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Allen Brain Atlas specifications


Unique identifier OMICS_03301
Name Allen Brain Atlas
Restrictions to use None
Maintained Yes


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus


  • person_outline Susan M. Sunkin

Publication for Allen Brain Atlas

Allen Brain Atlas citations


modCHIMERA: a novel murine closed head model of moderate traumatic brain injury

Sci Rep
PMCID: 5955903
PMID: 29769541
DOI: 10.1038/s41598-018-25737-6

[…] a Nikon Eclipse 80i epifluorescent microscope (Nikon Corporation, Tokyo, Japan) at 20× magnification. Bilateral hippocampi were analyzed from 3 sections per animal between Bregma −1.55 and −2.155 mm (Allen Brain Atlas, Allen Institute, Seattle, Washington, USA). For analysis of atrophy at 30 days post-injury (dpi), semi-automated thresholding was applied with ImageJ/FIJI to cresyl violet-stained s […]


A PCR Based Method for RNA Probes and Applications in Neuroscience

Front Neurosci
PMCID: 5942160
PMID: 29770110
DOI: 10.3389/fnins.2018.00266

[…] cific sequences containing both the RNA polymerase promoter and target DNA sequences, we designed two pairs of primers. The pairs of primer were obtained using NCBI's Primer Blast program or from the Allen Brain Atlas, and these were used to generate RNA probes for SST (391 nt corresponding to nucleotide 138–528, NM_009215.1), NPSR1 (741 nt corresponding to nucleotide 1897–2637, NM_175678.2), and […]


Structural covariance networks are coupled to expression of genes enriched in supragranular layers of the human cortex

PMCID: 5883331
PMID: 29274746
DOI: 10.1016/j.neuroimage.2017.12.060

[…] pection due to spatial distortions being introduced by coregistration of donors' brains to standard MNI-152 space. In this work, we provide a fully automated method for matching MRI parcellation with Allen Brain Atlas samples in each donor's native space in order to take into account inter-individual difference of cortical morphology. […]


Influence of full length dystrophin on brain volumes in mouse models of Duchenne muscular dystrophy

PLoS One
PMCID: 5877835
PMID: 29601589
DOI: 10.1371/journal.pone.0194636
call_split See protocol

[…] mplate brain, volumes of interest (VOIs) for the whole brain and 22 anatomical structures were manually segmented based on the Waxholm mouse brain atlas [], the Franklin and Paxinos atlas [,] and the Allen Brain Atlas [] using AMIRA (v5, FEI Software, Oregon, USA) []. Next to this, the 22 anatomical structures were either classified as white or grey matter, according to . The whole brain volume wa […]


An Ontology Systems Approach on Human Brain Expression and Metaproteomics

Front Microbiol
PMCID: 5852110
PMID: 29568289
DOI: 10.3389/fmicb.2018.00406

[…] ences (RefSeq-prot) database was downloaded from the NCBI ftp server (see Figure , data “RefSeq-prot”). Also, post-mortem human brain RNA-sequencing dataset (donor H0351.2001) was downloaded from the Allen Brain Atlas web page (see Figure , data “Allen exp.”), which contains three or four replicates per brain substructure.The metaproteome files were merged at the genus level to generate a single n […]


Foxj1 expressing ependymal cells do not contribute new cells to sites of injury or stroke in the mouse forebrain

Sci Rep
PMCID: 5789075
PMID: 29379049
DOI: 10.1038/s41598-018-19913-x

[…] e in each group (five sections containing intact olfactory bulbs, 20× objective, 1024 × 1024 resolution, 0.62 µm per pixel). DAPI counterstain was used to delineate architectonic boundaries using the Allen Brain Atlas P56 mouse sagittal reference panels ( Counting was conducted in ImageJ using the Cell Counter plugin (ImageJ, US National Institutes of Heal […]


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Allen Brain Atlas institution(s)
Allen Institute for Brain Science, Seattle, WA, USA

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