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Pattern formation is a widely observed phenomenon in diverse fields including materials physics, developmental biology and ecology, among many others. The physics underlying the patterns is specific to the mechanisms, and is encoded by partial differential equations (PDEs). With the aim of discovering hidden physics, we have previously presented a variational approach to identifying such systems of PDEs in the face of noisy data at varying fidelities (Computer Methods in Applied Mechanics and Engineering, 353:201-216, 2019). Here, we extend our variational system identification methods to address the challenges presented by image data on microstructures in materials physics. PDEs are formally posed as initial and boundary value problems over combinations of time intervals and spatial domains whose evolution is either fixed or can be tracked. However, the vast majority of microscopy techniques for evolving microstructure in a given material system deliver micrographs of pattern evolution over domains that bear no relation with each other at different time instants. The temporal resolution can rarely capture the fastest time scales that dominate the early dynamics, and noise abounds. Furthermore, data for evolution of the same phenomenon in a material system may well be obtained from different physical specimens. Against this backdrop of spatially unrelated, sparse and multi-source data, we exploit the variational framework to make judicious choices of weighting functions and identify PDE operators from the dynamics. A consistency condition arises for parsimonious inference of a minimal set of the spatial operators at steady state. It is complemented by a confirmation test that provides a sharp condition for acceptance of the inferred operators. The entire framework is demonstrated on synthetic data that reflect the characteristics of the experimental material microscopy images.