Quantifying the colocalisation of labels is a major application of fluorescent microscopy in plant biology. Pixel-based, i.e. Pearson's coefficient, quantification of colocalisation is a limited tool that gives limited information for further analysis. We show how applying bioimage informatics tools to a commonplace experiment allows further quantifiable results to be extracted. We use our object-based colocalisation technique to extract distance information, show temporal changes and demonstrate the advantages, and pitfalls, of using bioimage informatics for plant science.