masks_flows_to_seg#

cellpose_omni.io.masks_flows_to_seg(images, masks, flows, diams, file_names, channels=None)[source]#

save output of model eval to be loaded in GUI

can be list output (run on multiple images) or single output (run on single image)

saved to file_names[k]+'_seg.npy'

Parameters

  • images ((list of) 2D or 3D arrays) -- images input into cellpose

  • masks ((list of) 2D arrays, int) -- masks output from cellpose_omni.eval, where 0=NO masks; 1,2,...=mask labels

  • flows ((list of) list of ND arrays) -- flows output from cellpose_omni.eval

  • diams (float array) -- diameters used to run Cellpose

  • file_names ((list of) str) -- names of files of images

  • channels (list of int (optional, default None)) -- channels used to run Cellpose