The BrainGlobe Initiative

Image analysis in a common coordinate space

Igor Tatarnikov

Introduction to atlases
Counting cells in atlas space
Segmentation in atlas space
Visualisation in atlas space

Introduction to atlases

What is an atlas?

Template/Reference Image

Annotation Image

Why is an atlas useful?

A standardised annotation and coordinate system
A target for registering experimental data
A simple way to compare across multiple subjects

Building an atlas

Building an atlas

Building an atlas

BrainGlobe Atlas

Many similar communities working independently with brain atlases

Model species
Imaging modality
Anatomical focus
Developmental stage

`brainglobe-atlasapi`

from brainglobe_atlasapi import BrainGlobeAtlas
atlas = BrainGlobeAtlas("allen_mouse_25um")

reference_image = atlas.reference
print(reference_image.shape)
# (528, 320, 456)

annotation_image = atlas.annotation
print(annotation_image.shape)
# (528, 320, 456)

VISp = atlas.structures["VISp"]
print(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]}