Motivation: Study of brain images of rodent animals is the most straightforward way to understand brain functions and neural basis of physiological functions. An important step in brain image analysis is to precisely assign signal labels to specified brain regions through matching brain images to standardized brain reference atlases. However, no significant effort has been made to match different types of brain images to atlas images due to influence of artifact operation during slice preparation, relatively low resolution of images and large structural variations in individual brains. Results: In this study, we develop a novel image sequence matching procedure, termed accurate and robust matching brain image sequences (ARMBIS), to match brain image sequences to established atlas image sequences. First, for a given query image sequence a scaling factor is estimated to match a reference image sequence by a curve fitting algorithm based on geometric features. Then, the texture features as well as the scale and rotation invariant shape features are extracted, and a dynamic programming-based procedure is designed to select optimal image subsequences. Finally, a hierarchical decision approach is employed to find the best matched subsequence using regional textures. Our simulation studies show that ARMBIS is effective and robust to image deformations such as linear or non-linear scaling, 2D or 3D rotations, tissue tear and tissue loss. We demonstrate the superior performance of ARMBIS on three types of brain images including magnetic resonance imaging, mCherry with 4′,6-diamidino-2-phenylindole (DAPI) staining and green fluorescent protein without DAPI staining images.