Cooling experiments usually require using many thermocouples to better characterize the heat transfer processes, but there is usually a limitation on the maximum number of thermocouples to be used, because of either limited acquisition channels or limited budget. This paper presents an experimentdesign process to guide choosing the number of thermocouples to ensure a high-quality inversion and accurate heat flux estimations. Two main criteria define the quality of the instrumentation: 1) the agreement between the simulated heat flux (imposed in the numerical simulations) and that obtained by an inverse method, and 2) the agreement between the calculated temperature profiles along the sample thickness using the simulated and estimated heat fluxes. We found that large errors in the estimated heat flux can be captured by estimating the central thermocouples measurements, but not if the difference between estimated and simulated boundary conditions is small.