A novel data-driven real-time procedure based on diffuse approximation is proposed to characterize the mechanical behavior of liquid-core microcapsules from their deformed shape and identify the mechanical properties of the sub-micron-thick membrane that protects the inner core through inverse analysis. The method first consists of experimentally acquiring the deformed shape that a given microcapsule takes at steady-state when it flows through a microfluidic microchannel of comparable cross-sectional size. From the mid-plane capsule profile, we deduce a series of geometrical quantities that uniquely characterize the shape taken by the microcapsule under the external hydrodynamic stresses. To identify the value of the unknown rigidity of the membrane, we compare the set of geometrical quantities to all the ones predicted numerically using a fluid-structure-interaction model by solving the threedimensional capsule-flow interactions. The complete numerical data set is obtained off-line by systematically varying the governing parameters of the problem, i.e. the capsule-to-tube confinement ratio and the capillary number, ratio of the viscous to elastic forces. We show that diffuse approximation efficiently estimates the unknown mechanical resistance of the capsule membrane. We valide the data-driven procedure by applying it to the geometrical and mechanical characterization of ovalbumin microcapsules (diameter of the order of a few tens of microns). As soon as the capsule is sufficiently deformed to exhibit a parachute shape at the rear, the capsule size and surface shear modulus are determined with an accuracy of 0.3% and 8%, respectively, as compared to 2-3% and 25% without it, in the best cases (Hu et al. PRE 2013). Diffuse approximation thus allows to quasi-instantly provide the capsule size and resistance with a very high precision. It opens interesting perspectives for all the industrial applications that require a tight control of the capsule mechanical properties in order to secure their behavior when they transport active material.