diff --git a/panpipes/funcs/io.py b/panpipes/funcs/io.py index b50496da..af41d6ff 100644 --- a/panpipes/funcs/io.py +++ b/panpipes/funcs/io.py @@ -156,6 +156,15 @@ def gen_load_spatial_jobs(caf, mode_dictionary = {}, load_raw=True): spatial_filetype = None else: spatial_path = caf["spatial_path"][nn] + if caf['spatial_filetype'][nn]=="xenium": + spatial_filetype = caf['spatial_filetype'][nn] + visium_feature_bc_matrix = None + visium_fullres_image_file = None + visium_tissue_positions_file = None + visium_scalefactors_file = None + vpt_cell_by_gene = None + vpt_cell_metadata = None + vpt_cell_boundaries = None if caf['spatial_filetype'][nn]=="vizgen": visium_feature_bc_matrix = None visium_fullres_image_file = None diff --git a/panpipes/python_scripts/make_spatialData_from_csv.py b/panpipes/python_scripts/make_spatialData_from_csv.py index d34c4822..0d22a5c6 100644 --- a/panpipes/python_scripts/make_spatialData_from_csv.py +++ b/panpipes/python_scripts/make_spatialData_from_csv.py @@ -155,7 +155,9 @@ def check_dir_transform(infile_path, transform_file): tissue_positions_file=args.tissue_positions_file, scalefactors_file=args.scalefactors_file) - +elif args.spatial_filetype =="xenium": + sdata = sd_io.xenium(path = args.spatial_infile) + L.info("Resulting SpatialData is:") L.info(sdata) #L.info("Creating MuData with .mod['spatial']")