diff --git a/wsi_preprocessing/slides.py b/wsi_preprocessing/slides.py index b5a721e..c3a2c87 100644 --- a/wsi_preprocessing/slides.py +++ b/wsi_preprocessing/slides.py @@ -14,7 +14,7 @@ def list_slides(slides_dir, glob_pattern="*.svs"): return slides -def save_slides_mpp_otsu(slides, csv_fname, mpp_key="openslide.mpp-x"): +def save_slides_mpp_otsu(slides, csv_fname, mpp_key="openslide.mpp-x", level=2): d = {} d["slide_path"] = [] @@ -34,7 +34,7 @@ def save_slides_mpp_otsu(slides, csv_fname, mpp_key="openslide.mpp-x"): print(f"- finding slide resolution") - vi = utils.read_image(file, access="sequential", level=2) + vi = utils.read_image(file, access="sequential", level=level) try: # TODO: generalize the mpp_key?