Phenotypic drug discovery (PDD) is a powerful approach for identifying new drug targets and elucidating disease mechanisms. Current approaches for PDD mainly rely on either microscopy-based or flow cytometry-based technologies. Microscopy-based screening platforms are well established and obtain high content image information, however the current approaches lack versatility, are subject to well-to-well variation, and require time-intensive image processing and analysis. Conventional flow-based screening platforms allow for higher efficiencies and larger scale screening, but do not provide high content morphological information about cell phenotypes and only limited fluorescence resolution.