Example 12: Mouse Brain Atlas with Focused Ultrasound¶

Combines a BrainGlobe mouse brain atlas (allen_mouse_25um) with a concave bowl transducer and its simulated pressure field in a single 3-D scene.

What you will learn¶

Loading a BrainGlobe atlas and selecting brain regions
Simulating a small focal volume with a concave bowl transducer
Building a 4x4 affine transform to register the atlas to the transducer frame
Rendering anatomy, transducer, and pressure together in PyVista

Prerequisites¶

This example requires the BrainGlobe atlas API. The mouse atlas data (~500 MB) is downloaded automatically on first run.

Output¶

Mouse brain atlas with transducer and pressure field

Run it¶

uv run examples/example12_txconcave_mousebrain.py

Key code¶

from esdiva.utilities import BG_Atlas
from esdiva.transducers import ConcaveCircularTransducer

mouse_tx = ConcaveCircularTransducer(
    diameter_mm=10.0,
    focus_mm=10.0,
    no_sub_diameter=20,
    frequency_Hz=5e6,
)

mouse_atlas = BG_Atlas("allen_mouse_25um", region_names=("root", "Isocortex", "CA1"))
mouse_atlas.transform(T_matrix=T_matrix, inplace=True)

View full script on GitHub