stereo.image.segmentation_deepcell.segment.cell_seg_deepcell#

stereo.image.segmentation_deepcell.segment.cell_seg_deepcell(img_path, out_path, model_path=None, deep_crop_size=20000, overlap=100, post_processing_workers=10, tissue_seg_model_path=None, tissue_seg_staining_type=None, tissue_seg_num_threads=-1, gpu='-1')[source]#

Cell segmentation on regist.tif by deep cell model.

Parameters:

  • img_path (str) – the path of regist.tif without tissue segmentation.

  • out_path (str) – the path of directory to save the result cell mask.tif.

  • model_path (Optional[str]) – the path of deep cell model.

  • deep_crop_size (int) – deep crop size, defaults to 20000.

  • overlap (int) – over lap size, defaults to 100.

  • post_processing_workers (int) – the number of processes on post processing, defaults to 10.

  • tissue_seg_model_path (Optional[str]) – the path of model used to tissue segmentation, defaults to None.

  • tissue_seg_staining_type (Optional[str]) – the staining type of regist.mask, defaults to None.

  • tissue_seg_num_threads (int) – the number of threads when model work on cpu, -1 means using all the cores.

  • gpu (str) – the gpu on which the model works, available for both cell segmtation and tissue segmtation, ‘-1’ means working on cpu.