39The effector functions of macrophages across the spectrum of activation states in vitro are linked to 40 profound metabolic rewiring. However, the metabolism of macrophages remains poorly characterized in 41 vivo. To assess changes in the intracellular metabolism of macrophages in their native inflammatory 42 microenvironment, we employed two-photon fluorescence lifetime imaging microscopy (FLIM) of 43 metabolic coenzymes NAD(P)H and FAD. We found that pro-inflammatory activation of macrophages in 44 vivo was associated with a decrease in the optical redox ratio [NAD(P)H/(NAD(P)H+FAD)] relative to a 45 pro-resolving population during both infected and sterile inflammation. FLIM also resolved temporal 46 changes in the optical redox ratio and lifetime variables of NAD(P)H in macrophages over the course of 47 sterile inflammation. Collectively, we show that non-invasive and label-free imaging of autofluorescent 48 metabolic coenzymes is sensitive to dynamic changes in macrophage activation in interstitial tissues. This 49 imaging-based approach has broad applications in immunometabolism by probing in real time the 50 temporal and spatial metabolic regulation of immune cell function in a live organism. 51 52 Significance 53 Metabolic regulation of macrophage effector functions has recently emerged as a key concept in immune 54 cell biology. Studies rely on in vitro and ex vivo approaches to study macrophage metabolism, however 55 the high plasticity of these cells suggest that removal from their native microenvironment may induce 56 changes in their intracellular metabolism. Here, we show that fluorescence lifetime imaging microscopy 57 of metabolic coenzymes captures dynamic changes in the metabolic activity of macrophages while 58 maintaining them in their endogenous microenvironment. This approach also resolves variations on a 59 single-cell level, in contrast to bulk measurements provided by traditional biochemical assays, making it a 60 potentially valuable tool in the field of immunometabolism. 61 62 63 64 65 66 67 68 69 70 71 72 Nicotinamide adenine dinucleotide (NADH/NAD+) and flavin adenine dinucleotide (FADH 2 /FAD) are 97 endogenous metabolic coenzymes, and serve as electron carriers in numerous metabolic pathways 98including glycolysis, the Krebs cycle, electron transport chain and oxidative phosphorylation (17, 18). 99These coenzymes are autofluorescent when reduced and oxidized, respectively, and allow for 100 fluorescence lifetime imaging microscopy (FLIM) to quantify intracellular metabolism using intensity 101 and lifetime measurements (17, 18). NADH and NADPH have overlapping spectral properties, and for 102 accuracy NAD(P)H is used to reflect their combined signals (19). Fluorescence intensity can be used to 103 determine the optical redox ratio that provides an assessment of the redox state of the cell (20). Multiple 104 definitions of the optical redox ratio exist, but here we use NAD(P)H/(NAD(P)H+FAD), since an 105 increase in the optical redox ratio intuitively corresponds with an increase i...