diff --git a/README.md b/README.md index edcdf7c6..e2acd5b4 100644 --- a/README.md +++ b/README.md @@ -23,21 +23,23 @@ The brainglobe atlas API (brainglobe-atlasapi) provides a common interface for p A number of atlases are in development, but those available currently are: -- [Allen Mouse Brain Atlas](https://doi.org/10.1016/j.cell.2020.04.007) at 10, 25, 50 and 100 micron resolutions -- [Allen Human Brain Atlas](https://www.brain-map.org) at 100 micron resolution -- [Max Planck Zebrafish Brain Atlas](http://fishatlas.neuro.mpg.de) at 1 micron resolution -- [Enhanced and Unified Mouse Brain Atlas](https://kimlab.io/brain-map/atlas/) at 10, 25, 50 and 100 micron resolutions -- [Smoothed version of the Kim et al. mouse reference atlas](https://doi.org/10.1016/j.celrep.2014.12.014) at 10, 25, 50 and 100 micron resolutions -- [Gubra's LSFM mouse brain atlas](https://doi.org/10.1007/s12021-020-09490-8) at 20 micron resolution -- [3D version of the Allen mouse spinal cord atlas](https://doi.org/10.1101/2021.05.06.443008) at 20 x 10 x 10 micron resolution -- [AZBA: A 3D Adult Zebrafish Brain Atlas](https://doi.org/10.1101/2021.05.04.442625) at 4 micron resolution -- [Waxholm Space atlas of the Sprague Dawley rat brain](https://doi.org/10.1038/s41592-023-02034-3) at 39 micron resolution -- [3D Edge-Aware Refined Atlases Derived from the Allen Developing Mouse Brain Atlases](https://doi.org/10.7554/eLife.61408) (E13, E15, E18, P4, P14, P28 & P56) -- [Princeton Mouse Brain Atlas](https://brainmaps.princeton.edu/2020/09/princeton-mouse-brain-atlas-links) at 20 micron resolution -- [Kim Lab Developmental CCF (P56)](https://data.mendeley.com/datasets/2svx788ddf/1) at 10 micron resolution with 8 reference images - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2) -- [Blind Mexican Cavefish Brain Atlas](https://doi.org/10.7554/eLife.80777) at 2 micron resolution -- [BlueBrain Barrel Cortex Atlas](https://doi.org/10.1162/imag_a_00209) at 10 and 25 micron resolution -- [UNAM Axolotl Brain Atlas](https://doi.org/10.1038/s41598-021-89357-3) at 40 micron resolution +| 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 | 1 year | 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 ## Installation