Upload Colony_Analyzer_AI_zstack2_HF.py

Colony_Analyzer_AI_zstack2_HF.py

@@ -268,13 +268,16 @@ def main(args):
         else:
            colonies = compare_frames(frame, colonies)
     if len(colonies) <=0:
+        img = np.array(files[0])
+        if img.ndim == 2:
+            img = cv2.cvtColor(img, cv2.COLOR_GRAY2BGR)
     	caption = np.ones((150, 2048, 3), dtype=np.uint8) * 255  # Multiply by 255 to make it white
     	cv2.putText(caption, 'No colonies detected.', (40, 40), cv2.FONT_HERSHEY_SIMPLEX, 1, (0, 0, 0), 3)
-    	cv2.imwrite('results.png', np.vstack((np.array(files[0]), caption)))
+    	cv2.imwrite('results.png', np.vstack(img, caption)))
     	colonies = pd.DataFrame({"Colony Number":[], 'Colony volume':[], "colony_area":[],'mean_pixel_value':[], "centroid":[], "necrotic_area":[],"percent_necrotic":[]})
     	with pd.ExcelWriter('results.xlsx') as writer:
             colonies.to_excel(writer, sheet_name="Colony data", index=False)
-    	return(np.vstack((files[0], caption)), 'results.png', 'results.xlsx')
+    	return(np.vstack((img, caption)), 'results.png', 'results.xlsx')
     counts = {}
     for x in range(len(files)):
         counts[x] = list(colonies["source"]).count(x)