pysted.base.TemporalDatamap

class pysted.base.TemporalDatamap(whole_datamap, datamap_pixelsize, synapses)

Implements a dynamic datamap

This class inherits from Datamap, adding the t dimension to it for managing Ca2+ flashes and diffusion. The TemporalDatamap object is split into subdatamaps. In the simplest case, the only subdatamap is the base, which does not change with time (unless being acquired on with bleaching). In the case of Ca2+ flashes, we can add a subdatamap containing the flashes separately from the base datamap. Thus, for a certain time step t, the whole_datamap is the sum of the base and the flash at idx t.

Currently, as there is only the Ca2+ flash dynamics implemented, the TemporalDatamap is initialized by passing the whole molecule disposition and the pixelsize, as for Datamap, with the addition of a list containing all of the synapse objects in the Datamap.

Parameters:

  • whole_datamap – The disposition of the molecules in the sample. This represents the whole sample, from which only a region will be imaged (roi). (numpy array)

  • datamap_pixelsize – The size of a pixel of the datamap. (m)

  • synapses – The list of synapses present in the whole_datamap

TemporalDatamap.bleach_future(indices, ...)

Applies bleaching to the future flash subdatamaps according to the bleaching that occured to the current flash subdatamap

TemporalDatamap.create_t_stack_dmap(...)

Generates the flashes for the TemporalDatamap.

TemporalDatamap.set_bleached_datamap(...)

Updates the datamap.

TemporalDatamap.set_roi(laser[, intervals])

Sets the Region of Interest for the acquisition.

TemporalDatamap.update_dicts(indices)

Method used to update the dicts of the temporal datamap.

TemporalDatamap.update_whole_datamap(flash_idx)

Method used to update the whole datamap using the indices of the sub datamaps.