP-expressing interneurons in the anterior insular cortex contribute to sensory processing to regulate adaptive behavior

(2022) Arnau Ramos-Prats et al.   Cell Reports

SMART: An Open-Source Extension of WholeBrain for Intact Mouse Brain Registration and Segmentation

(2022) Michelle Jin et al.   eNeuro

Bi-channel Image Registration and Deep-learning Segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brain

(2021) Xuechun Wang et al.   eLife

Supervised Learning With Perceptual Similarity for Multimodal Gene Expression Registration of a Mouse Brain Atlas

(2021) Jan Krepl et al.   Frontiers in Neuroinformatics

Cross-modal coherent registration of whole mouse brains

(2021) Lei Qu et al.   NATURE METHODS

A Robust Image Registration Interface for Large Volume Brain Atlas

(2020) Hong Ni et al.   Scientific Reports

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

(2020) Quanxin Wang et al.   CELL

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

Automatic navigation system for the mouse brain

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

Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool

(2019) Maja A. Puchades et al.   PLoS One

Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)

(2019) Niklas Pallast et al.   JOURNAL OF NEUROSCIENCE METHODS

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

(2019) Yimin Wang et al.   Nature Communications

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

(2019) Asim Iqbal et al.   Scientific Reports

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

(2018) Rui Lin et al.   NATURE METHODS

Mapping Histological Slice Sequences to the Allen Mouse Brain Atlas Without 3D Reconstruction

(2018) Jing Xiong et al.   Frontiers in Neuroinformatics

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

Possum—A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections

(2015) Piotr Majka et al.   NEUROINFORMATICS

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

(2015) Yongsoo Kim et al.   Cell Reports

Automatic Registration of Mass Spectrometry Imaging Data Sets to the Allen Brain Atlas

(2014) Walid M. Abdelmoula et al.   ANALYTICAL CHEMISTRY

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Waxholm Space atlas of the Sprague Dawley rat brain

(2014) Eszter A. Papp et al.   NEUROIMAGE

Atlas-based automatic mouse brain image segmentation revisited: model complexity vs. image registration

(2012) Jordan Bai et al.   MAGNETIC RESONANCE IMAGING

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

(2012) Timothy Ragan et al.   NATURE METHODS

Cortical representations of olfactory input by trans-synaptic tracing

(2010) Kazunari Miyamichi et al.   NATURE

Automated cross-sectional and longitudinal hippocampal volume measurement in mild cognitive impairment and Alzheimer's disease

(2010) Kelvin K. Leung et al.   NEUROIMAGE