title: Algae through the looking glass.
abstract: 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.
authors.affiliation: Istituto Scienza e Tecnologie dell'Informazione, CNR, Via Moruzzi 1, Pisa, 56124, Italy.
authors.forename: Primo
authors.initials: P
authors.lastname: Coltelli
authors.affiliation: Istituto di Biofisica, CNR, Via Moruzzi 1, Pisa, 56124, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Barsanti
authors.affiliation: Istituto di Biofisica, CNR, Via Moruzzi 1, Pisa, 56124, Italy.
authors.forename: Valter
authors.initials: V
authors.lastname: Evangelista
authors.affiliation: Istituto di Biofisica, CNR, Via Moruzzi 1, Pisa, 56124, Italy.
authors.forename: Paolo
authors.identifier: http://orcid.org/0000-0001-7203-948X
authors.initials: P
authors.lastname: Gualtieri
mesh_terms: D002857:Chromium / Q000737:chemistry; D003116:Color; D005055:Euglena / Q000737:chemistry / Q000166:cytology / Q000648:ultrastructure; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D058086:Microalgae / Q000737:chemistry / Q000166:cytology / Q000378:metabolism* / Q000648:ultrastructure*; D008853:Microscopy / Q000379:methods*; D009068:Movement; D020283:Photoreceptors, Microbial / Q000648:ultrastructure; D013057:Spectrum Analysis
chemical_list: D020283:Photoreceptors, Microbial; D002857:Chromium
keywords: automatic identification; automatic track reconstruction; digital microscopy; microalgae; microspectroscopy