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Large particle flow cytometers from Union Biometrica provide automation for the analysis and dispensing of intact cell clusters. Cells growing in clusters communicate with each other and behave differently than cells grown as monolayers or in suspension. Many cell types will naturally form cell clusters when given the opportunity. These organoids and spheroids are believed to more closely recapitulate a normal physiological state. Research using stem cell clusters, organoids, tumor spheres and other types of 3D cultures are important biological systems for the discovery of signals responsible for normal development as well as the abnormal disease states. The COPAS Vision instrument can characterize these sample types with measurements typical of flow cytometry, like size, optical density, and fluorescence. In addition, the COPAS Vision collects brightfield images of the cell clusters during analysis. The COPAS Vision instrument provides automation for unbiased analysis, handling of large numbers of cell clusters, and dispensing of these sample types in a multiwell plate format. This approach can be used to characterize populations of organoids and organoid bodies of various types. Dispensing to wells of multiwell plates provides an approach to using these 3D cultures in large scale biological assays and screens.