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The present study introduces a new MATLAB toolbox, called MatMouse, suitable for the performance of experimental studies based on mouse movements tracking and analysis. MatMouse supports the implementation of task-based visual search experiments. The proposed toolbox provides specific functions which can be utilized for the experimental building and mouse tracking processes, the analysis of the recorded data in specific metrics, the production of related visualizations, as well as for the generation of statistical grayscale heatmaps which could serve as an objective ground truth product. MatMouse can be executed as a standalone package or integrated in existing MATLAB scripts and/or toolboxes. In order to highlight the functionalities of the introduced toolbox, a complete case study example is presented. MatMouse is freely distributed to the scientific community under the third version of GNU General Public License (GPL v3) on GitHub platform.