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3D maps of the extinction density in the Galaxy can be built through the inversion of catalogues of distance-extinction pairs for individual target stars. The spatial resolution of the maps that can be achieved increases with the spatial density of the targets, and subsequently with the combination of catalogues. However, this requires their careful inter-calibration. Our aim is to develop methods of inter-calibration of two different catalogues. We used as reference a spectrophotometric catalogue. A principal component analysis was performed in G,GB,GR,J,H,K multi-colour space for the second catalog. The subspace constituted by the two first components was split into cells in which we estimated deviations from the reference. The deviations were computed using all targets from the reference located at a short spatial distance of each secondary target. Corrections and filtering were deduced for each cell in the multi-colour space. We applied the technique to two different datasets: on the one hand, the spectrophotometric catalogue, and, on the other hand, a catalogue of extinctions based on photometry of Gaia eDR3 and 2MASS. After calibration, the dispersion of the extinction among neighbouring points in the second catalogue is reduced, regardless of whether reference targets are present locally. Weak structures are then more apparent. The extinction of high Galactic latitude targets is more tightly correlated with the dust emission, a property acquired from the first catalogue. A hierarchical inversion technique was applied to the two merged inter-calibrated catalogues to produce 3D extinction density maps corresponding to different volumes and maximum spatial resolution. The maximum resolution is 10pc for a 3000x3000x800pc3 volume around the Sun, and the maximum size of the maps is 10x10x0.8 kpc3 for a resolution of 50pc. Maps can be downloaded or used by means of on-line tools.