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An alignment method for holographic data storage system (HDSS) is proposed in this paper. Due to several types of noises encountered in the HDSS, the signal-to-noise ratio (SNR) is degraded. Errors can be corrected using a channel code for some sorts of noise, while it may require a high quality optical system to reduce the error probability for the other types of noise. A checkerboard pattern is proposed using intensity weighting to find the fiducial points, which could work in a lower SNR system and thus reduce the error likelihood effectively. Reed-solomon (RS) code and oversampling are both made available in the HDSS. As a consequence, the aberration effects are eliminated using the fiducial points, leading to a low SNR system clear of errors after performing decoding. The lowest SNR system is out of error-free recovery condition, so that all the alignment methods proposed in this paper could not reduce the aberration effects to restore the images into the original data.