
The steps to perform the analysis of a short movie are

1. run Deconvolve.exe (if needed, unlock the file by changing the file properties; Windows Attachment Manager may recognize .exe files as unsafe)
2. start with pre-processing the Raw Files 
3. choose a data folder containing the sample .xlsx file, for instance sampleShort
4. choose extension, for instance xls
5. select Show Plots
6. Process; Figure 1 pops-up with the timeseries for each transcription site in the dataset
7. Back
8. Deconvolve
9. Select data folder, for instance, sampleShort again
10. Set Parameters (data dependent, values below are for sampleShort)
	- polymerase speed = 45
	- length of null signal = 0
	- length of MS2 signal = 1292
	- length of stable signal = 4526
	- Minimum distance between two polymerase = 30
	- Frame length = 3.9
11. Pick a name for saving these parameters, for instance sampleShort
12. Save and Load Parameters
13. select Perform deconvolution
14. check max number of threads available
15. choose a number smaller thant the max available
16. maximum number of generation (needed for the genetic algorithm) for instance 200
17. select perform fit 2 states and 3 states
18. analyze. 
	-the progress bar will show you how far you are in the process (this may take long for computers with a number of threads
	less than the number of transcription sites)
	-when deconvolution finishes, the model fits are launched the results of the analysis are stored in the selected folder 
	(the one containing data) 
		-sampleShort images contains figure1 showing the data
		-npzdatafiles/resultDec contains the .npz file with the result of the deconvolution
		-npzdatafiles/Results contains the fit results. 
		-the xlsx files contain the parameters of the 2 states and 3 states models
		-the folder with the name of the dataset contains 
			-DataExp, DataPred : heatmaps showing the data the deconvolution fit
			-figure 1 contains the same thing but as 1D plots. data is in blck, deconvolution fit in red
			-Fig2States shows the parametric fit of the survival function using 2 exponentials
			-Fig3states M1 and M2 should be identical : they are parametric fits with 3 exponentials
			-FitCDF shows the fit of cumulative distribution functions
			-Pospred shows the distribution of polymerase positions as a heatmap. 