Computer-assisted live cell analysis of mitochondrial membrane potential, morphology and calcium handling

Mitochondria are crucial for many aspects of cellular homeostasis and a sufficiently negative membrane potential (Deltapsi) across the mitochondrial inner membrane (MIM) is required to sustain most mitochondrial functions including ATP generation, MIM fusion, and calcium uptake and release. Here, we present a microscopy approach for automated quantification of Deltapsi and mitochondrial position, shape and calcium handling in individual living cells. In the base protocol, cells are stained with tetramethyl rhodamine methyl ester (TMRM), a fluorescent cation that accumulates in the mitochondrial matrix according to Deltapsi, and visualized using video-microscopy. Next, the acquired images are processed to generate a mitochondria-specific binary image (mask) allowing simultaneous quantification of mitochondrial TMRM fluorescence intensity, shape and position. In a more advanced version of this protocol a mitochondria-targeted variant of green fluorescent protein (mitoAcGFP1) is expressed to allow mask making in TMRM-stained cells. The latter approach allows quantification of Deltapsi in cells with a substantially depolarized Deltapsi. For automated quantification of mitochondrial calcium handling in space and time mitoAcGFP1-expressing cells are stained with rhod-2, a fluorescent calcium indicator that accumulates in the mitochondrial matrix. In this paper, a detailed step-by-step description of the above approaches and its pitfalls is provided.