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Microstructure refers to the spatial organization of phases in a material. A perfectly uniform crystalline (or, even non-crystalline) material has no microstructure. Thus, microstructures, at some level, are brought about by defects -- in particular, extended defects such as dislocations, grain boundaries (boundaries between crystals of the same phase) and interfaces between crystals of different phases.
For example, in a single phase material -- say, a piece of aluminum -- is composed of many small crystallites (grains); within each grain, the crystal has a certain orientation which is different from that of the neighboring grains. The (thin) region of orientational mismatch between two grains is referred to as grain boundaries. Thus, in a single phase material, microstructure is described by grain size, grain size distribution, and distribution of grain orientations. This description can be further augmented by the correlation between orientations of neighboring grains.