stereo.tools.tissue_extraction.tissue_extraction_to_bgef#
- stereo.tools.tissue_extraction.tissue_extraction_to_bgef(src_gef_path, dst_bgef_path, dst_mask_dir_path, staining_type=None, model_path='', src_img_path='', rna_tissue_cut_bin_size=1, gpu='-1', num_threads=-1)[source]#
- Parameters:
src_gef_path (
Optional[str]) – the gef will be extracted by mask.tif from tissue cut.dst_bgef_path (
Optional[str]) – result bgef path, contains file name.dst_mask_dir_path (
Optional[str]) – save tissue cut result mask.tif to this directory.staining_type (
Optional[str]) – the staining type of regist.tif, available values include ‘ssDNA’, ‘dapi’, ‘HE’, ‘mIF’ and ‘RNA’, except ‘RNA’ staining type,src_img_pathis required, while setting to ‘RNA’, the mask.tif will be generated from src gef.model_path (
Optional[str]) – the path if model used to generated mask.tif, it has to be matched with staining type.src_img_path (
Optional[str]) – the path of regist.tif which is used to generated mask.tif.rna_tissue_cut_bin_size (
Optional[int]) – fixed value 1.gpu (
Union[int,str]) – the gpu on which the model will work, -1 means working on cpu.num_threads (
int) – the number of threads when model work on cpu, -1 means using all the cores.
- Returns:
the dst_bgef_path