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With the growth of the scale, depth, and resolution of astronomical imaging surveys, there is an increased need for highly accurate automated detection and extraction of astronomical sources from images. This also means there is a need for objective quality criteria, and automated methods to optimise parameter settings for these software tools. We present a comparison of several tools which have been developed to perform this task: namely SExtractor, ProFound, NoiseChisel, and MTObjects. In particular, we focus on evaluating performance in situations which present challenges for detection -- for example, faint and diffuse galaxies; extended structures, such as streams; and objects close to bright sources. Furthermore, we develop an automated method to optimise the parameters for the above tools. We present four different objective segmentation quality measures, based on precision, recall, and a new measure for the correctly identified area of sources. Bayesian optimisation is used to find optimal parameter settings for each of the four tools on simulated data, for which a ground truth is known. After training, the tools are tested on similar simulated data, to provide a performance baseline. We then qualitatively assess tool performance on real astronomical images from two different surveys. We determine that when area is disregarded, all four tools are capable of broadly similar levels of detection completeness, while only NoiseChisel and MTObjects are capable of locating the faint outskirts of objects. MTObjects produces the highest scores on all tests on all four quality measures, whilst SExtractor obtains the highest speeds. No tool has sufficient speed and accuracy to be well-suited to large-scale automated segmentation in its current form.