pysted.microscopes.DyMINRESCueMicroscope.get_signal_and_bleach

DyMINRESCueMicroscope.get_signal_and_bleach(datamap, pixelsize, pdt, p_ex, p_sted, indices=None, acquired_intensity=None, pixel_list=None, bleach=True, update=True, seed=None, filter_bypass=False, bleach_func=<cyfunction default_update_survival_probabilities>, sample_func=<cyfunction sample_molecules>)

This function acquires the signal and bleaches simultaneously.

Parameters:

  • datamap – The datamap on which the acquisition is done, either a Datamap object or TemporalDatamap

  • pixelsize – The pixelsize of the acquisition. (m)

  • pdt – The pixel dwelltime. Can be either a single float value or an array of the same size as the ROI being imaged. (s)

  • p_ex – The excitation beam power. Can be either a single float value or an array of the same size as the ROI being imaged. (W)

  • p_sted – The depletion beam power. Can be either a single float value or an array of the same size as the ROI being imaged. (W)

  • indices – A dictionary containing the indices of the subdatamaps used. This is used to apply bleaching to the future subdatamaps. If acquiring on a static Datamap, leave as None.

  • acquired_intensity – The result of the last incomplete acquisition. This is useful in a time routine where flashes can occur mid acquisition. Leave as None if it is not the case. (array)

  • pixel_list – The list of pixels to be iterated on. If none, a pixel_list of a raster scan will be generated. (list of tuples (row, col))

  • bleach – Determines whether bleaching is active or not. (Bool)

  • update – Determines whether the datamap is updated in place. If set to false, the datamap can still be updated later with the returned bleached datamap. (Bool)

  • seed – Sets a seed for the random number generator.

  • filter_bypass – Whether or not to filter the pixel list. This is useful if you know your pixel list is adequate and ordered differently from a raster scan (i.e. a left to right, row by row scan), as filtering the list return it in raster order. If pixel_list is none, this must be True then.

  • bleach_func – The bleaching function to be applied.

  • steps – list containing the pixeldwelltimes for the sub steps of an acquisition. Is none by default. Should be used if trying to implement a DyMin type acquisition, where decisions are made after some time on whether or not to continue the acq.

Returns:

returned_acquired_photons, the acquired photon for the acquisition. bleached_sub_datamaps_dict, a dict containing the results of bleaching on the subdatamaps acquired_intensity, the intensity of the acquisition, used for interrupted acquisitions