Full-heart conduction system example

This example demonstrates how to build a conduction system for a full-heart model, including the Purkinje network and other conduction pathways.

Note

The fractal tree used in this example was generated with LS-DYNA and is based on: F. Sahli Costabal, D. Hurtado and E. Kuhl. Generating Purkinje networks in the human heart. 2016, Journal of Biomechanics.

Overview

In addition to the Purkinje fibers, this example defines other key conduction pathways, such as the sinoatrial (SA) node to atrioventricular (AV) node path, the Bachmann bundle, the His bundle and its bifurcation, as well as the left and right bundle branches. Each conduction path is constructed using anatomical landmarks and keypoints, and is integrated into the heart model.

Required imports

from pathlib import Path

import numpy as np
import pyvista as pv

from ansys.health.heart.examples import (
    get_fractal_tree_purkinje,
    get_preprocessed_fullheart,
)
import ansys.health.heart.models as models
from ansys.health.heart.models_utils import HeartModelUtils
from ansys.health.heart.pre.conduction_path import ConductionPath, ConductionPathType

# Set the working directory and path to the model.
workdir = Path.home() / "pyansys-heart" / "downloads" / "Rodero2021" / "01" / "FullHeart"
path_to_model, path_to_partinfo, _ = get_preprocessed_fullheart(resolution="2.0mm")

Load the full-heart model

model: models.FullHeart = models.FullHeart.load_model(
    path_to_model, path_to_partinfo, working_directory=workdir
)

Create conduction paths for the Purkinje network

# Load precomputed Purkinje network meshes
left_purkinje, right_purkinje = get_fractal_tree_purkinje()

# Create left Purkinje network conduction path
left_purkinje = ConductionPath(
    name=ConductionPathType.LEFT_PURKINJE,
    mesh=left_purkinje,
    is_connected=np.zeros(left_purkinje.n_points),
    id=1,
    relying_surface=model.left_ventricle.endocardium,
)

# Add Purkinje-myocardial junctions (PMJs) at terminal nodes
pmj_nodes_left = left_purkinje.get_terminal_nodes()
pmj_coordinates_left = left_purkinje.get_terminal_coordinates()
left_purkinje.add_pmj_path(pmj_list=pmj_nodes_left)

# Visualize the left Purkinje network
left_purkinje.plot()

Static Scene

Interactive Scene

Create right Purkinje network

right_purkinje = ConductionPath(
    name=ConductionPathType.RIGHT_PURKINJE,
    mesh=right_purkinje,
    is_connected=np.zeros(right_purkinje.n_points),
    id=2,
    relying_surface=model.right_ventricle.endocardium,
)

# Add Purkinje-myocardial junctions (PMJs) at terminal nodes
pmj_nodes_right = right_purkinje.get_terminal_nodes()
pmj_coordinates_right = right_purkinje.get_terminal_coordinates()
right_purkinje.add_pmj_path(pmj_list=pmj_nodes_right)

# Visualize the right Purkinje network
right_purkinje.plot()

Static Scene

Interactive Scene

Visualize both Purkinje networks and PMJ points together

Combine PMJ coordinates for visualization

pmj_points = pv.PolyData(np.vstack([pmj_coordinates_left, pmj_coordinates_right]))

# Create a plotter and add all relevant meshes
plotter = pv.Plotter()
plotter.add_mesh(pmj_points, color="r", render_points_as_spheres=True, point_size=5)
plotter.add_mesh(pv.merge([left_purkinje.mesh, right_purkinje.mesh]), line_width=2)
plotter.add_mesh(
    pv.merge([left_purkinje.relying_surface, right_purkinje.relying_surface]),
    opacity=0.5,
    color="white",
)
plotter.add_text("Left and right Purkinje networks.", position="upper_edge")
plotter.show()

Static Scene

Interactive Scene

Create the SA-AV node conduction path

sa = HeartModelUtils.define_sino_atrial_node(model, target_coord=[6, 66, 88])
av = HeartModelUtils.define_atrio_ventricular_node(model)
# Create the SA-AV node conduction path. The default option is to connect the
# SA node and AV node by a geodesic path.
sa_av = ConductionPath.create_from_keypoints(
    name=ConductionPathType.SAN_AVN,
    keypoints=[sa.xyz, av.xyz],
    id=3,
    base_mesh=model.right_atrium.endocardium,
    connection="first",
    line_length=None,
    center=True,
)

# Add PMJ nodes at every 4th node along the SA-AV path (excluding endpoints)
sa_av.add_pmj_path(list(range(1, sa_av.mesh.n_points - 1, 4)))

# Visualize the SA-AV node conduction path
sa_av.plot()

Static Scene

Interactive Scene

Create the His bundle and its bifurcation

The His bundle is constructuted inside the myocardium, not on a surface.

Note

You can modify the conduction velocity in his_top.ep_material to induce a delay in activation.

