Ground-based observations at thermal infrared wavelengths suffer from large background radiation due to the sky, telescope and warm surfaces in the instrument. This significantly limits the sensitivity of ground-based observations at wavelengths longer than 3 microns. We analyzed this background emission in infrared high contrast imaging data, show how it can be modelled and subtracted and demonstrate that it can improve the detection of faint sources, such as exoplanets. We applied principal component analysis to model and subtract the thermal background emission in three archival high contrast angular differential imaging datasets in the M and L filter. We describe how the algorithm works and explain how it can be applied. The results of the background subtraction are compared to the results from a conventional mean background subtraction scheme. Finally, both methods for background subtraction are also compared by performing complete data reductions. We analyze the results from the M dataset of HD100546 qualitatively. For the M band dataset of beta Pic and the L band dataset of HD169142, which was obtained with an annular groove phase mask vortex vector coronagraph, we also calculate and analyze the achieved signal to noise (S/N). We show that applying PCA is an effective way to remove spatially and temporarily varying thermal background emission down to close to the background limit. The procedure also proves to be very successful at reconstructing the background that is hidden behind the PSF. In the complete data reductions, we find at least qualitative improvements for HD100546 and HD169142, however, we fail to find a significant increase in S/N of beta Pic b. We discuss these findings and argue that in particular datasets with strongly varying observing conditions or infrequently sampled sky background will benefit from the new approach.
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