Monitoring of cell metabolism represents an important application area for fluorescence lifetime imaging microscopy (FLIM). In particular, assessment of mitochondrial membrane potential (MMP) in complex three-dimensional multicellular in vitro, ex vivo, and in vivo models would enable improved segmentation and functional discrimination of cell types, directly report on the mitochondrial function and complement the quenched-phosphorescence detection of cellular O 2 and two-photon excited FLIM of endogenous NAD(P)H. Here, we report the green and orange-emitting fluorescent dyes SYTO and tetramethylrhodamine methyl ester (TMRM) as potential FLIM probes for MMP. In addition to nuclear, SYTO 16 and 24 dyes also display mitochondrial accumulation. FLIM with the culture of human colon cancer HCT116 cells allowed observation of the heterogeneity of mitochondrial polarization during the cell cycle progression. The dyes also demonstrated good performance with 3D cultures of Lgr5-GFP mouse intestinal organoids, providing efficient and quick cell staining and compatibility with two-photon excitation. Multiplexed imaging of Lgr5-GFP, proliferating cells (Hoechst 33342-aided FLIM), and TMRM-FLIM allowed us to identify the population of metabolically active cells in stem cell niche. TMRM-FLIM enabled to visualize the differences in membrane potential between Lgr5-positive and other proliferating and differentiated cell types. Altogether, SYTO 24 and TMRM dyes represent promising markers for advanced FLIM-based studies of cell bioenergetics with complex 3D and in vivo models.Key terms FLIM; intestinal organoids; Lgr5-GFP; mitochondrial membrane potential; SYTO; tetramethylrhodamine methyl ester Energy production and regulation of cell metabolism are essential for the living cell. Corresponding biomarkers are important for cancer, stem and basic cell biology, drug screening and discovery, cell death and toxicity, and tissue engineering (1-4). Quantitative assessment of cell metabolism and mitochondrial function is possible via a number of techniques, which include analyses of oxygenation and oxygen consumption rate (OCR), mitochondrial membrane potential (MMP), glycolytic flux, ATP and redox status, analysis of metabolome and other approaches (5-8). Photoluminescence (i.e., fluorescence and phosphorescence)-based methods enable quantification of these parameters in formats of a plate reader, fluorescence microscope, and other readouts compatible with various cells and tissues. For in vivo and advanced microscopy applications, quantitative analysis of mitochondrial function is possible only by limited number of probes and approaches, such as measurement of cell oxygenation by phosphorescence quenching method (9,10), analysis of redox status by imaging of NAD(P)H, FAD + , and tryptophan autofluorescence by FLIM or by using various genetically-encoded fluorescent biosensors (11-15). The quantitative assessment of the direct indicator of mitochondrial function, MMP, remains a challenging task (16). This situation creates a gap in the...