Visualize ReaDDy simulation trajectories

Notebook contains steps for visualizing ReaDDy simulations of a single actin fiber using Simularium.

if __name__ != "__main__":
    raise ImportError("This module is a notebook and is not meant to be imported")

from pathlib import Path

from subcell_pipeline.analysis.compression_metrics.compression_metric import (
    CompressionMetric,
)
from subcell_pipeline.visualization.individual_trajectory import (
    visualize_individual_readdy_trajectories,
)

Define visualization settings

Define simulation and visualization settings that are shared between different simulation series.

# S3 bucket for input and output files
bucket: str = "s3://readdy-working-bucket"

# Number of simulation replicates
n_replicates: int = 5

# Number of timepoints
n_timepoints = 200

# Number of monomer points per fiber
n_monomer_points = 200

# Specify whether the visualization should be recalculated. Set this to true if
# you make changes to any visualization functions.
recalculate: bool = True

# Temporary path to save downloaded trajectories
temp_path: Path = Path(__file__).parents[2] / "viz_outputs"
temp_path.mkdir(parents=True, exist_ok=True)

# List of compression metrics to include
metrics = [
    CompressionMetric.NON_COPLANARITY,
    CompressionMetric.PEAK_ASYMMETRY,
    CompressionMetric.AVERAGE_PERP_DISTANCE,
    CompressionMetric.CONTOUR_LENGTH,
    CompressionMetric.COMPRESSION_RATIO,
]

Visualize compression simulations

The ACTIN_COMPRESSION_VELOCITY simulation series compresses a single 500 nm actin fiber at four different velocities (4.7, 15, 47, and 150 μm/s) with five replicates each.

Iterate through all condition keys and replicates to load simulation output files and visualize them. If the visualization file for a given condition key and replicate already exists and recalculate is False, visualization is skipped.

  • Input: (series_name)/outputs/(series_name)_(condition_key)_(index + 1).h5

  • Output: (series_name)/viz/(series_name)_(condition_key)_(index + 1).simularium

# Name of the simulation series
compression_series_name: str = "ACTIN_COMPRESSION_VELOCITY"

# List of condition file keys for each velocity
compression_condition_keys: list[str] = ["0047", "0150", "0470", "1500"]

# Total number of steps for each condition
compression_total_steps: dict[str, int] = {
    "0047": int(3.2e8),
    "0150": int(1e8),
    "0470": int(3.2e7),
    "1500": int(1e7),
}

visualize_individual_readdy_trajectories(
    bucket,
    compression_series_name,
    compression_condition_keys,
    n_replicates,
    n_timepoints,
    n_monomer_points,
    compression_total_steps,
    str(temp_path),
    metrics=metrics,
    recalculate=recalculate,
)

Visualize no compression simulations

The ACTIN_NO_COMPRESSION simulation series simulates a single actin fiber with a free barbed end across five replicates.

Iterate through all replicates to load simulation output files and visualize them. If the visualization file for a given replicate already exists and recalculate is False, visualization is skipped.

  • Input: (series_name)/outputs/(series_name)_(index + 1).h5

  • Output: (series_name)/viz/(series_name)_(index + 1).simularium

# Name of the simulation series
no_compression_series_name: str = "ACTIN_NO_COMPRESSION"

# Total number of steps for each condition
no_compression_total_steps: dict[str, int] = {"": int(1e7)}

visualize_individual_readdy_trajectories(
    bucket,
    no_compression_series_name,
    [""],
    n_replicates,
    n_timepoints,
    n_monomer_points,
    no_compression_total_steps,
    str(temp_path),
    metrics=metrics,
    recalculate=recalculate,
)