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Scalable Brain Atlas specifications


Unique identifier OMICS_24787
Name Scalable Brain Atlas
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


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Publication for Scalable Brain Atlas

Scalable Brain Atlas citations


The Brain/MINDS 3D digital marmoset brain atlas

Sci Data
PMCID: 5810420
PMID: 29437168
DOI: 10.1038/sdata.2018.9

[…] ed as the standard reference). Digital versions of the cortical regions (for one hemisphere) of the Paxinos et al. atlas can be found at a number of sites online, e.g. Majka and Kowalski, or from The Scalable Brain Atlas website (Bakker et al.). The original Nissl histology images are also available online at Tokuno et al.. The cortical parcellation and subsampled Nissl data can be downloaded as s […]


Building the Ferretome

Front Neuroinform
PMCID: 4861729
PMID: 27242503
DOI: 10.3389/fninf.2016.00016

[…] to extract data of all modalities (including computed brain maps relations) in a variety of formats in order to integrate well with analysis and simulation platforms and (online) atlases, such as the Scalable Brain Atlas (). The export of connectivity data in XML and JSON formats is already available and more formats are planned. Integration with atlases will be useful not only for visualization, […]


Characterizing blood–brain barrier perturbations after exposure to human triglyceride‐rich lipoprotein lipolysis products using MRI in a rat model

Magn Reson Med
PMCID: 4838551
PMID: 26485349
DOI: 10.1002/mrm.25985

[…] s were placed supine on a custom made Plexiglas stage. The stage and rat were then placed into a 72‐mm radio frequency probe inside the 7T magnet centering 2 mm rostral to the bregma [slice 44 in the Scalable Brain Atlas ]. A previously described rapid‐acquisition refocused‐echo (RARE) sequence was used to create T1 maps . In brief, images were captured using a 64‐mm field‐of‐view with a matrix of […]


Dynamic Data Visualization with Weave and Brain Choropleths

PLoS One
PMCID: 4587848
PMID: 26418012
DOI: 10.1371/journal.pone.0139453

[…] We chose a mapping format, GeoJSON, as the image format for our brain atlas. An alternative image format, the general-purpose scalable vector graphic (SVG), has been used successfully in the Scalable Brain Atlas [,]. GeoJSON and SVG are both human readable vector graphics formats well suited to the web. They are based on different data interchange formats: JavaScript Object Notation (JSON […]


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

[…] Examples of reconstructions based on these volumetric datasets are shown in Fig. . Fig. 11The last group of available CAF datasets were created using interoperability with the Scalable Brain Atlas. Three Scalable Brain Atlas templates were converted into CAF: Paxinos Rhesus Monkey atlas (PHT00, Paxinos et al. ()), NeuroMaps Macaque atlas (DB08, Wu et al. ()) and Waxholm Spa […]


Knowledge Synthesis with Maps of Neural Connectivity

Front Neuroinform
PMCID: 3205380
PMID: 22053155
DOI: 10.3389/fninf.2011.00024

[…] mapping systems includes several notable development efforts from large, well-supported teams such as Elsevier’s Brain Navigator, the International Neuroinformatics Coordinating Facility’s (INCF’s) “Scalable Brain Atlas” system, the Allen Institute’s Mouse, and Human Brain Atlases, The University of California, Los Angeles (UCLA) Laboratory of NeuroImaging’s (LONI) Mouse Brain Atlasing Toolkit (M […]


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Scalable Brain Atlas institution(s)
Department of Neuroinformatics, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen, Nijmegen, Netherlands; Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), Jülich Research Centre and JARA, Jülich, Germany; Centre for Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
Scalable Brain Atlas funding source(s)
Supported by the International Neuroinformatics Coordinating Facility (INCF) and the Donders Institute for Brain, Cognition and Behaviour of the Radboud University and UMC Nijmegen.

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