The extension of imaging flow cytometry (IFC) with snapshot-mosaic cameras is a novel approach for the in-flow characterization of bioparticles. With this innovative approach, cells at the single cell level as well as whole cell populations can be analyzed and counted. Spatial and spectrally resolving snapshot-mosaic cameras and real time capable multivariate data processing extend the possibilities for automated and in-flow characterization and analysis of mixed bioparticle populations. Cells move through a microfluidic chip for analysis and measurement as well as classification. For consistent imaging quality the cells passing an innovative 3-step microfluidic focusing unit. For the investigations we used the microalgae Haematococcus pluvialis (HP). These microalgae are used commercially to produce the red carotenoid pigment astaxanthin. Therefore, HP is suitable to practically demonstrate the usability of the developed system.