🔬 ThermalShift — Simulations & Analysis Toolkit

This repository contains the codebase for analyzing and simulating thermal lensing effects in two-photon light-sheet microscopy, as presented in our preprint:

Hubert, A., Trentesaux, H., Pujol, T., Debrégeas, G., & Bormuth, V. (2025).
Thermal Lensing Effects in Two-Photon Light-Sheet Microscopy.
Biomedical Optics Express, 17, 1064–1073.

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📂 Project Overview

🧪 Notebooks

• ThermalShift_main_code.ipynb: main notebook for processing experimental beam propagation data (Python)
• ThermalShift_simulations.ipynb: notebook for simulating thermal lensing and beam dynamics (Julia)

⚙️ Code Modules

• simulations_codes/: contains all Julia functions and parameters for simulating Gaussian beam propagation under thermal lensing
• wvlengths.csv: absorption coefficients vs wavelength (interpolated from Hale & Querry, 1973)

🗃️ Dataset

• Raw data available on request
• Pre-processed data is included under the dataset/ folder.

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📝 Citation

If you use this repository, please cite our preprint:

@article{hubert2026thermal,
  title   = {Thermal lensing effects in two-photon light-sheet microscopy},
  author  = {Hubert, Antoine and Trentesaux, Hugo and Pujol, Thomas and Debrégeas, Georges and Bormuth, Volker},
  journal = {Biomedical Optics Express},
  volume  = {17},
  pages   = {1064--1073},
  year    = {2026}
}