Introduction
Web-Based Interactive Brain Atlas
Core Features of the SBA
Methods
Importing Atlases into the SBA
Template | Title | Primary publication/site | Parcellation | Imaging modalities |
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Mouse | ||||
ABA2012 | Allen Mouse Brain 2012 | Dong (2008) | 667 areas incl. layer subdivision | Nissl |
WHS12 | Waxholm Space atlas 2012 | Johnson et al. (2010) | 39 areas | Nissl and 21.5 μm resolution MR (T1, T2w, T2*) |
Rat | ||||
PLCJB14 | Waxholm space Sprague Dawley reference atlas | Papp et al. (2014) | 97 areas (neocortex = 1 area) | 39 μm T2*, DTI, DWI, fractional anisotropy |
CBWJ13_age_P80 | MR-Histology atlas at postnatal day 80 | Calabrese et al. (2013) | 27 areas | 25 μm resolution MR (T2*/GRE) |
VSNetal11 | Wistar rat in vivo MRI template | Valdés-Hernández et al. (2011) | 129 cortical areas | T2w, white/gray matter, csf |
RMJetal13_age_P72 | DTI Atlas of the Rat Brain (age P72) | Rumple et al. (2013) | 29 areas | 160 μm DTI |
VLAetal11 | Population-averaged DTI atlas | Veraart et al. (2011) | 14 areas | T1w, DWI, FA |
Marmoset | ||||
PWPRT12 | Marmoset Cortical structures provided by M. Rosa | Paxinos et al. (2012) | 116 cortical areas | Nissl, plus seven other stains via marmoset-brain.org |
Macaque | ||||
PHT00 | Rhesis monkey in stereotaxic coordinates | Paxinos, Huang, Toga (2000) | 283 areasa: cortex, amygdala, thalamus, striatum | – |
DB08 | NeuroMaps Macaque atlas | Dubach, Bowden (2009) | 384 anatomically defined areas | T1 |
FVE91_on_F99b
| Felleman and Van Essen 1991 in F99 space | Felleman and Van Essen (1991) | 73 cortical areas | T1 |
LVE00_on_F99b
| Lewis and Van Essen 2000 in F99 space | Lewis, Van Essen (2000) | 87 cortical areas | T1 |
MMFetal11_on_F99b
| Markov et al. 2011 in F99 space | Markov et al. (2011) | 81 cortical areas | T1 |
MERetal12_on_F99b
| Markov et al. 2012 in F99 space | Markov et al. (2012) | 93 cortical areas | T1 |
RM_on_F99b
| Regional Map in F99 space | Kötter and Wanke (2005) | 41 anatomical areas | T1 |
Opossum | ||||
OPSM14 | Multimodal atlas of gray short-tailed opossum brain | 105 areas (neocortex = 1 area) | ||
Human | ||||
EAZ05 | JuBrain cytoarchitectonic parcellation | Eickhoff et al. (2005) | 76 cyto-architectonic areas | averaged MRI template |
LPBA40_on_SRI24 | LBPA40 areas in SRI24 space | SRI24: Rohlfing et al. (2010) LBPA40: Shattuck et al. (2008) | 56 cortical areas incl. Left/Right division | T1w, T2w, rho |
B05_on_Conte69 | Brodmannd areas in Conte69 space | Glasser and Van Essen (2011) | 47 Brodmann cortical areas | T1w, T2w, T1w/T2w |
BIGB13 | Bigbrain, resampled at 400 μm | Amunts et al (2013) | – | Nissl, resampled at 400 μm |
Creating Interactive SVG-Based Webpages
Creating Plugins
Bilateral Client-Server Communication
Creating Services
Imported Atlas Templates
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is publicly accessible
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is described in a peer-reviewed publication
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contains both a brain parcellation and underlying data modality
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is part of a resource that contains valuable neuroscience data
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is (becoming) a standard reference space
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is available in parseable format (NIfTI-1, CAF)
Citation Policy
Waxholm Space
Services
Atlas Viewer (Main/Coronal3d.php)
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region (the brain region to highlight). It is first matched with the list of region abbreviations that comes with the template. If that fails, the alias list is search, then the full names, and finally a case-insensitive match is tried.
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plugin (the plugin to activate). If the plugin starts with http:// or https://, it is assumed that an external plugin is intended. External plugins must be white listed to prevent abuse.
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underlay2d (the image modality to display in the slice panel).