follow_flows#

cellpose_omni.dynamics.follow_flows(dP, mask=None, inds=None, niter=200, interp=True, use_gpu=True, device=None, omni=False, calc_trace=False)[source]#

define pixels and run dynamics to recover masks in 2D

Pixels are meshgrid. Only pixels with non-zero cell-probability are used (as defined by inds)

Parameters
  • dP (float32, 3D or 4D array) -- flows [axis x Ly x Lx] or [axis x Lz x Ly x Lx]

  • mask ((optional, default None)) -- pixel mask to seed masks. Useful when flows have low magnitudes.

  • niter (int (optional, default 200)) -- number of iterations of dynamics to run

  • interp (bool (optional, default True)) -- interpolate during 2D dynamics (not available in 3D) (in previous versions + paper it was False)

  • use_gpu (bool (optional, default False)) -- use GPU to run interpolated dynamics (faster than CPU)

Returns

p -- final locations of each pixel after dynamics

Return type

float32, 3D array