stereo.algorithm.st_gears.StGears.stack_slices_pairwise_elas_field

StGears.stack_slices_pairwise_elas_field(pixel_size, fil_pc=20, sigma=1, set_as_position=False, res_key='st_gears')[source]

Eliminating distorsions through Gaussian Smoothed Elastic Fields

Parameters:

  • pixel_size (float) – Edge length of single pixel, when generating elastic field. Input a rough average of spots distance here

  • fil_pc (float) – Percentage of ranked probabilities in transition matrix, after which probabilities will be filtered, defaults to 20

  • sigma (float) – sigma value of gaussina kernel, when filtering noises in elastic registration field, with a higher value indicating a smoother elastic field. Refer to this website to decide sigma according to your desired range of convolution, defaults to 1

  • set_as_position (bool) – Whether to use the new coordinates calculated by this method as the cells/bins position, defaults to False

  • res_key (str) – Must be the same as res_key in main function, defaults to ‘st_gears’