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We present a statistically motivated method to extract magnonic contrast from time-resolved scanning transmission x-ray microscopy (TR-STXM) measurements. TR-STXM is an element-specific method for resolving spin-dynamics in space and time. It offers nanometer spatial resolution and picosecond temporal resolution. The presented method makes it possible to obtain phase and amplitude profiles of spin-waves from STXM measurements. Furthermore, it allows for a rigorous transformation to reciprocal magnon k⃗-space, revealing k⃗-dependent magnon properties such as the magnon dispersion in three dimensions and for all directions of the magnetic anisotropy. We demonstrate our method using X-band ferromagnetic resonance on a micrometer-sized permalloy assembly.