Waxholm Space Atlas of the Sprague Dawley Rat Brain

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Open access volumetric atlas of the Sprague Dawley rat brain. The delineations are defined in isotropic magnetic resonance (39 μm) and diffusion tensor (78 μm) images acquired ex vivo from an 80 day old male rat at the Duke Center for In Vivo Microscopy. Coordinates for navigating the volume are provided by the Waxholm Space coordinate system. The location of bregma and lambda are also identified as anchors towards stereotaxic space.

The atlas delineations and the MRI/DTI reference data are shared along with labels and configuration files for ITK-SNAP, the Mouse BIRN Atlasing Toolkit, and PMOD. The latest atlas version contains 222 structures. For more information, see MediaWiki.

The atlas has been adopted as the standard rat brain atlas for the EBRAINS infrastructure, see https://ebrains.eu/service/rat-brain-atl...

The atlas is shared under the CC BY 4.0 licence, see Citation for instructions on how to cite.

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Specifications

Category:
Atlas Data, Atlas Application
License:
Attribution
Diagnosis:
Amyotrophic Lateral Sclerosis, Brain Injuries, Huntington Disease, Parkinson Disease, Stroke
Domain:
MR, PET/SPECT
Funding Initiative:
Human Brain Project (Europe)
Operating System:
OS Independent
Supported Data Format:
NIfTI-1
Other Keywords:
DTI, MRI, Template, Volumetric atlas, Waxholm Space

Associations

images available at:
Scalable Brain Atlas
works well with:
CutNII - Custom-angle slicer for brain atlas volumes
ITK-SNAP
MeshGen - Surface meshes from volumetric segmentation data
MouseBIRN Atlasing Toolkit (MBAT)
QuickNII - Serial section aligner to volumetric atlases
VisuAlign - Nonlinear adjustments after QuickNII
MeshView for brain atlases
QCAlign - quality control for the QUINT workflow

Statistics more information

Home Page

RRID: SCR_017124

Funding:

Supported by the HBP Neuroinformatics Platform funded from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreements Nos. 720270 and 785907 (Human Brain Project) and The Research Council of Norway. MR imaging was performed at the Duke Center for In Vivo Microscopy, a NIH/NCRR National Biomedical Technology Research Center (P41 EB015897) and Small Animal Imaging Resource Program (U24 CA092656) member.

Documents: 12

PubMed Mentions: 25

Forums: 44 messages in 1 forum

News Items: 0

Total Downloads: 37162

Registered: Nov 22, 2016

Organization: University of Oslo

Center: Neural Systems Laboratory, Institute of Basic Medical Sciences

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