This repository contains several .zip archives containing scripts used within the paper:
"Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical Nanopores"
Here is a description of the content of the individual archives:

* FDTD simulations
	* This folder contains the project files for running lumerical simulations, both of the excitation field and for the emission fields used in the fluorescence enhancement.
* Plotting_of_experimental_data
	* Filenames need some adjustment (watch out for /media/work_data/Analyses/ in the path)
	* Contains the plotting scripts to reproduce the experimental plots in the manuscript from the experimental data.
	* pip_requirements should contain the required python packages (and versions) to run the scripts.
	* functions.py is an assembly of functions used in the scripts.
	* The workflow to get from the photon_hdf5s to the result_hdf5 is the following:
		* use function init_results_hdf5 to initialize the results hdf5 file
		* gen_fcs to compute the fcs curves
		* get_cps is the main function to find the events using the changepoint algorithm
		* generate_event_stats generates statistics of the events
		* sort_hsnr_states dismisses low nignal to noise ratio events
		* generate_event_stats as well for the sorted events
		* then most of the plotting should work right away.

	