polyTEM.tomography.alignment.find_markers¶

polyTEM.tomography.alignment.find_markers(imgarray, num_markers: int, contrast: str = 'bright', kernel_size=25, kernel_step=5, max_iter=5, _recursion_count=0, debug=False)¶

Find gold fiduciary markers in image

Relies on large contrast of gold to identify nanoparticles. Uses otsu’s threshold, image opening, and kmeans clustering.

Parameters:

imgarray – numpy 2D array of image
contrast – string signally whether the gold are the “bright” or “dark” spots in image
num_markers – number of gold particles in image

Returns:

row,col locations of the markers