Merge pull request #77 from zcoman/cellmaskC&D

Updating ranges and ease of batch processing for masks C and D workflows
ndcn · Apr 12, 2024 · 6b0b04e · 6b0b04e
2 parents b48e1fa + 42337b6
commit 6b0b04e
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Showing 3 changed files with 17 additions and 8 deletions.
diff --git a/infer_subc/organelles/membrane.py b/infer_subc/organelles/membrane.py
@@ -235,11 +235,13 @@ def double_watershed(nuc: np.ndarray,
                                      method=Watershed_Method)
 
     cm_combo = cm_A.astype(bool) + cm_B.astype(bool)
-    out_img = close_and_fill(in_img=cm_combo,
+    cm_out = close_and_fill(in_img=cm_combo,
                              Min_Hole_Width=Min_Hole_Width,
                              Max_Hole_Width=Max_Hole_Width,
                              Method=Method,
                              Size=Size)
+
+    out_img = np.stack([nuc, cm_out], axis=0)
 
     return out_img
 

diff --git a/infer_subc/organelles_config/all_functions.json b/infer_subc/organelles_config/all_functions.json
@@ -2221,7 +2221,7 @@
             "Thresh_Adj": {
                 "data_type": "float",
                 "increment": 0.1,
-                "max": 5,
+                "max": 10,
                 "min": 0,
                 "widget_type": "slider"
             }
@@ -2286,14 +2286,14 @@
             "Min_Hole_Width": {
                 "data_type": "int",
                 "increment": 1,
-                "max": 40,
+                "max": 1000,
                 "min": 0,
                 "widget_type": "slider"
             },
             "Max_Hole_Width": {
                 "data_type": "int",
                 "increment": 1,
-                "max": 40,
+                "max": 1000,
                 "min": 4,
                 "widget_type": "slider"
             },
@@ -2344,14 +2344,14 @@
             "Min_Hole_Width": {
                 "data_type": "int",
                 "increment": 1,
-                "max": 40,
+                "max": 1000,
                 "min": 0,
                 "widget_type": "slider"
             },
             "Max_Hole_Width": {
                 "data_type": "int",
                 "increment": 1,
-                "max": 40,
+                "max": 1000,
                 "min": 4,
                 "widget_type": "slider"
             },
@@ -2380,14 +2380,14 @@
             "Min_Hole_Width": {
                 "data_type": "int",
                 "increment": 1,
-                "max": 40,
+                "max": 10000,
                 "min": 0,
                 "widget_type": "slider"
             },
             "Max_Hole_Width": {
                 "data_type": "int",
                 "increment": 1,
-                "max": 40,
+                "max": 10000,
                 "min": 4,
                 "widget_type": "slider"
             },

diff --git a/infer_subc/organelles_config/conf_0.1.masks_D.json b/infer_subc/organelles_config/conf_0.1.masks_D.json
@@ -53,5 +53,12 @@
         "parameter_values": null,
         "parent": [1,2,3],
         "annotation": "singles out one cell from the watershed"
+    },
+    "5":{
+        "category": "export",
+        "function": "stack_layers",
+        "parameter_values": null,
+        "parent": [2, 4],
+        "annotation": "stacks nuclei and cellmask for batch processing and export"
     }
 }