This repository holds material for:

Valentin Kapitany, Vytautas Zickus, Areeba Fatima, Guillem Carles & Daniele Faccio 
"Single-shot time-folded fluorescence lifetime imaging" 

This repository is published under a CC BY-NC 4.0 License. The corresponding authors are 
Mr. Valentin Kapitany (v.kapitany.1@research.gla.ac.uk) and Prof. Daniele Faccio (daniele.faccio@glasgow.uk)

Contents:

data (contains all the data relevant to the project)
	- exp_predictions (Fig. 3 and Fig. 4 and Supplementary Fig. S3 and Supplementary Fig. S4 and Supplementary Fig. S7)
	- exp_processed 
		- FLIMERA beads (fits for Supplementary Fig. S2)
		- IR_intermediate (pre-processed data to be implemented with IR)
	- exp_raw (raw measurements and systems parameters)
		- 2um_and_4um_beads (raw data for Fig. 3)
		- convallaria (raw data for Fig. 4 and Supplementary Fig. S3 and Supplementary Fig. S4)
		- experimental_parameters (system parameters inc. iCCD gate gain profile)
		- FLIMERA beads (raw measurement for Supplementary Fig. S2)
	- synth_predictions
		- set of test set input-label-prediction images. Generated from ../notebooks/train.ipynb
	- synth_raw 
		- synthetic training/validation/testing data for NN. Generated from ../notebooks/datagen.ipynb

figures (contains all the figures as svg and pdf files)
	- fig1 
	- fig2 [(a) run - ../notebooks/cavity_bayes_uncertainty.ipynb)]
	- fig3 [(c-d) data in ../exp_predictions/NN, or run ../notebooks/eval_beads.ipynb]
		 [(e-f) data in ../exp_predictions/IR, or run ../IR/codes_final/Cav_FLIM_beads_09_11_12.m]
	- fig4 [(a)(iii)-(b)(iii) data in ../exp_predictions/NN, or run ../notebooks/eval_convallaria.ipynb]
		 [(a)(iv)-(b)(iv) data in ../exp_predictions/IR, or run ../IR/codes_final/Cav_FLIM_convallaria_09_11_12.m]
	- sf1 [data in ../data/exp_raw/experimental_parameters/2022_02_21_defaults/gate_full.mat]
	- sf3 [run ../notebooks/eval_convallaria.ipynb]
	- sf3 [run ../notebooks/eval_convallaria.ipynb]
	- sf4 [run ../notebooks/eval_convallaria.ipynb]
	- sf5 [data in ../data/exp_processed/FLIMERA_beads, or run ../notebooks/mle_lifetime_extraction_for_general_purpose_use.py]	
	- sf6 [run ../notebooks/cavity_bayes_uncertainty.ipynb]
	- sf7 [run ../notebooks/eval_beads.ipynb]

IR (contains a copy of all the inverse retrieval (IR) code)

models (made via ../notebooks/train.ipynb)
	- fusion_model_test_10k_centre.h5 (NN model)
	- fusion_history_test_10k_centre.csv (training_history)
	- fusion_training_loss_test_10k_centre.svg (training_history as image)

	#(used for SF7, modified and retrained version model_test10k_0.h5 that uses only the iCCD input to predict lifetime.)
	- iccd_only_model_test_10k_centre.h5 (NN model)
	- iccd_only_history_test_10k_centre.csv (training_history)
	- iccd_only_training_loss_test_10k_centre.svg (training_history as image)

notebooks (contains all the notebooks, except the IR matlab code. Their use is detailed in the descriptions of the various directories in this repository)

src (imports used by notebooks)

LICENSE.txt - CC BY 4.0 License detailing the authors' copyright, and public redistribution rights

requirements.txt - python installation requirements