Example Atlas Assets

This page shows example atlas assets currently available in the Allen Atlas Assets repository, illustrating how the naming conventions and organizational structure apply 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 that ABA was 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