# Define three keypoints for the His bundle
his_bif = HeartModelUtils.define_his_bundle_bifurcation_node(model)
his_left_point = HeartModelUtils.define_his_bundle_end_node(model, side="left")
his_right_point = HeartModelUtils.define_his_bundle_end_node(model, side="right")

# Top part of the His bundle.
his_top = ConductionPath.create_from_keypoints(
    name=ConductionPathType.HIS_TOP,
    keypoints=[av.xyz, his_bif.xyz],
    id=4,
    base_mesh=model.mesh.extract_cells_by_type(10),
)
his_top.up_path = sa_av

# Create branches for the left and right bundle branches
his_left = ConductionPath.create_from_keypoints(
    name=ConductionPathType.HIS_LEFT,
    keypoints=[his_bif.xyz, his_left_point.xyz],
    id=5,
    base_mesh=model.mesh.extract_cells_by_type(pv.CellType.TETRA),
)
his_left.up_path = his_top
his_right = ConductionPath.create_from_keypoints(
    name=ConductionPathType.HIS_RIGHT,
    keypoints=[his_bif.xyz, his_right_point.xyz],
    id=6,
    base_mesh=model.mesh.extract_cells_by_type(pv.CellType.TETRA),
)
his_right.up_path = his_top

Create the left and right bundle branches

Create the left and right bundle branches by defining their keypoints

left_bundle = ConductionPath.create_from_keypoints(
    name=ConductionPathType.LEFT_BUNDLE_BRANCH,
    keypoints=[his_left_point.xyz, model.left_ventricle.apex_points[0].xyz],
    id=7,
    base_mesh=model.left_ventricle.endocardium,
    line_length=None,
    center=True,
)
# Connect the left bundle branch to the septum by adding additional Purkinje-myocardial junctions
pmj_list = list(
    range(
        int((0.4 * left_bundle.mesh.n_points)),
        int((0.9 * left_bundle.mesh.n_points)),
        4,  # every 4 nodes
    )
)
left_bundle.add_pmj_path(pmj_list, merge_with="node")
left_bundle.up_path = his_left
left_bundle.down_path = left_purkinje

# Build the right bundle branch
surface_ids = [
    model.right_ventricle.endocardium.id,
    model.right_ventricle.septum.id,
]
endo_surface = model.mesh.get_surface(surface_ids)
right_bundle = ConductionPath.create_from_keypoints(
    name=ConductionPathType.RIGHT_BUNDLE_BRANCH,
    keypoints=[his_right_point.xyz, model.right_ventricle.apex_points[0].xyz],
    id=8,
    base_mesh=endo_surface,
    line_length=None,
)
right_bundle.up_path = his_right
right_bundle.down_path = right_purkinje

Create the Bachmann bundle

surface_ids = [
    model.left_atrium.epicardium.id,
    model.right_atrium.epicardium.id,
]
surface = model.mesh.get_surface(surface_ids)
bachman_bundle = ConductionPath.create_from_keypoints(
    name=ConductionPathType.BACHMANN_BUNDLE,
    keypoints=[sa.xyz, [46, 102, 97]],
    id=9,
    base_mesh=surface,
    line_length=None,
    center=True,
)
bachman_bundle.add_pmj_path(list(range(1, bachman_bundle.mesh.n_points - 1, 4)))
bachman_bundle.up_path = sa_av

Create the mid and post SA-AV node conduction paths

# The mid and post SA-AV node conduction paths are created by providing a list of keypoints.
mid_sa_av = ConductionPath.create_from_keypoints(
    name=ConductionPathType.MID_SAN_AVN,
    keypoints=[
        sa.xyz,
        [10, 79, 64],
        [18, 95, 41],
        [32, 93, 31],
        [43, 88, 26],
        av.xyz,
    ],
    id=10,
    base_mesh=model.right_atrium.endocardium,
    line_length=None,
    center=True,
)
mid_sa_av.add_pmj_path(list(range(5, mid_sa_av.mesh.n_points - 5, 4)))
mid_sa_av.up_path = sa_av
mid_sa_av.down_path = sa_av
post_sa_av = ConductionPath.create_from_keypoints(
    name=ConductionPathType.POST_SAN_AVN,
    keypoints=[sa.xyz, [2, 65, 53], [6, 73, 34], [25, 75, 26], av.xyz],
    id=11,
    base_mesh=model.right_atrium.endocardium,
    line_length=None,
    center=True,
)
post_sa_av.add_pmj_path(list(range(5, post_sa_av.mesh.n_points - 5, 4)))
post_sa_av.up_path = sa_av
post_sa_av.down_path = sa_av

Assign all conduction paths to the model and visualize the complete system

model.assign_conduction_paths(
    [
        left_purkinje,
        right_purkinje,
        sa_av,
        his_top,
        his_left,
        his_right,
        left_bundle,
        right_bundle,
        bachman_bundle,
        mid_sa_av,
        post_sa_av,
    ]
)

# Visualize the entire conduction system
model.plot_purkinje()

Static Scene

Interactive Scene