ALLEN HUMAN REFERENCE ATLAS - 3D, 2020
The Allen Human Reference Atlas - 3D is a parcellation of the adult human brain in 3D, labeling every voxel with a brain structure spanning 141 structures. These parcellations were drawn by Song-Lin Ding, and adapted from his prior 2D version of an adult human brain atlas.
A 2D sagittal cross-section overlaid on MNI space and 3D medial and lateral rendering of the new human parcellation volume visualized using ITK-SNAP application.
Example python scripts have been included to demonstrate:
- how to download structure information and ontology from the Allen Brain API
- use of the annotation volume in context of a hierarchical ontology
- creation of ITK-SNAP compatible files to visualize the parcellation in 2D and 3D
Citation of these materials should conform to the Allen Institute Citation Policy: https://alleninstitute.org/legal/citation-policy/
Allen Human Reference Atlas - 3D, 2020 Citation information:
|Resource Name:||Allen Human Reference Atlas – 3D, 2020|
|Research Resource Identifier (RRID):||RRID:SCR_017764|
|Copyright notice:||© 2019 Allen Institute for Brain Science|
|Dataset citation:||Song‐Lin Ding, Joshua J. Royall, Susan M. Sunkin, Benjamin A.C. Facer, Phil Lesnar, Amy Bernard, Lydia Ng, Ed S. Lein (2020). “Allen Human Reference Atlas – 3D, 2020," RRID:SCR_017764, version 1.0.0.|
The anatomic structure ontology adapted for use in the 3D atlas was based on the 2016 version of the 2D atlas, published in final form here.
|Publication Citation for structure ontology:||Ding, S.L., Royall, J.J., […], Lein, E.S. Comprehensive cellular‐resolution atlas of the adult human brain. Journal of Comparative Neurology, Volume 524:16, pages 3127–3481, 1 November 2016, DOI 10.1002/cne.24080.|
These materials are provided as-is, without direct support. Community discussion around this resource is available here at https://community.brain-map.org/.
Creation of the 3D parcellation volume was supported by the Allen Institute for Brain Science, and by the National Institute of Mental Health under Award Number 1U01MH114812-01 (PI: Ed Lein, Allen Institute for Brain Science).
The 2D atlas and anatomic structural ontology upon which it was based was supported by the Allen Institute for Brain Science, and by the National Institute of Mental Health under Award Number RC2MH089921 (PIs: Ed Lein & Michael Hawrylycz, Allen Institute for Brain Science).