High-fidelity identification of guest species in porous materials

Host-guest chemistry in microporous crystals underpins key applications in catalysis¹, separation² and sensing³, yet the unambiguous identification of guest species within host frameworks remains a central challenge. Recent advances in low-dose phase-contrast electron microscopy have enabled real-space imaging of guest moieties and transformed this field^4,5. Here, however, we show that standard implementations of these techniques can generate artefactual in-pore contrast owing to non-ideal contrast transfer, thus compromising the reliability of guest identification. We address this limitation with a reconstruction method based on Gaussian-apodized single-sideband electron ptychography, which suppresses such artefacts and yields chemically interpretable phase images. We apply this method to an important catalytic system, achieving unbiased identification of guest metal-oxo clusters within microporous zeolite hosts. Our results are supported by complementary diffraction and spectroscopy. Beyond revealing previously unreported framework-confined metal active sites in zeolites, this method is expected to enable high-fidelity visualization of a broad range of local inhomogeneities across crystalline porous materials.