brainglobe-atlasapi
The BrainGlobe Atlas API (brainglobe-atlasapi) provides a common interface for programmers to download and process brain atlas data from multiple sources.
Atlases available
A number of atlases are in development; those available currently are shown in the table below. The table is synced from the BrainGlobe documentation repository—to update it locally after changes there, run python tools/update_atlas_table.py.
Acronyms:
- dpf: Days Post Fertilisation
- E: Embryonic day
- FISH: Fluorescent In Situ Hybridisation
- IHC: Immunohistochemistry
- LSFM: Light Sheet Fluorescent Microscopy
- MRI: Magnetic Resonance Imaging
- P: Post natal day
- STPT: Serial Two Photon Tomography
Installation
brainglobe-atlasapi can be installed from PyPI with:
pip install brainglobe-atlasapi
Usage
Full information can be found in the documentation
Python API
List of atlases
To see a list of atlases use brainglobe_atlasapi.show_atlases
from brainglobe_atlasapi import show_atlases
show_atlases()
# Brainglobe Atlases
# ╭──────────────────────────────────┬────────────┬───────────────┬──────────────╮
# │ Name │ Downloaded │ Local version │ Latest │
# │ │ │ │ version │
# ├──────────────────────────────────┼────────────┼───────────────┼──────────────┤
# │ allen_human_500um │ ✔ │ 0.1 │ 0.1 │
# │ mpin_zfish_1um │ ✔ │ 0.3 │ 0.3 │
# │ allen_mouse_50um │ ✔ │ 0.3 │ 0.3 │
# │ kim_unified_25um │ ✔ │ 0.1 │ 0.1 │
# │ allen_mouse_25um │ ✔ │ 0.3 │ 0.3 │
# │ allen_mouse_10um │ ✔ │ 0.3 │ 0.3 │
# │ example_mouse_100um │ --- │ --- │ 0.3 │
# ╰──────────────────────────────────┴────────────┴───────────────┴──────────────╯
Using the atlases
All the features of each atlas can be accessed via the BrainGlobeAtlas class.
e.g. for the 25um Allen Mouse Brain Atlas:
from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas
atlas = BrainGlobeAtlas("allen_mouse_25um")
The various files associated with the atlas can then be accessed as attributes of the class:
# template image
template_image = atlas.template
print(template_image.shape)
# (528, 320, 456)
# annotation image
annotation_image = atlas.annotation
print(annotation_image.shape)
# (528, 320, 456)
# a hemispheres image (value 1 in left hemisphere, 2 in right) can be generated
hemispheres_image = atlas.hemispheres
print(hemispheres_image.shape)
# (528, 320, 456)
Pass dask=True to BrainGlobeAtlas to return dask arrays for these images; index/slice them as usual, then call .compute() when you need the numpy result.
Brain regions
There are multiple ways to work with individual brain regions. To see a dataframe of each brain region, with it's unique ID, acronym and full name, use atlas.lookup_df:
atlas.lookup_df.head(8)
# acronym id name
# 0 root 997 root
# 1 grey 8 Basic cell groups and regions
# 2 CH 567 Cerebrum
# 3 CTX 688 Cerebral cortex
# 4 CTXpl 695 Cortical plate
# 5 Isocortex 315 Isocortex
# 6 FRP 184 Frontal pole, cerebral cortex
# 7 FRP1 68 Frontal pole, layer 1
Each brain region can also be accessed by the acronym, e.g. for primary visual cortex (VISp):
from pprint import pprint
VISp = atlas.structures["VISp"]
pprint(VISp)
# {'acronym': 'VISp',
# 'id': 385,
# 'mesh': None,
# 'mesh_filename': PosixPath('/home/user/.brainglobe/allen_mouse_25um_v0.3/meshes/385.obj'),
# 'name': 'Primary visual area',
# 'rgb_triplet': [8, 133, 140],
# 'structure_id_path': [997, 8, 567, 688, 695, 315, 669, 385]}
Note on coordinates in brainglobe-atlasapi
Working with both image coordinates and cartesian coordinates in the same space can be confusing!
In brainglobe-atlasapi, the origin is always assumed to be in the upper left corner of the image (sectioning along the first dimension), the "ij" convention.
This means that when plotting meshes and points using cartesian systems, you might encounter confusing behaviors coming from the fact that in cartesian plots one axis is inverted with respect to ij coordinates (vertical axis increases going up, image row indexes increase going down).
To make things as consistent as possible, in brainglobe-atlasapi the 0 of the meshes coordinates is assumed to coincide with the 0 index of the images stack, and meshes coordinates increase following the direction stack indexes increase.
To deal with transformations between your data space and brainglobe-atlasapi, you might find the brainglobe-space package helpful.
Seeking help or contributing
We are always happy to help users of our tools, and welcome any contributions. If you would like to get in contact with us for any reason, please see the contact page of our website. To contribute to brainglobe-atlasapi, please see the BrainGlobe developer's guide.
Citation
If you find the BrainGlobe Atlas API useful, please cite the paper in your work:
Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W. and Portugues, R. (2020). BrainGlobe Atlas API: a common interface for neuroanatomical atlases. Journal of Open Source Software, 5(54), 2668, https://doi.org/10.21105/joss.02668
Don't forget to cite the developers of the atlas that you used!
Atlas Generation and Adding a New Atlas
For full instructions to add a new BrainGlobe atlas, please see here.
The brainglobe_atlasapi.atlas_generation submodule contains code for the generation of cleaned-up data, for the main brainglobe_atlasapi module.
This code was previously the bg-atlasgen module.
To contribute
- Fork this repo
- Clone your repo
- Run
git clone https://github.com/brainglobe/brainglobe-atlasapi
- Install an editable version of the package; by running
pip install -e . within the cloned directory
- Create a script to package your atlas, and place into
brainglobe_atlasapi/atlas_generation/atlas_scripts. Please see other scripts for examples.
Your script should contain everything required to run.
The raw data should be hosted on a publicly accessible repository so that anyone can run the script to recreate the atlas.
If you need to add any dependencies, please add them as an extra in the pyproject.toml file, e.g.:
[project.optional-dependencies]
allenmouse = ["allensdk"]
newatlas = ["dependency_1", "dependency_2"]
