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Waxholm Space specifications


Unique identifier OMICS_24765
Name Waxholm Space
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • Rodents
    • Mus musculus


  • person_outline Allan Johnson

Additional information

Users have to contact the maintainer to access this atlas.

Publication for Waxholm Space

Waxholm Space citations


Longitudinal investigation of neuroinflammation and metabolite profiles in the APP swe×PS1Δe9 transgenic mouse model of Alzheimer's disease

PMCID: 5846890
PMID: 29124761
DOI: 10.1111/jnc.14251

[…] st (ROI)‐opt method. Dynamic PET images were analysed using Brainvisa and Anatomist software (http://brainvisa.info/web/index.html) and quantified using the magnetic resonance imaging (MRI) template (Waxholm space) created by Johnson et al. (). This MRI mouse brain template was used to create three brain ROIs (all cortical areas and whole hippocampus, subcortical regions and cerebellum) large enou […]


Mapping and Analysis of the Connectome of Sympathetic Premotor Neurons in the Rostral Ventrolateral Medulla of the Rat Using a Volumetric Brain Atlas

Front Neural Circuits
PMCID: 5331070
PMID: 28298886
DOI: 10.3389/fncir.2017.00009

[…] o the Biorad format in ImageJ. Each segmented area was individually rendered using the Imaris “contour surface” function, resulting in a surface-rendered model that incorporates regions demarcated in Waxholm space. Tabulated Waxholm coordinates of Input, non-C1 starter, and C1 starter neurons were then imported using a Python script (“CreateSpotsFromFile,” http://open.bitplane.com/tabid/235/Defaul […]


Was it a pain or a sound? Across species variability in sensory sensitivity

PMCID: 4764020
PMID: 26270592
DOI: 10.1097/j.pain.0000000000000316

[…] ry somatosensory cortex (S1). The locations of the forelimb and hindlimb S1 were determined using the 3D Paxinos and Watson atlas of the rat brain, and displayed on the 3D brain mask surface from the Waxholm Space atlas of the rat brain., […]


Web tools for large scale 3D biological images and atlases

BMC Bioinformatics
PMCID: 3412715
PMID: 22676296
DOI: 10.1186/1471-2105-13-122

[…] between the two marked points. In Figure b we show the multi-channel display capability of the IIP3D viewer. For this example we have used the set of five 3D reconstructed images that are part of the Waxholm space atlas standard. These are three MR images (T2*, T2 weighted, T1), stained histology and a labelled tissue segmentation. Applications currently available are not able to simultaneously di […]


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

PMCID: 3325030
PMID: 22227717
DOI: 10.1007/s12021-011-9138-6

[…] at the INCF Software Center (http://software.incf.org/software/waxholm-space) and was extended with a simple hierarchy. Reconstructions created by 3dBAR using this template are also localized in the Waxholm Space spatial reference system.Another dataset derived from a volumetric source atlas is the average-shape atlas of the honeybee brain (Brandt et al. ) created using confocal imaging of 20 spe […]


An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

Front Neuroinform
PMCID: 3254174
PMID: 22275894
DOI: 10.3389/fninf.2011.00026
call_split See protocol

[…] 4 mm, and −18.07 to 13.81 mm, respectively. The origin (anterior commissure) and orientation of the coordinate system is very similar to the convention established in (Hawrylycz et al., ), i.e., the “Waxholm space.” Voxel size (isotropic 1.25 mm3) is the actual value multiplied by 10 to make images usable in standard human software like SPM, i.e., 1 mm means 100 μm. The orientation of the images i […]


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Waxholm Space institution(s)
Duke Center for In Vivo Microscopy, Radiology, Duke University Medical Center, Durham, NC, USA; Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, USA; Department of Basic Sciences, Touro University Nevada, Henderson, NV, USA
Waxholm Space funding source(s)
Supported by the Mouse Biomedical Informatics Research Network (MBIRN) (U24 RR021760) and the International Neuroinformatics Coordinating Facility (INCF).

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