Photon Flux Estimation

A Python library for estimating photon flux from multiphoton imaging data. This package provides tools to compute photon sensitivity and generate photon flux visualizations from imaging data.

Installation

pip install photon-flux-estimation

Features

• Compute photon sensitivity from imaging data
• Generate photon transfer curve visualizations
• Calculate photon flux estimates
• Visualize coefficient of variation
• Demo notebook with DANDI dataset integration

Usage

from photon_flux_estimation import PhotonFluxAnalyzer

# Load your imaging data (height, width, time)
movie = your_data_loading_function()

# Create estimator and compute sensitivity
estimator = PhotonFluxEstimator(movie)
results = estimator.compute_sensitivity()

print(f"Sensitivity: {results['sensitivity']:.2f}")
print(f"Zero level: {results['zero_level']:.2f}")

# Get photon flux movie
photon_flux = estimator.compute_photon_flux()

# Generate visualization
from photon_flux_estimation import (
    plot_photon_transfer_curve,
    plot_average_intensity,
    plot_coefficient_variation,
    plot_photon_flux,
)

plot_average_intensity(
    movie=movie,
    title="Average Intensity",
    save_path=str(figure_filename) + "-A.png",
)
plot_photon_transfer_curve(
    results=results,
    title="Photon Transfer Curve",
    save_path=str(figure_filename) + "-B.png",
)
plot_coefficient_variation(
    movie=movie,
    results=results,
    title="Coefficient of Variation",
    save_path=str(figure_filename) + "-C.png",
)
plot_photon_flux(
    movie=movie,
    results=results,
    title="Average Photon Flux",
    save_path=str(figure_filename) + "-D.png",
)

Citation

This package is based on code from the compress-multiphoton repository. If you use this package in your research, please cite both this package and the original repository.

Documentation

For detailed documentation and examples, please see the demo notebook.

License

MIT License. See LICENSE for details.