An automatic sample centering system is underway at the protein crystallography beam line of the Pohang Light Source to improve the efficiency of the crystal screening process. A sample pin which contains a protein crystal is mounted on a goniometer head. Then the crystal should be moved to the center of X-ray beam by controlling the motorized goniometer to obtain diffraction data. Since the X-ray beam is located at the center of the image obtained from the CCD camera when the image of the sample pin is in focus, an auto-focusing algorithm is a very important part in the auto-sample-centering system. However the results of applying several well-known auto focusing algorithms directly to the images are not satisfactory owing to the following factors: misalignment of CCD camera, non-uniform cryo-stream in the background of the image and the supporter of the loop. The performance of an auto-focusing algorithm can be increased if the algorithm is applied to only the loop region identified. Non-uniform cryo-stream and a various illumination condition and a stain, which is shown in the image, are main obstacles to loop region identification. In this paper, a simple loop region identification algorithm, which can solve these problems, is proposed and the effective ness of the proposed scheme is shown by applying the auto-focusing algorithm to the loop region identified.