def test_tractography():
scene = Scene()
analyzer = ABA()
p0 = scene.get_region_CenterOfMass("ZI")
tract = analyzer.get_projection_tracts_to_target(p0=p0)
scene.add_tractography(tract, display_injection_structure=False, color_by="target_region",
VIP_regions=['MOs'], VIP_color="red", others_color="ivory")
def ConnectivityScene():
scene = Scene()
p0 = scene.get_region_CenterOfMass("ZI")
# Then we se these coordinates to get tractography data, note: any set of X,Y,Z coordinates would do.
tract = aba.get_projection_tracts_to_target(p0=p0)
scene.add_tractography(tract, display_injection_structure=False, color_by="region",
display_injection_volume=True, others_alpha=.25)
scene.add_brain_regions(['ZI'], colors="ivory", alpha=1)
set_camera(scene)
scene.render()
def test_tractography():
from brainrender.Utils.ABA.connectome import ABA
# Create a scene
scene = Scene()
# Get the center of mass of the region of interest
p0 = scene.get_region_CenterOfMass("ZI")
# Get projections to that point
analyzer = ABA()
tract = analyzer.get_projection_tracts_to_target(p0=p0)
# Add the brain regions and the projections to it
scene.add_brain_regions(['ZI'], alpha=.4, use_original_color=True)
scene.add_tractography(tract, display_injection_structure=False, color_by="region")
scene.render(interactive=False, )
scene.close()
"""
This tutorial shows how download and rendered afferent mesoscale projection data
using the AllenBrainAtlas (ABA) and Scene classes
"""
import brainrender
brainrender.SHADER_STYLE = 'cartoon'
from brainrender.scene import Scene
from brainrender.atlases.aba import ABA
# Create a scene
scene = Scene()
# Get the center of mass of the region of interest
p0 = scene.get_region_CenterOfMass("ZI")
# Get projections to that point
analyzer = ABA()
tract = analyzer.get_projection_tracts_to_target(p0=p0)
# Add the brain regions and the projections to it
scene.add_brain_regions(['ZI'], alpha=.4, use_original_color=True)
scene.add_tractography(tract, display_injection_structure=False, color_by="region")
scene.render()
