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Foci picking.

Finds foci using a Laplacian convolution. See https://scikit-image.org/docs/stable/auto_examples/features_detection/plot_blob.html for details. Foci are linked to the cell objects in which they appear.

Input

  • .pkl file of cell objects from Track widget.

Output

  • .pkl file with a dictionary of cell objects, with x, y and time positions of foci detections stored as attributes of the corresponding cell objects.

Parameters

  • LoG_min_sig : Minimum sigma of laplacian to convolve in pixels. Scales with minimum foci width to detect as 2*sqrt(2)*minsig
  • LoG_max_sig: Maximum sigma of laplacian to convolve in pixels. Scales with maximum foci width to detect as 2*sqrt(2)*maxsig
  • LoG_threshold : Absolute threshold laplacian must reach to record potential foci. Keep low to detect dimmer spots.
  • LoG_peak_ratio : Focus peaks must be this many times greater than median cell intensity. Think signal to noise ratio