This workshop aims to provide an opportunity to those involved in the cytometry area to become familiar with the fundamentals and applications of microfluidics, in other words, how these microfluidic devices are operated toward the development of next-generation of flow cytometry devices. At first, the principles and practical notes for designing a microfluidic channel in commercially available software packages are stated. Afterwards, a brief discussion on the fabrication of microfluidic devices will be provided. For this aim, conventional and emerging fabrication methods will be evaluated, and the merits and demerits of each will be counted. Moreover, various microfluidic devices aiming for samples preparation and reagent mixing will be introduced and explored. After that, particle manipulation techniques within microfluidic devices will be discussed, and various methods for particle sorting, enrichment, isolation, and focusing will be discussed. For this particular aim, various active and passive microfluidic devices will be introduced, and their functionality will be compared. In the end, the most recent development and new aspects of microfluidic compartmentalisation research that cover flow cytometry will be discussed. We hope this workshop can initiate a synergy with graduate and PhD students, postdocs, academics, and industrials partners toward the accomplishment of interdisciplinary research activities