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Colony_Analyzer_AI2_HF.py

@@ -243,7 +243,7 @@ def main(args):
     colonies = colonies.drop('nec_contours', axis=1)
     
     colonies.insert(loc=0, column="Colony Number", value=[str(x) for x in range(1, len(colonies)+1)])
-    total_area_dark = sum(colonies['necrosis_area'])
+    total_area_dark = sum(colonies['necrotic_area'])
     total_area_light = sum(colonies['colony_area'])
     ratio = total_area_dark/(abs(total_area_light)+1)
     radii = [np.sqrt(x/3.1415) for x in list(colonies['colony_area'])]

Colony_Analyzer_AI_zstack2_HF.py

@@ -349,7 +349,7 @@ def main(args):
     img = cv2.copyMakeBorder(img,top=10, bottom=0,left=10,right=0, borderType=cv2.BORDER_CONSTANT,  value=[255, 255, 255]) 
     
     colonies.insert(loc=0, column="Colony Number", value=[str(x) for x in range(1, len(colonies)+1)])
-    total_area_dark = sum(colonies['necrosis_area'])
+    total_area_dark = sum(colonies['necrotic_area'])
     total_area_light = sum(colonies['colony_area'])
     ratio = total_area_dark/(abs(total_area_light)+1)
     radii = [np.sqrt(x/3.1415) for x in list(colonies['colony_area'])]