This paper describes the adoption and validation of two innovative methods for the automated count of Ostreopsis spp. concentration in sea water: a molecular assay based on RT-qPCR and an opto-electronic device implementing automatic recognition algorithms. The proposed approaches were tested on samples coming from different locations along the Mediterranean Sea and compared with the standard counting method based on microscopy observation by a taxonomy expert. The results demonstrate the effectiveness of both automatic approaches which provide a valuable tool, mostly cost and time effective, for the establishment of wide pan-Mediterranean monitoring strategies of Ostreopsis spp. blooms. Moreover, the two automatic methods demonstrated the ability to discriminate for the presence of a different but similar species, O. fattorussoi, for which new species-specific qPCR primers were developed.

Microalgae are one of the most suitable subjects for testing the potentiality of light microscopy and image analysis, because of the size of single cells, their endogenous chromaticity, and their metabolic and physiological characteristics. Microscope observations and image analysis can use microalgal cells from lab cultures or collected from water bodies as model to investigate metabolic processes, behavior/reaction of cells under chemical or photic stimuli, and dynamics of population in the natural environment in response to changing conditions. In this paper we will describe the original microscope we set up together with the image processing techniques we improved to deal with these topics. Our system detects and recognizes in-focus cells, extracts their features, measures cell concentration in multi-algal samples, reconstructs swimming cell tracks, monitors metabolic processes, and measure absorption and fluorescent spectra of subcellular compartments. It can be used as digital microscopy station for algal cell biology and behavioral studies, and field analysis applications.

Quality loss during storage is often associated to changes in relevant product colors and/or to the appearance of new pigments. Computer Vision System (CVS) for non-destructive quality evaluation often relies on human knowledge provided by operators to identify these relevant colors and their features. The approach described in this paper automatically identifies the most significant colors in unevenly colored products to evaluate their quality level. Its performance was compared with results obtained by exploiting human training. The new method improved quality evaluation and reduced the subjectivity and the inconsistency potentially induced by operators.

alpha-Helices are peculiar atomic arrangements characterizing protein structures. Their occurrence can be used within crystallographic methods as minimal a priori information to drive the phasing process towards solution. Recently, brute-force methods have been developed which search for all possible positions of alpha-helices in the crystal cell by molecular replacement and explore all of them systematically. Knowing the alpha-helix orientations in advance would be a great advantage for this kind of approach. For this purpose, a fully automatic procedure to find alpha-helix orientations within the Patterson map has been developed. The method is based on Fourier techniques specifically addressed to the identification of helical shapes and operating on Patterson maps described in spherical coordinates. It supplies a list of candidate orientations, which are then refined by using a figure of merit based on a rotation function calculated for a template polyalanine helix oriented along the current direction. The orientation search algorithm has been optimized to work at 3 A resolution, while the candidates are refined against all measured reflections. The procedure has been applied to a large number of protein test structures, showing an overall efficiency of 77% in finding alpha-helix orientations, which decreases to 48% on limiting the number of candidate solutions (to 13 on average). The information obtained may be used in many aspects in the framework of molecular-replacement phasing, as well as to constrain the generation of models in computational modelling programs. The procedure will be accessible through the next release of IL MILIONE and could be decisive in the solution of new unknown structures.