pysted.raster

Cython implementations of the raster functions

This module contains the Cython implementations of the raster functions. These functions are used to simulate the acquisition of a STED microscopy image. The Cython implementation is used to speed up the calculation of the raster function.

Functions

raster_func_c_self_bleach_split_g(self, ...)

Raster and photobleaching implementation of a STED microscope acquisition.

raster_func_dymin(self, datamap, ...)

Implements the raster scanning and photobleaching of DyMIN microscopy

raster_func_rescue(self, datamap, ...)

Implements the raster scanning and photobleaching of RESCue microscopy

reset_prob(mask, prob_ex, prob_sted)

Resets the probability of survival of the fluorophores in the mask to 1.0
pysted.raster.raster_func_c_self_bleach_split_g(self, datamap, acquired_intensity, pixel_list, ratio, rows_pad, cols_pad, laser_pad, prob_ex, prob_sted, pdt_roi, p_ex_roi, p_sted_roi, bleach, bleached_sub_datamaps_dict, seed, bleach_func, sample_func, steps)

Raster and photobleaching implementation of a STED microscope acquisition.

raster_func_c_self_bleach executes the simultaneous acquisition and bleaching routine for the case where the excitation power (p_ex) AND/OR sted power (p_sted) AND/OR pixel dwell time vary through the sample. This function thus requires these parameters to be passed as arrays of floats the same size as the ROI being imaged.

Additionally, this function seperately bleaches the different parts composing the datamap (i.e. the base and flash components of the datamap are bleached separately).

To speed up the calculation, the position of the emitters are kept in memory and only those positions are updated by the bleaching method.

Parameters:

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

  • acquired_intensity – 2D array to store the acquired intensity

  • pixel_list – 2D array with the position of the pixels to be acquired

  • ratio – The ratio of the pixel size to the datamap pixel size

  • rows_pad – The number of rows to pad the datamap

  • cols_pad – The number of columns to pad the datamap

  • laser_pad – The number of pixels to pad the laser

  • prob_ex – 2D array with the probability of survival of the fluorophores under excitation

  • prob_sted – 2D array with the probability of survival of the fluorophores under sted

  • pdt_roi – 2D array with the pixel dwell time

  • p_ex_roi – 2D array with the excitation power

  • p_sted_roi – 2D array with the sted power

  • bleach – Boolean to indicate if the sample should be bleached

  • bleached_sub_datamaps_dict – Dictionary with the different parts of the datamap to be bleached

  • seed – Seed for the random number generator

  • bleach_func – Function to bleach the sample

  • sample_func – Function to sample the sample

  • steps – List with the different steps of the acquisition

pysted.raster.raster_func_dymin(self, datamap, acquired_intensity, pixel_list, ratio, rows_pad, cols_pad, laser_pad, prob_ex, prob_sted, returned_photons, scaled_power, pdt_roi, p_ex_roi, p_sted_roi, bleach, bleached_sub_datamaps_dict, seed, bleach_func, sample_func, steps)

Implements the raster scanning and photobleaching of DyMIN microscopy

Parameters:

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

  • acquired_intensity – 2D array to store the acquired intensity

  • pixel_list – 2D array with the position of the pixels to be acquired

  • ratio – The ratio of the pixel size to the datamap pixel size

  • rows_pad – The number of rows to pad the datamap

  • cols_pad – The number of columns to pad the datamap

  • laser_pad – The number of pixels to pad the laser

  • prob_ex – 2D array with the probability of survival of the fluorophores under excitation

  • prob_sted – 2D array with the probability of survival of the fluorophores under sted

  • pdt_roi – 2D array with the pixel dwell time

  • p_ex_roi – 2D array with the excitation power

  • p_sted_roi – 2D array with the sted power

  • bleach – Boolean to indicate if the sample should be bleached

  • bleached_sub_datamaps_dict – Dictionary with the different parts of the datamap to be bleached

  • seed – Seed for the random number generator

  • bleach_func – Function to bleach the sample

  • sample_func – Function to sample the sample

  • steps – List with the different steps of the acquisition

pysted.raster.raster_func_rescue(self, datamap, acquired_intensity, pixel_list, ratio, rows_pad, cols_pad, laser_pad, prob_ex, prob_sted, returned_photons, thresholds, pdt_roi, p_ex_roi, p_sted_roi, bleach, bleached_sub_datamaps_dict, seed, bleach_func, sample_func, steps)

Implements the raster scanning and photobleaching of RESCue microscopy

Parameters:

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

  • acquired_intensity – 2D array to store the acquired intensity

  • pixel_list – 2D array with the position of the pixels to be acquired

  • ratio – The ratio of the pixel size to the datamap pixel size

  • rows_pad – The number of rows to pad the datamap

  • cols_pad – The number of columns to pad the datamap

  • laser_pad – The number of pixels to pad the laser

  • prob_ex – 2D array with the probability of survival of the fluorophores under excitation

  • prob_sted – 2D array with the probability of survival of the fluorophores under sted

  • pdt_roi – 2D array with the pixel dwell time

  • p_ex_roi – 2D array with the excitation power

  • p_sted_roi – 2D array with the sted power

  • bleach – Boolean to indicate if the sample should be bleached

  • bleached_sub_datamaps_dict – Dictionary with the different parts of the datamap to be bleached

  • seed – Seed for the random number generator

  • bleach_func – Function to bleach the sample

  • sample_func – Function to sample the sample

  • steps – List with the different steps of the acquisition

pysted.raster.reset_prob(mask, prob_ex, prob_sted)

Resets the probability of survival of the fluorophores in the mask to 1.0

Parameters:

  • mask – list of tuples with the position of the fluorophores

  • prob_ex – 2D array with the probability of survival of the fluorophores under excitation

  • prob_sted – 2D array with the probability of survival of the fluorophores under sted