Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Jun 28, 2026

Whole-Brain 3D Activation and Functional Connectivity Mapping in Mice using Transcranial Functional Ultrasound Imaging

Whole-Brain 3D Activation and Functional Connectivity Mapping in Mice using Transcranial Functional Ultrasound Imaging

Published on: February 24, 2021

Three-dimensional atlas system for mouse and rat brain imaging data.

Trine Hjornevik¹, Trygve B Leergaard, Dmitri Darine

¹Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo Norway.

Frontiers in Neuroinformatics

|November 1, 2008

Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Improved multimodal prediction of progression from MCI to Alzheimer's disease combining genetics with quantitative brain MRI and cognitive measures.

Alzheimer's & dementia : the journal of the Alzheimer's Association·2023

Same author

Childhood Disadvantage Moderates Late Midlife Default Mode Network Cortical Microstructure and Visual Memory Association.

The journals of gerontology. Series A, Biological sciences and medical sciences·2023

Same author

Heritability Estimation of Cognitive Phenotypes in the ABCD Study<sup>®</sup> Using Mixed Models.

Behavior genetics·2023

Same author

Task fMRI paradigms may capture more behaviorally relevant information than resting-state functional connectivity.

NeuroImage·2023

Same author

Identification of novel genomic risk loci shared between common epilepsies and psychiatric disorders.

Brain : a journal of neurology·2023

Same author

A Multicompartmental Diffusion Model for Improved Assessment of Whole-Body Diffusion-weighted Imaging Data and Evaluation of Prostate Cancer Bone Metastases.

Radiology. Imaging cancer·2023

This study introduces a method to create 3D rodent brain atlases from 2D diagrams, improving anatomical localization for neuroimaging like PET and MRI. The developed tool aids in analyzing and visualizing brain structures in experimental data.

Area of Science:

Neuroscience
Medical Imaging
Computational Biology

Background:

Tomographic neuroimaging (PET, MRI) visualizes rodent brain signals but often lacks structural detail for accurate anatomical localization.
Interpreting low-resolution, low-contrast images is challenging due to the limitations of 2D atlases and the absence of integrated analytical environments.
Accurate anatomical identification is crucial for understanding functional and structural signals in rodent brains.

Purpose of the Study:

To develop a method for reconstructing 3D rodent brain atlases from existing 2D atlas diagrams.
To create a versatile tool for analyzing and visualizing neuroimaging data within these 3D atlas spaces.
To enhance the assignment of anatomical locations and facilitate comparative analyses of signal data in tomographic neuroimaging.

Keywords:

3-D reconstruction atlas brain imaging magnetic resonance imaging positron emission tomography stereotaxic visualization

More Related Videos

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

Published on: September 5, 2018

Cerebrovascular Casting of the Adult Mouse for 3D Imaging and Morphological Analysis

Cerebrovascular Casting of the Adult Mouse for 3D Imaging and Morphological Analysis

Published on: November 30, 2011

Related Experiment Videos

Last Updated: Jun 28, 2026

Whole-Brain 3D Activation and Functional Connectivity Mapping in Mice using Transcranial Functional Ultrasound Imaging

Whole-Brain 3D Activation and Functional Connectivity Mapping in Mice using Transcranial Functional Ultrasound Imaging

Published on: February 24, 2021

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

Published on: September 5, 2018

Cerebrovascular Casting of the Adult Mouse for 3D Imaging and Morphological Analysis

Cerebrovascular Casting of the Adult Mouse for 3D Imaging and Morphological Analysis

Published on: November 30, 2011

Main Methods:

Reconstruction of 3D brain atlases from digital 2D stereotaxic atlas diagrams.
Development of a multi-platform software tool (The Rodent Workbench) for 3D atlas visualization and data integration.
Exemplification of 3D atlas-based analysis using Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) data.

Main Results:

Successful reconstruction of 3D atlases for 30 mouse and 60 rat brain structures.
A functional tool enabling combined visualization of experimental neuroimaging data within the 3D atlas space.
Facilitation of precise anatomical localization and comparative analysis for low-contrast neuroimaging datasets.

Conclusions:

The developed 3D atlas reconstruction method and associated software tool significantly improve anatomical referencing in rodent neuroimaging.
This approach addresses the limitations of 2D atlases and low-resolution imaging, enabling more accurate interpretation of functional and structural brain data.
The Rodent Workbench provides a valuable platform for integrative analysis of tomographic neuroimaging data in neuroscience research.