Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

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

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

The Human Brain Project—Synergy between neuroscience, computing, informatics, and brain-inspired technologies

(2019) Katrin Amunts et al.   PLOS BIOLOGY

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

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

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

Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging

(2019) Kirsten K. Osen et al.   NEUROIMAGE

QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain

(2019) Sharon C. Yates et al.   Frontiers in Neuroinformatics

Data integration through brain atlasing: Human Brain Project tools and strategies

(2018) Ingvild E. Bjerke et al.   EUROPEAN PSYCHIATRY

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

(2018) Jing Xiong et al.   Frontiers in Neuroinformatics

An interactive framework for whole-brain maps at cellular resolution

(2017) Daniel Fürth et al.   NATURE NEUROSCIENCE

Development of a 2D Image Reconstruction and Viewing System for Histological Images from Multiple Tissue Blocks: Towards High-Resolution Whole-Organ 3D Histological Images

(2016) Noriaki Hashimoto et al.   PATHOBIOLOGY

High-throughput 3D whole-brain quantitative histopathology in rodents

(2016) Michel E. Vandenberghe et al.   Scientific Reports

Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging

(2015) Lisa J. Kjonigsen et al.   NEUROIMAGE

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

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Common Atlas Format and 3D Brain Atlas Reconstructor: Infrastructure for Constructing 3D Brain Atlases

(2012) Piotr Majka et al.   NEUROINFORMATICS

HistoStitcher©: An interactive program for accurate and rapid reconstruction of digitized whole histological sections from tissue fragments

(2011) Jonathan Chappelow et al.   COMPUTERIZED MEDICAL IMAGING AND GRAPHICS

Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy

(2009) Jason W. Bohland et al.   METHODS