Visualise blackcap traced cells alongside injection site

blackcap_atlas_vis.py

from pathlib import Path

from brainrender.scene import Scene
from brainrender.actors import Points, Cylinder
from brainrender import settings

from myterial import indigo_darker, light_green, amber, salmon, blue_light, green

settings.SHADER_STYLE = "plastic"
settings.SHOW_AXES = False


cells_path = Path("/Users/adamtyson/UCL Dropbox/Adam Tyson/AT/data_analysis/blackcap_analysis/2024-11-25/brainmapper") / "points.npy"

# Create a brainrender scene
scene = Scene(atlas_name="oldenburg_blackcap_25um", inset=False)

# Create points actor & add cells
cells = Points(cells_path, radius=25, colors=blue_light, alpha=0.9)
scene.add(cells)

# Add "top" brain regions
scene.add_brain_region("H", color=green, alpha=0.2)
scene.add_brain_region("HP", color=amber, alpha=0.2)
scene.add_brain_region("M", color=salmon, alpha=0.2)


# Coordinate picked in image, then multipled by 25 to get into micron space
coords = [3000, 1825, 8575]

injection_cylinder = Cylinder(
    coords,  # center the cylinder at the center of mass of th
    scene.root,
    radius=100
)
scene.add(injection_cylinder)

scene.render()