Upload Organoid_Analyzer_AI_zstack2_HF.py

Organoid_Analyzer_AI_zstack2_HF.py

@@ -284,14 +284,14 @@ def contour_overlap(contour1, contour2, centroid1, centroid2, area1, area2, cent
     else:
         return 1  # Some overlap but not meeting strict criteria
     
-def compare_frames(frame1, frame2):
+def compare_frames(frame1, frame2, centroid_dist=30, overlap_area=.4):
     for i in range(1, len(frame1)+1):
         if frame1.loc[i,"exclude"] == True:
             continue
         for j in range(1, len(frame2)+1):
             if frame2.loc[j,"exclude"] == True:
                 continue
-            temp = contour_overlap(frame1.loc[i, "contour"], frame2.loc[j, "contour"], frame1.loc[i, "centroid"], frame2.loc[j, "centroid"], frame1.loc[i, "organoid_area"], frame2.loc[j, "organoid_area"])
+            temp = contour_overlap(frame1.loc[i, "contour"], frame2.loc[j, "contour"], frame1.loc[i, "centroid"], frame2.loc[j, "centroid"], frame1.loc[i, "organoid_area"], frame2.loc[j, "organoid_area"],centroid_dist, overlap_area)
             if temp ==2:
                 frame2.loc[j,"exclude"] = True
             elif temp ==3:
@@ -306,7 +306,7 @@ def compare_frames(frame1, frame2):
 def main(args):
     min_size = args[1]
     min_circ = args[2]
-    do_necrosis = args[3]
+    do_necrosis = args[5]
     colonies = {}
     files = args[0]
     for idx,x in enumerate(files):
@@ -321,7 +321,7 @@ def main(args):
         if isinstance(colonies, dict):
             colonies = frame
         else:
-           colonies = compare_frames(frame, colonies)
+           colonies = compare_frames(frame, colonies, args[3], args[4])
     if len(colonies) <=0:
         img = pad(np.array(files[0]))
         if img.ndim == 2: