Example 13: Rat Brain Zone Focusing¶

Demonstrates focused ultrasound simulation targeting specific anatomical zones of a rat brain using a BrainGlobe atlas and a linear array transducer.

What you will learn¶

• Loading the rat atlas (whs_sd_rat_39um) and selecting motor/somatosensory regions
• Scaling the atlas by the lambda-bregma distance for a specific animal
• Combining atlas, transducer delays, and pressure field in one 3-D scene
• Positioning the brain relative to the transducer with affine transforms

Prerequisites¶

This example requires the BrainGlobe atlas API. The rat atlas data is downloaded automatically on first run.

Output¶

Run it¶

uv run examples/example13_txlinear_ratbrainzones.py

Key code¶

from esdiva.utilities import BG_Atlas

brain_atlas = BG_Atlas("whs_sd_rat_39um", region_names=("root", "M1", "S1-hl"))

# Scale by animal-specific lambda-bregma distance
scale = np.eye(4)
scale[:3, :3] *= 8.0  # mm

# Transform and render
brain_atlas.transform(T_matrix=T_matrix, inplace=True)

View full script on GitHub