PYME.IO.FileUtils.readSpeckle module

Created on Thu Jul 9 13:46:29 2015

@author: david

PYME.IO.FileUtils.readSpeckle.gen_traces_from_speckles(speckles, leadFrames=10, followFrames=50, seriesLength=1000000, clipRegion=[0, 0, 512, 512])

Generate pseudo particle trajectories from speckle data.

These trajectories look like they were generated using the normal particle tracking methods, but are centered at the detected speckle position. They extend before the start of the speckle trace (to establish a baseline), and after the end of the speckle trace (to look at the diffusion of the membrane label away from the point of fusion.

Parameters

speckleslist

list of [x,y,t]xN arrays containing the trace for each speckle

leadFramesint

Number of frames to extract before the start of the speckle for establishing the baseline

followFramesint

Number of frames to extract after the end of the speckle to follow the diffusion of the fused dyes.

seriesLengthint

the length of the image series - traces will not extend beyond the end of the series.

Returns

a numpy recarray containing x, y, t, and clumpIndex columns

PYME.IO.FileUtils.readSpeckle.readSpeckles(filename)