Scanning transmission electron microscopy-energy-dispersive X-ray (STEM-EDX) spectroscopy is a popular method of material analysis used for elemental and phase mapping. It is corrupted by noise due to a limited electron dose used to reduce the operating time or sample damage. To extract chemically meaningful spectra from noisy spectroscopic data, multivariate analysis methods were used and developed . Among them, principal component analysis (PCA) uniquely projects data onto the underlying low-dimensional subspace, and is one of the most popular, well-established techniques used for noise reduction .