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Add vole atlas and add api atlas names to table (#256)
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adamltyson authored Oct 31, 2024
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35 changes: 18 additions & 17 deletions docs/source/documentation/brainglobe-atlasapi/index.md
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A number of atlases are in development, but those available currently are:

| Atlas Name | Resolution | Ages | Reference Images |
|----------------------------------------------------------------------------------------------------------------------------|----------------------------|-----------------------------------|--------------------------------------------------------|
| [Allen Mouse Brain Atlas](https://doi.org/10.1016/j.cell.2020.04.007) | 10, 25, 50, and 100 micron | P56 | STPT |
| [Allen Human Brain Atlas](https://www.brain-map.org) | 100 micron | Adult | MRI |
| [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) | 1 micron | 6-dpf | FISH |
| [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) | 10, 25, 50, and 100 micron | P56 | STPT |
| [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) | 10, 25, 50 and 100 micron | P56 | STPT |
| [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) | 20 micron | 8 to 10 weeks post natal | LSFM |
| [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) | 20 x 10 x 10 micron | Adult | Nissl |
| [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) | 4 micron | 15-16 weeks post natal | LSFM |
| [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3) | 39 micron | P80 | MRI |
| [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) | 16, 16.75, and 25 micron | E13, E15, E18, P4, P14, P28 & P56 | Nissl |
| [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) | 20 micron | >P56 (older animals included) | LSFM |
| [Kim Lab Developmental CCF](https://data.mendeley.com/datasets/2svx788ddf/1) | 10 micron | P56 | STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2) |
| [Blind Mexican Cavefish Brain Atlas](https://doi.org/10.7554/eLife.80777) | 2 micron | 6-dpf | IHC |
| [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) | 10 and 25 micron | P56 | STPT |
| [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3) | 40 micron | ~ 3 months post hatching | MRI |
| Atlas Name | Resolution | Ages | Reference Images | Name in API
| --- | --- | --- | --- | --- |
| [Allen Mouse Brain Atlas](https://doi.org/10.1016/j.cell.2020.04.007) | 10, 25, 50, and 100 micron | P56 | STPT | allen_mouse_10um, allen_mouse_25um, allen_mouse_100um
| [Allen Human Brain Atlas](https://www.brain-map.org) | 500 micron | Adult | MRI | allen_human_500um
| [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) | 1 micron | 6-dpf | FISH | mpin_zfish_1um
| [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) | 10, 25, 50, and 100 micron | P56 | STPT | kim_mouse_10um, kim_mouse_25um, kim_mouse_50um, kim_mouse_100um
| [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) | 10, 25, 50 and 100 micron | P56 | STPT | osten_mouse_10um,osten_mouse_25um, kim_mouse_50um, kim_mouse_100um
| [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) | 20 micron | 8 to 10 weeks post natal | LSFM | perens_lsfm_mouse_20um
| [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) | 20 x 10 x 10 micron | Adult | Nissl | allen_cord_20um
| [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) | 4 micron | 15-16 weeks post natal | LSFM | azba_zfish_4um
| [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3) | 39 micron | P80 | MRI | whs_sd_rat_39um
| [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) | 16, 16.75, and 25 micron | E13, E15, E18, P4, P14, P28 & P56 | Nissl | admba_3d_e11_5_mouse_16um, admba_3d_e13_5_mouse_16um, admba_3d_e15_5_mouse_16um, admba_3d_e18_5_mouse_16um, admba_3d_p14_mouse_16.752um, admba_3d_p28_mouse_16.752um, admba_3d_p4_mouse_16.752um, admba_3d_p56_mouse_25um
| [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) | 20 micron | >P56 (older animals included) | LSFM | princeton_mouse_20um
| [Kim Lab Developmental CCF](https://data.mendeley.com/datasets/2svx788ddf/1) | 10 micron | P56 | STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2) | kim_dev_mouse_stp_10um, kim_dev_mouse_idisco_10um, kim_dev_mouse_mri_a0_10um, kim_dev_mouse_mri_adc_10um, kim_dev_mouse_mri_dwi_10um, kim_dev_mouse_mri_fa_10um, kim_dev_mouse_mri_mtr_10um, kim_dev_mouse_mri_t2_10um
| [Blind Mexican Cavefish Brain Atlas](https://doi.org/10.7554/eLife.80777) | 2 micron | 6 days post fertilisation | IHC | sju_cavefish_2um
| [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) | 10 and 25 micron | P56 | STPT | allen_mouse_bluebrain_barrels_10um, allen_mouse_bluebrain_barrels_25um
| [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3) | 40 micron | ~ 3 months post hatching | MRI | unam_axolotl_40um
| [Prairie Vole Brain Atlas](https://doi.org/10.7554/eLife.87029.3.sa0) | 25 micron | Unknown | LSFM | prairie_vole_25um

## Installation

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19 changes: 13 additions & 6 deletions docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md
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* `kim_mouse_50um` - 50μm resolution
* `kim_mouse_100um` - 100μm resolution



### [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8)
This atlas from [Perens et al. (2020)](https://doi.org/10.1007/s12021-020-09490-8) provides a version of the Allen
Adult Mouse Brain Atlas, based on solvent-cleared brains imaged with LSFM. This atlas may be a
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This atlas is only available at 39μm resolution:
* `whs_sd_rat_39um`

## Other rodent
### [Prairie vole brain atlas](https://doi.org/10.7554/eLife.87029.3.sa0)
This is a brain atlas of the Prairie vole (Microtus ochrogaster) from
[Gustison et al. (2024)](https://doi.org/10.7554/eLife.87029.3.sa0).
This atlas is only available at 25μm resolution:
* `sju_cavefish_2um`

## Fish
### [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de)
### [Max Planck zebrafish brain atlas](http://fishatlas.neuro.mpg.de)
This atlas is only available at 1μm resolution:
* `mpin_zfish_1um`

### [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625)
### [AZBA: A 3D Adult zebrafish brain atlas](https://doi.org/10.1101/2021.05.04.442625)
This atlas is only available at 4μm resolution:
* `azba_zfish_4um`

### [Blind Mexican cavefish Brain Atlas](https://elifesciences.org/articles/80777)
### [Blind Mexican cavefish brain atlas](https://elifesciences.org/articles/80777)
This is a brain atlas of the blind Mexican cavefish (Astyanax mexicanus) from
[Kozol et al. (2023)](https://elifesciences.org/articles/80777). For more details please
see [the blogpost](/blog/cavefish-atlas-added).

This atlas is only available at 2μm resolution:
* `sju_cavefish_2um`




## Amphibian
### [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3)
This is a magnetic resonance imaging based atlas of the Axolotl (Ambystoma mexicanum) from
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