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We propose a neurobiologically inspired visual simultaneous localization and mapping (SLAM) system based on direction sparse method to real-time build cognitive maps of large-scale environments from a moving stereo camera. The core SLAM system mainly comprises a Bayesian attractor network, which utilizes neural responses of head direction (HD) cells in the hippocampus and grid cells in the medial entorhinal cortex (MEC) to represent the head direction and the position of the robot in the environment, respectively. Direct sparse method is employed to accurately and robustly estimate velocity information from a stereo camera. Input rotational and translational velocities are integrated by the HD cell and grid cell networks, respectively. We demonstrated our neurobiologically inspired stereo visual SLAM system on the KITTI odometry benchmark datasets. Our proposed SLAM system is robust to real-time build a coherent semi-metric topological map from a stereo camera. Qualitative evaluation on cognitive maps shows that our proposed neurobiologically inspired stereo visual SLAM system outperforms our previous brain-inspired algorithms and the neurobiologically inspired monocular visual SLAM system both in terms of tracking accuracy and robustness, which is closer to the traditional state-of-the-art one.