Small fixes

Author: schilling40

reproducibility/label_components/repro_label_components.py

@@ -32,7 +32,6 @@ def repro_label_components(
     for dic in param_dicts:
         cochlea = dic["cochlea"]
         print(f"Labeling components for {cochlea}.")
-        unet_version = dic["unet_version"]
 
         threshold_erode = dic["threshold_erode"] if "threshold_erode" in dic else default_threshold_erode
         min_component_length = dic["min_component_length"] if "min_component_length" in dic else default_min_length

scripts/dilate_sgns.py

@@ -7,6 +7,7 @@
 
 LOWER_RESOLUTION_DIR = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/lower_resolution"
 
+
 def dilate_sgns(in_path, out_path, dilation_distance, block_shape=[64, 128, 128], halo=[8, 16, 16]):
     print(f"Dilating {in_path} with dilation distance {dilation_distance}.")
     seg = tifffile.imread(in_path).astype("uint32")

scripts/measurements/sgn_subtypes.py

@@ -135,6 +135,13 @@ def stain_to_type(stain):
         # Prph is isolated.
         "Prph+": "Type II",
         "Prph-": "Type I",
+
+        # Combinations of CR and Ntng1
+        "CR+/Ntng1+": "Type Ib",
+        "CR+/Ntng1-": "Type Ia",
+        "CR-/Ntng1+": "Type Ic",
+        "CR-/Ntng1-": "inconclusive",
+
     }
 
     if stain_norm not in stain_to_type: