From c5411ba3943d6be92b7b6e3b6361cdfc9a19f43e Mon Sep 17 00:00:00 2001 From: Adam Tyson Date: Thu, 31 Oct 2024 09:36:49 +0000 Subject: [PATCH] Add vole atlas and add api atlas names to table (#256) --- .../brainglobe-atlasapi/index.md | 35 ++++++++++--------- .../usage/atlas-details.md | 19 ++++++---- 2 files changed, 31 insertions(+), 23 deletions(-) diff --git a/docs/source/documentation/brainglobe-atlasapi/index.md b/docs/source/documentation/brainglobe-atlasapi/index.md index 3144136e..90a47849 100644 --- a/docs/source/documentation/brainglobe-atlasapi/index.md +++ b/docs/source/documentation/brainglobe-atlasapi/index.md @@ -19,23 +19,24 @@ Each atlas consists of data files in a common format: 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 diff --git a/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md b/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md index 75ba8b3f..77375c7d 100644 --- a/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md +++ b/docs/source/documentation/brainglobe-atlasapi/usage/atlas-details.md @@ -47,8 +47,6 @@ Available versions: * `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 @@ -132,23 +130,32 @@ Available versions: 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