Increment cores are often used in wood science for measuring wood density of trees non destructively and at large scale, for instance with the objective to assess the available biomass in a forest resource. This paper presents a software allowing to measure by X-ray computed tomography (CT) the wood density of thousands increment cores. The software is able to process 3000 cores per hour semi-automatically. Manual intervention may be required to control and eventually adjust the positioning of the cores. The software was tested on 30 trees from 13 temperate species. Two increment cores were taken from each tree: one 5 mm diameter core and one 4 mm diameter core. The obtained CT density of the cores was compared to reference data obtained by volume and mass measurement on the 5 mm cores. The reference data were used for tuning the software settings by leave-one-out cross validation method. The obtained root mean square error was below 10 kg/m3 (1.7%) for the 5 mm cores. For the 4 mm cores, the root mean square difference with the reference density of the 5 mm cores was 25 kg/m(3) (4.2%).