## 1 Introduction  
Diatoms are a major group of algae and are among the most common microorganisms in marine and freshwater habitats. They are important contributors to the primary production in aquatic ecosystems, placed at the bottom of the food chain. The diatoms have been shown to be increasingly important worldwide in studies related to climate change, as well as in the development of functions that allow the modeling of such change. Moreover, they are good indicators of environmental conditions and are commonly used in water quality assessment [1,2]. Diatom indices are known to correlate more significantly with water chemical variables, within continental waters, while macroinvertebrate- or plant-based methods are more sensitive to changes affecting structural parameters [3]. Diatoms have several advantages over other indicators that make them ideal as indicators of water quality. These features are: (a) their ability to spread over a variety of habitats; (b) they are relatively easy to sample, and such sampling has no impact on the ecosystem during collection; (c) they have a quick response to variation in environmental conditions; and (d) they are sensitive to changes in environmental conditions that may not be observed in other communities. Diatom cells are enclosed within a unique silica cell wall known as a frustule made up of two valves, which fit into each other like a pill box. The frustules show a wide diversity of shapes and sizes, though mainly, they can be divided into centric diatoms (radial symmetry, rounded) and pennate diatoms (bilateral symmetry, elongated). The main taxonomic features used in diatom identification are related to the morphology and ornamentation of the frustule. The presence of raphe and the ornamentation of the frustule, stigmata and other features are important in identifying these organisms [4]. The diatom size, in the range of 2-2000 \(\upmu\)m, is suitable for observation of most species using an optical microscope. However, diatoms require specialized skills for their classification, that is trained diatomists (phyclologists specializing in diatom taxonomy). As stated in [5], more than 200,000 diatom species are estimated to exist, although just half of them have been described. Several intercalibration tests have shown that the results of biological indices based on diatoms are highly sensitive to the level of accuracy in taxonomic classification [6]. The identification task is very difficult due to the huge number of species estimated to exist [7]. Classical taxonomic diagnosis is performed using key features or by visual comparison with type samples or reference iconographies [8]. The conventional approach is to analyze these microalgae using light microscopy (brightfield, DIC, RIC, etc.). Diatom-based metrics are calculated based on the relative abundance of different taxa in an assemblage and the autecological parameters characterizing each species. However, the current manual analysis of images is tedious, requiring highly qualified staff, and it is time consuming. This is the case when diatoms are used in the context of water quality, as in this study. According to a European directive, in order to compute an index score, the identification of a minimum of 400 valves per sample is required [9]. In the case of transparent specimens such as diatoms, brightfield microscopy presents some difficulties. Some details are barely distinguishable from the background, and some other alternative modalities such as phase contrast, DIC or dark field need to be considered. There are few species of the _Nitzschia_, which are good examples of that (_Nitzschia coseti_, _Nitzschia frustulum var frustulum_ and _Nitzschia inconspicua_). This is probably due to a not well-developed silicification process. Phase contrast microscopy is a suitable technique for visualizing transparent specimens. However, it produces some artifacts (halos and shading-off) that limit its usefulness in some applications.