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Automated systems can be used to facilitate continual collection of biological information from a large number of samples over long periods of time. The proper combination of automated systems with fluorescent reporter genes offers the potential for non-destructive analysis of gene expression over time. One of the fluorescent genes more commonly used in many different areas of biology is the green fluorescent protein (GFP) gene from jellyfish. The expression of this reporter gene can be detected in the tissues of any transgenic organism by using a microscope equipped with special illumination and emission filters. The main aim of this work was to develop a computer-controlled automated system to monitor GFP gene expression over time. The automated system consists of a two-dimensional belt-driven positioning table, a custom-designed sample holder, and a charged-coupled device (CCD) camera mounted on a stereomicroscope equipped for GFP fluorescence detection. To precisely control the system, software with custom applications was generated. The automated system was used to monitor the response of GFP-expressing Agrobacterium to plant tissues in vitro. Gene expression and bacterial growth were successfully monitored and quantified using image analysis. Our results showed that bacterial colonies growing in the presence of plant tissue had faster growth than those growing in the absence of plant tissues.