Atlas & Template

Database

• • BrainMap: search papers by brain coordinate for meta-analysis

• • Scalable Brain Atlas, INCF: mouse, macaque, human

  • LONI Atlases: human, monkey, rat, mouse, mouse neonate

Human brain

• • Multi-modal Parcellation of Human Cerebral Cortex into 180 areas based on HCP data

  • Excellent collection of cortical and subcortical atlas by Lead DBS

  • Harvard Ascending Arousal Network Atlas

  • Cerebellum atlases

  • NextBrain: histology-driven brain MRI segmentation into 330+ regions.

  • Julich Atlas: histology atlas.

Human brain: Developmental Atlas

• • UNC Infant 0-1-2 Atlases

  • USC Neurodevelopmental MRI Database: span from infant to adult, including a lot of time points in 0 to 5 years old.

  • MNI 0 - 4.5y: T1w, T2w, PDw but no segmented tissue.

  • Imperial College: T1w, T2w, probabilistic atlas from fetal, neonate to pediatric.

Human brain: Connectivity Atlas

• • Susumu Mori's Lab, Johns Hopkins

  • DTI Atlas of Human Brain (online)

  • Functional connectivity parcellation (cortex) and striatum and cerebellum by Thomas Yeo

  • Functional ROI of whole brain by Craddock, HBM 2012 -- suitable for whole brain seed point analysis

  • Functional network ROI by Greicius (FIND lab) in Stanford

Non-human primate brain

• • MNI Macaque Atlas: average of 25 normal adult MRI with Paxions label. No tissue segmented.

  • 3D Template Atlas of Macaque Brain: highly detailed MRI atlas with 3D and surface mapping.

  • UNC primate brain: aged 16-34 months. T1-weighted MRI and tissue segmentation probability maps.

  • BrainInfo: labeled atlas template

  • BrainMap: labeled histology atlas

  • PRIMatE Data Exchange: open NHP imaging resource

Rabbit brain

• • Rabbit Brain Atlas

Rat brain

• • Rat brain template only template, no label. (Karolinska Institutet, Sweden)

  • OSF rat brain template: ex vivo MRI Wistar rat brain template with correct GM, WM, CSF segmentation. No label.

  • Wistar rat brain template in vivo T2w MRI with GM, WM, CSF probabilistic segmented and 48 cortical areas labelled (Tohoku Univ, Japan). *NOTE: the WM segment is wrong.

  • Sprague Dawley rat brain ex vivo T2*w MRI and DTI atlas in Waxholm & Stereotaxic Space with 79 regions labelled (no cortical label). 

  • Rodent Brain Workbench: various regional atlas (histology based) and connectivity atlas (Univ Oslo, Norway)

  • 3D DTI rat brain template: P5, P15 & adult

Mouse brain

• • Allen Brain Atlas: The most comprehensive atlas, including gene expression, connectivity, development

    • Methods for download ABA atlas data

    • Download and manipulate ABA Mouse Connectivity

    • Download template and annotation image files.  

    • Allen Brain Explorer

  • AMBMC Atlas: A detailed atlas compatible with the Paxinos and Watson's stereotaxic atlas (made by Australian Mouse Brain Mapping Consortium (AMBMC) together with Prof Watsons).

  • Mouse Connectome Project: 3D atlas of >240 intracortical connection mapped.

  • Whole-Brain Cellular Connectomics: cellular-level circuitry.

  • MouseLight: whole brain cellular circuit by Janelia Farm.

  • Blue Brain Cell Atlas: cellular-level whole brain atlas.

  • Mouse Brain Architecture: mesoscale connectivity and cell type mapping by Cold Spring Harbor Laboratory.

  • Mouse MRI Atlas (Mouse Imaging Center, Toronto Centre for Phenogenomics)

    • includes Variational Brain Atlas, Cerebral Vascular Atlas, & Neuroanatomy Atlas of the C57Bl/6j Mouse

  • SPMmouse

  • CT-MRI Stereotaxic Mouse Atlas (Lab of Brain Anatomical MRI, Johns Hopkins Medical Institute)

    • A developmental atlas of C57BL6 mice from neonate to adult. Segmented brain included.

  • The mouse brain proteome

Whole-body Atlas

• • The Visible Mouse

  • Digimouse: 3D atlas based on cryosection, CT and PET