Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy

Quantitative analysis of biological image data generally involves the detection of many subresolution spots. Especially in live cell imaging, for which fluorescence microscopy is often used, the signal-to-noise ratio (SNR) can be extremely low, making automated spot detection a very challenging task. In the past, many methods have been proposed to perform this task, but a thorough quantitative evaluation and comparison of these methods is lacking in the literature. In this paper, we evaluate the performance of the most frequently used detection methods for this purpose. These include seven unsupervised and two supervised methods. We perform experiments on synthetic images of three different types, for which the ground truth was available, as well as on real image data sets acquired for two different biological studies, for which we obtained expert manual annotations to compare with. The results from both types of experiments suggest that for very low SNRs (approximate to 2), the supervised (machine learning) methods perform best overall. Of the unsupervised methods, the detectors based on the so-called h-dome transform from mathematical morphology or the multiscale variance-stabilizing transform perform comparably, and have the advantage that they do not require a cumbersome learning stage. At high SNRs (> 5), the difference in performance of all considered detectors becomes negligible.