cows.find_filaments

cows.find_filaments(skel, periodic=False)[source]

Find individual filament.

Connects all cells that are neighbours within a 3x3x3 neihbourhood. The set of connected cells are labled with a unique ID.

Parameters:

  • skel (ndarray, 3D) – An array containing the classified and separated skeleton. Zeros represent background, ones are endpoints and twos are regular cells.

  • periodic (bool) – If True, the skeletonization uses periodic boundary conditions for the input array. Input array must be 3D.

Returns:

  • result (ndarray, 3D) – An array with skel.shape containing the sets of connected cells (filaments) with their respective ID.

  • catalogue (ndarray, 2D) – A catalogue containing, for each cell, a row of ID, X-, Y- and Z- position.