Reference Atlases

Cell Locator bundles the files associated with the reference atlases described below.

Allen Mouse Brain Common Coordinate Framework (CCF)

Version 3

Allen Mouse Brain Common Coordinate Framework (CCFv3) is a 3D reference space by creating an average brain at 10um voxel resolution from serial two-photon tomography images of 1,675 young adult C57Bl6/J mice.

Using multimodal reference data, the entire brain was directly parcellated in 3D, labeling every voxel with a brain structure spanning 43 isocortical areas and their layers, 314 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.

Allen Mouse Brain Common Coordinate Framework (CCFv3):

Details: https://community.brain-map.org/t/allen-mouse-ccf-accessing-and-using-related-data-and-tools/359
Research Resource Identifier (RRID): RRID:SCR_020999

Annotation Volume
Download	http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/
Filename	`annotation_25.nrrd`
Checksum (SHA256)	`c620cbcc562183e4dcd40250d440130501781f74b41de35b1c1bdabace290c42`

Reference Volume
Download	http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/average_template/
Filename	`average_template_25.nrrd`
Checksum (SHA256)	`e4a2b483e842b4c8c1b5452d940ea59e14bc1ebaa38fe6a9c3bacac6db2a8f4b`

Allen Human Reference Atlas - 3D

Version 1.0.0 (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.

Annotation Volume	`Allen Human Reference Atlas - 3D, 2020`
Version	1.0.0
Details	https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405
Research Resource Identifier (RRID)	RRID:SCR_017764
Download	http://download.alleninstitute.org/informatics-archive/allen_human_reference_atlas_3d_2020/version_1/
Filename	`mni_annotation_full.nii.gz`
Checksum (SHA256)	`2b05581e39c44f2623d9b0a69f64e3df0823c20d054abef92973812313335dc3`

These parcellations were drawn on the MRI reference brain volume “ICBM 2009b Nonlinear Symmetric”, a non-linear average of the MNI152 database of 152 normal brain images.

Reference Volume	`ICBM 152 Nonlinear Symmetric`
Version	2009b
Details & Download	https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
Filename	`mni_icbm152_t1_tal_nlin_sym_09b_hires.nii`
Checksum (SHA256)	`b2ca5ca7c94471f0ca77b64485c0d9655737b9029ec19ef7486ab89f1ce4bf79`