Example Atlas Assets

This page provides examples of actual atlas assets currently available in the Allen Atlas Assets repository, showing how the naming conventions and organization structure are applied in practice.

s3://allen-atlas-assets/
├── annotation-sets/
│   ├── allen-adult-mouse-annotation/
│   │   ├── 2011/  # 2D ABA drawings aligned to 3D nissl template
│   │   ├── 2015/  # 3D drawings on 2p template ("ccfv1")
│   │   ├── 2016/  # 3D drawings on 2p template ("ccfv2")
│   │   ├── 2017/  # 3D drawings on 2p template ("ccfv3")
│   │   └── 2020/  # 2017 drawings with new ontology identifiers ("ccf 2020")
│   │
│   ├── allen-adult-mouse-spim-lca-annotation/
│   │   └── 2024-05/  # ccfv3 drawings aligned to smartspim template
│   │
│   └── allen-dev-p56-mouse-annotation/
│       └── 2012/  # 2D devmouse drawings aligned to nissl template
│
├── templates/
│   ├── allen-adult-mouse-stpt-template/
│   │   └── 2015/  # the tissuecyte template, used in all "CCFs"
│   │
│   ├── allen-adult-mouse-nissl-template/
│   │   └── 2011/  # the coregistered 3D nissl slices ABA was all aligned to
│   │
│   └── allen-adult-mouse-spim-lca-template/
│       └── 2024-05/  # the SmartSPIM template in production now
│
├── coordinate-transformations/
│   └── allen-adult-mouse-spim-lca-2024-05_to_allen-adult-mouse-stpt-2015/
│       └── 2024-05/  # transformation between SmartSPIM template and 2p template
│
├── coordinate-spaces/
│   ├── allen-adult-mouse-ccf-space/
│   │   ├── 2011/
│   │   └── 2015/
│   │
│   └── allen-adult-mouse-ccf-stereotaxic-space/
│       └── 2020/
│
├── atlases/
│   ├── allen-adult-mouse-ccf-atlas/
│   │   ├── 2011/  # nissl template 2011, 2017 ontology, 2011 annotations
│   │   ├── 2015/  # 2p template 2015, 2017 ontology, 2015 annotations (CCFv1)
│   │   ├── 2016/  # 2p template 2015, 2017 ontology, 2016 annotations (CCFv2)
│   │   └── 2017/  # 2p template 2015, 2017 ontology, 2017 annotations (CCFv3)
│   │
│   ├── allen-adult-mouse-ccf-stereotaxic-atlas/
│   │   └── 2020/  # 2p template 2015, 2020 ontology, 2020 annotations (CCF 2020)
│   │
│   └── allen-dev-mouse-atlas/
│       └── 2012/  # nissl template 2011, 2012 devmouse ontology, 2012 annotations
│
└── terminologies/
    ├── allen-adult-mouse-terminology/
    │   ├── 2017/  # original ids (CCFv1-3)
    │   └── 2020/  # new ids (CCF2020)
    │
    └── allen-dev-mouse-terminology/
        └── 2012/  # puelles taxonomy