The BrainGlobe atlas API includes a number of atlases in a standardised form that vary based on:
Reference image modality
Brain region annotations
Sometimes choosing the most appropriate atlas for a specific question is easy (e.g., there is currently only one rat atlas in the API). However, in some cases (e.g. adult mouse brains) there are many options. In some cases the annotations included with an atlas will dictate the choice — if the brain region you are studying is not included in an atlas, it is not much use! In other cases the reference image will be important. If you have imaged your sample with lightsheet microscopy (LSFM) it may be useful to use an atlas that also uses this modality. An atlas using a different modality (such as serial section two-photon, STP) may produce inferior registration results.
In most software you can choose the atlas from a list, but if using a command line tool, or the API directly, the
unique key (e.g.
example_mouse_100um must be used).
For many researchers working with mice, this is the “default” atlas for a variety of tasks. It is also the basis for the most commonly used common coordinate space (CCFv3). It is usually the best mouse atlas to start with, but it has some disadvantages. It has a reference image based on STP, which may not produce the best results for other imaging modalities, and you may want to try atlases based on other modalities (see below). It also has limited annotations in some regions (alternatives such as the Enhanced and Unified Mouse Brain Atlas may be better if the Allen Adult Mouse Brain Atlas is not annotated sufficiently).
allen_mouse_10um- 10μm resolution
allen_mouse_25um- 25μm resolution
allen_mouse_50um- 50μm resolution
allen_mouse_100um- 100μm resolution
This atlas from Chon et al. (2019) is very similar to the Allen Adult Mouse Brain Atlas (it has the same reference image), but it includes additional annotations (e.g. from the Franklin-Paxinos atlas). This atlas may be a good choice for those brain regions not annotated sufficiently in the Allen Adult Mouse Brain Atlas.
kim_mouse_10um- 10μm resolution
kim_mouse_25um- 25μm resolution
kim_mouse_50um- 50μm resolution
kim_mouse_100um- 100μm resolution
This atlas from Perens et al. (2020) provides a version of the Allen Adult Mouse Brain Atlas, based on solvent-cleared brains imaged with LSFM. This atlas may be a good choice for registering other similar images. However, please note that this atlas is in a different coordinate space to the original Allen atlas (CCFv3).
This atlas is only available at 20μm resolution:
This atlas from Pisano et al. (2021) is a version of the Allen Adult Mouse Brain Atlas with two main differences. Unlike the Allen Adult Mouse Brain Atlas it includes a full cerebellum, and the reference image is based on LSFM rather than STP.
This atlas is only available at 20μm resolution:
These atlases from Young et al. (2021) are 3D reconstructions of the eight developmental stages from the Allen Developing Mouse Brain Atlas. This allows them to be used in automated 3D registration pipelines.
These atlases vary slightly, as the E11.5, E13.5 and E15.5 atlases contain the complete embryo. The other atlases (E18.5, P4, P14, P28 and P56) only contain the brain.
admba_3d_e11_5_mouse_16um- E11.5 at 16μm resolution
admba_3d_e13_5_mouse_16um- E13.5 at 16μm resolution
admba_3d_e15_5_mouse_16um- E15.5 at 16μm resolution
admba_3d_e18_5_mouse_16um- E18.5 at 16μm resolution
admba_3d_p4_mouse_16.752um- P4 at 16.752μm resolution
admba_3d_p14_mouse_16.752um- P14 at 16.752μm resolution
admba_3d_p28_mouse_16.752um- P28 at 16.752μm resolution
admba_3d_p56_mouse_25um- P56 at 25μm resolution
This atlas is part of a new developmental atlas following Luis Puelles’ Developmental Vertebrate Ontology. BrainGlobe currently hosts the P56 version of this atlas at 10μm resolution with eight versions, each with a different reference image - STP, LSFM (iDISCO) and MRI (a0, adc, dwo, fa, MTR, T2).
kim_dev_mouse_stp_10um- “normal” CCF serial 2p template at 10μm resolution
kim_dev_mouse_idisco_10um- iDISCO LSFM template at 10μm resolution
kim_dev_mouse_mri_a0_10um- MRI a0 template at 10μm resolution
kim_dev_mouse_mri_adc_10um- MRI ADC (apparent diffusion coefficient) template at 10μm resolution
kim_dev_mouse_mri_dwi_10um- MRI DWI (diffusion-weighted imaging) template at 10μm resolution
kim_dev_mouse_mri_fa_10um- MRI FA (fractional anisotropy) template at 10μm resolution
kim_dev_mouse_mri_mtr_10um- MRI MTR (magnetic transfer ratio) template at 10μm resolution
kim_dev_mouse_mri_t2_10um- MRI T2 template at 10μm resolution
This atlas is only available at a single (20 x 10 x 10μm) resolution:
This atlas is part of the API to support some existing projects. We do not recommend it for any new projects (use the Allen Adult Mouse Brain Atlas instead).
osten_mouse_10um- 10μm resolution
osten_mouse_25um- 25μm resolution
osten_mouse_50um- 50μm resolution
osten_mouse_100um- 100μm resolution
Waxholm Space atlas of the Sprague Dawley rat brain at 39 micron resolution#
This atlas is only available at 39μm resolution:
whs_sd_rat_39um- 39μm resolution
This atlas is only available at 1μm resolution:
This atlas is only available at 4μm resolution:
This atlas is included mostly for visualisation and comparison to the other atlases. Note that it is also only a single hemisphere. There are many better atlases (and indeed software tools) for the analysis of human neuroimaging data.
This atlas is only available at 500μm resolution: