Dwell time analysis

Dwell time analysis#

Dwell times can be extracted from the overall classification using the determine_dwells_from_classification method:.

determine_dwells_from_classification(variable='FRET', selected=True)

The method will create an additional .nc file named <filename>_dwells.nc. From which the contents can be obtained using:

file.dwells

For each dwell the following information is provided:

  • file: the file from which it originates

  • molecule_in_file: the molecule index in the original file

  • state: the state of the dwell

  • frame_count: the dwell duration in frames

  • duration: the dwell duration in time

  • mean_<variable_name>: the mean of the used variable

The dwells with positive states that have a negative state neighbor are inactivated (i.e. set to state -128) by default.

The dwell times can be analyzed using

file.analyze_dwells(plot=True, state_names={0: 'Low FRET state', 1: 'High FRET state'}, logy=False):

The analyze_dwells method will construct a dwell time histogram for each of the given states and will fit a single decaying exponential function

\[count = Ae^{-kt}\]

The method will create a new file named <filename>_dwell_analysis.nc containing the fit values, errors and covariance. In addition, if plot is set to True, the plot of the histogram and fit will be saved. The logy variable can be set to True for a logarithmic y-axis.