diff --git a/eyelign/gui_manual_align.py b/eyelign/gui_manual_align.py
new file mode 100644
index 0000000..415caf6
--- /dev/null
+++ b/eyelign/gui_manual_align.py
@@ -0,0 +1,72 @@
+import logging
+import cv2
+import os
+import click
+import json
+import shutil
+logging.basicConfig(
+    level=logging.INFO,
+    format="%(asctime)s [%(levelname)s]: %(message)s",
+    datefmt="%Y-%m-%d %H:%M:%S",
+)
+
+
+@click.command()
+@click.argument(
+    "input_dir",
+    type=click.Path(exists=True, readable=True),
+    envvar="EYELIGN_INPUT_DIR",
+)
+
+def cli(
+    input_dir
+):
+    logging.info('Click left eye and right eye in order\n \
+                If click wrong, press ESC to exit and align agin\n \
+                    Aligned image info would not lost')
+    read_json_path=os.path.join(input_dir,'.eyelign')
+    align_file=json.load(open(read_json_path,'r'))
+    
+    # mouse callback helper function
+    feature_points_2d = []
+    FEATURE_NUM = 2
+    def draw_circle(event, x, y, flags, param):
+        if event == cv2.EVENT_LBUTTONDOWN:
+            cv2.circle(img,(x,y),10,(0,0,255),-1)
+            feature_points_2d.append([x, y])
+    
+    exit_flag=False
+    for file_name in align_file:
+        ## Check if the eyes are detected
+        data=align_file[file_name]
+        lx=data['lx']
+        if lx is None:
+            logging.info(f'Manual align file {file_name}')
+            img_path=os.path.join(input_dir,file_name)
+            img = cv2.imread(img_path)
+            cv2.namedWindow("image")
+            cv2.setMouseCallback("image", draw_circle)
+            while True:
+                cv2.imshow("image", img)
+                if len(feature_points_2d) == FEATURE_NUM:
+                    if len(feature_points_2d)==2:
+                        align_file[file_name]['lx']=feature_points_2d[0][0]
+                        align_file[file_name]['ly']=feature_points_2d[0][1]
+                        align_file[file_name]['rx']=feature_points_2d[1][0]
+                        align_file[file_name]['ry']=feature_points_2d[1][1]
+                    feature_points_2d = [] # reset
+                    break
+                if (cv2.waitKey(20) & 0xFF == 27):
+                    exit_flag=True
+                    break
+        if exit_flag is True:
+            break
+    backup_path=os.path.join(input_dir,'.eyelign.bak')
+    shutil.copy(read_json_path,backup_path)
+    logging.info(f'Backup the original align file to {backup_path}')
+    with open(read_json_path, 'w') as outfile:
+        json.dump(align_file, outfile,indent=2)
+
+
+if __name__ == "__main__":
+    cli()