locate_specimens

shampoo.locate_specimens(wave_cube, positions, labels, distances, plots=False)

Identify the (x, y, z) coordinates of a specimen.

Parameters:

wave_cube : ndarray

Cube of reconstructed waves

positions : ndarray

(x,y,z) positions of objects detected by the blob finder

labels : ndarray

Clustering labels for each (x,y,z) coordinate, identifying groups of positions, i.e., single particles detected at multiple z-planes

distances : ndarray

Propagation distances, same length as the first axis of complex_cube

Returns:

specimen_coordinates : ndarray

(x, y, z) coordinates of each detected specimen

specimen_coordinates : ndarray

Significance of each specimen detection. See docs of find_focus_plane for hints on how to interpret the significance quantity.