ovrlpy.detect_doublets

ovrlpy.detect_doublets(integrity_map, signal_map, min_distance=10, integrity_threshold=0.7, minimum_signal_strength=3, integrity_sigma=None)

This function is used to find individual low peaks of signal integrity in the tissue map as an indicator of single occurrences overlapping cells.

Parameters:

• integrity_map (ndarray) – Pixel map of signal integrity obtained from ovrlpy analysis

• signal_map (ndarray) – Signal strength map from ovrlpy analysis

• min_distance (int, optional) – Minimum distance between reported peaks

• integrity_threshold (float, optional) – Threhold of signal integrity value. A peak with an signal integrity > integrity_threshold is not considered.

• minimum_signal_strength (float, optional) – Minimum signal value for a peak to be considered

• integrity_sigma (float, optional) – Optional sigma value for gaussian filtering of the integrity map, which leads to the detection of overlap regions with larger spatial extent.