Entanglement is a fundamental resource for quantum information processing, occurring naturally in many-body systems at low temperatures. The presence of entanglement and, in particular, its scaling with the size of system partitions underlies the complexity of quantum many-body states. The quantitative estimation of entanglement in many-body systems represents a major challenge as it requires either full state tomography, scaling exponentially in the system size, or the assumption of unverified system characteristics such as its Hamiltonian or temperature. Here we adopt recently developed approaches for the determination of rigorous lower entanglement bounds from readily accessible measurements and apply them in an experiment of ultracold interacting bosons in optical lattices of approximately $10^5$ sites. We then study the behaviour of spatial entanglement between the sites when crossing the superfluid-Mott insulator transition and when varying temperature. This constitutes the first rigorous experimental large-scale entanglement quantification in a scalable quantum simulator.
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