Deep Learning Versus Classic Methods for Multi-taxon Diatom Segmentation

Diatom identification is a crucial process to estimate water quality, which is essential in biological studies. This process can be automated with machine learning algorithms. For this purpose, a dataset with 10 common taxa is collected, with annotations provided by an expert diatomist. In this work, a comparison of the classical state-of-the-art general purpose methods along with two different deep learning approaches is carried out. The classical methods are based on Viola-Jones and scale and curvature invariant ridge object detectors. The deep learning based methods are Semantic Segmentation and YOLO. This is the first time that Viola-Jones and Semantic Segmentation techniques are applied and compared for diatom segmentation in microscopic images containing several taxon shells. While all methods provide relatively good results in specific species, the deep learning approaches are consistently better in terms of sensitivity and specificity (up to 0.99 for some taxa) and up to 0.86 precision.