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IgorTatarnikov merged 1 commit into from
Aug 12, 2026
Merged

provide ng links for ccfv2 mouse atlases which are now on s3 #540

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6 changes: 6 additions & 0 deletions docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md
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Expand Up @@ -477,6 +477,8 @@ reference is an average template based on serial two-photon tomography, and is m
Available versions:
* `ccfv2_mouse_25um`

[![View in neuroglancer](https://img.shields.io/badge/Neuroglancer-View%20atlas-blue)](https://neuroglancer-demo.appspot.com/#!https://brainglobe.s3.amazonaws.com/ng_state_files/ccfv2_mouse.json)

### [Allen CCFv2 Mouse Fiber Tracts Atlas](https://doi.org/10.1038/nature13186)
This is a mouse brain fiber tract atlas using version 2 of the commonly used Allen Common Coordinate Framework. Where
the CCFv2 Mouse Brain atlas only provides information on the grey matter and ventricular systems of the mouse brain,
Expand All @@ -488,6 +490,8 @@ the original Nissl template.
Available versions:
* `ccfv2_fiber_mouse_25um`

[![View in neuroglancer](https://img.shields.io/badge/Neuroglancer-View%20atlas-blue)](https://neuroglancer-demo.appspot.com/#!https://brainglobe.s3.amazonaws.com/ng_state_files/ccfv2_fiber_mouse.json)

### [Allen CCFv2 Developmental Mouse Brain Atlas](https://doi.org/10.1038/nature13186)
This is a developmental mouse brain atlas using version 2 of the commonly used Allen Common Coordinate Framework.
The template is based on 528 Nissl-stained coronal slices from the mouse specimen used in the Allen Reference Atlas.
Expand All @@ -498,6 +502,8 @@ misaligned with the original Nissl template.
Available versions:
* `ccfv2_dev_mouse_25um`

[![View in neuroglancer](https://img.shields.io/badge/Neuroglancer-View%20atlas-blue)](https://neuroglancer-demo.appspot.com/#!https://brainglobe.s3.amazonaws.com/ng_state_files/ccfv2_dev_mouse.json)

## Rat
### [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3)
The Waxholm Space rat brain atlas features annotations of 222 structures, alongside a 39μm MRI template. It provides detailed delineations
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