Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add api name of atlases to readme #422

Merged
merged 1 commit into from
Oct 30, 2024
+17 −17
Merged

Add api name of atlases to readme #422

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
34 changes: 17 additions & 17 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,23 +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:

| 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) | 500 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 days post fertilisation | 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

## Installation

Expand Down
Loading