3D Orientation Tomography and Order Parameter Analysis Using Polarized Lanthanide Emission

This repository contains example analysis code and datasets used to perform 3D orientation tomography and order parameter mapping in assemblies of lanthanide-doped nanorods. Additionally, scripts are provided to evaluate the reference spectra and to simulate polarized optical microscopy (POM) images from computed director profiles. The scripts are structured into Jupyter-style code cells using the # %% notation.They can be run directly in Visual Studio Code using the Python extension with Jupyter Notebook support, which allows interactive execution of each cell, similar to a notebook environment. Example datasets are included so all scripts can be run immediately (unzip the Data.zip file in the same directory as the code). Included Scripts homeotropic_order_parameter.pyComputes the order parameter S for a homeotropic (θ = 0) nanorod assembly by spectral fitting. orientation_cross_section_microfluidic_channel.pyDetermines the order parameter S and in-plane orientation φ across the Y–Z cross-section of a microfluidic channel. Assumes a tilt profile for θ across the channel height. orientation_middle_plane_microfluidic_channel.pyComputes S and φ in the X–Y middle plane of a microfluidic channel, assuming planar alignment (θ = 90°). orientation_tomography_LC.pyPerforms full 3D orientation tomography in a liquid crystal assembly with a fixed value for S. POM_image_simulation.pySimulates polarized optical microscopy (POM) images from computed director fields, enabling comparison between reconstructed orientation maps and observed optical textures. reference_evaluation.pyEvaluates and validates polarized reference spectra (Iπ and Iσ) by simulating the isotropic spectrum and comparing it to the measured one common_imports.pyCentralized imports for numerical, plotting, and fitting libraries global_functions.pyShared functions for data processing and visualization