How to use the software:

The raw data can be downloaded from: 

https://doi.org/10.4121/12888455

this is in the format of photon-hdf5 files, have a look with hdfview to get a feeling of the datastructure. All of the metadata is stored in the users group, see here for the units:
* 'user' → grp
	* 'picoquant_meta' → grp
	* 'meas_spec' → grp
		* 'nranalytes' → int
		* 'voltage' → str
		* 'bgrd_file' → str
		* 'analyte_short_' + nr → str
		* 'analyte_descr_' + nr → str
		* 'analyte_' + nr → str
		* 'analyte_pltclr_' + nr → str
		* 'analyte_conc_' + nr → str
		* 'analyte_dye_'  + nr → str
		* 'analyte_comments_' + nr → str
		* 'analyte_time_threshold_' + nr → float 
		* 'analyte_diff_coeff' → float (μm²/s)
		* 'analyte_diff_coeff_err' → float (μm²/s)
		* 'chip' → str
		* 'coating' → str
		* 'pore_diam' → str
		* 'pore_area' → str
		* 'res_buf' → str
		* 'mem_buf' → str
		* 'others' → str

They have been generated from the raw .ptu output of the microscope software using phconvert module: https://pypi.org/project/phconvert/ using a modified version of the loader.nsalex_pq function.

Please see requirements_pip.txt for the requirements of the scripts.

Then you need to run a basic analysis on the file, which detects the fluorescence bursts from the timetrace by running analyse.py . It creates the _results.hdf5 files, where all the basic results such as eventrate etc. are stored. It uses the changepoint program from https://doi.org/10.5281/zenodo.3987514 . You need to compile it on your computer and set the location of it to the analyse.py 

Additionally analyse.py needs to reach the file functions.py and import it.

The jupyter notebooks then only run on the _results.hdf5 files and were used for the figures in the publication.

