Abstract: A novel technique for automated analysis of organisms like insects, shrimp and fish. The technique comprises detection of structures and/or organs in the organisms in a flow-system. Alternatively or in addition, the technique may comprise sorting of the organisms, for example sex separation of the organisms in the flow system. The technique may comprise steps of: (a) illuminating the organisms in a detection region, (b) imaging the organisms in the detection region, with an extended depth of field that spans at least one-fourth of their thickness and from at least two different directions; (c) analyzing the images for the presence of one or more features, structures and/or organs of interest.