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Cobalt-based Fischer-Tropsch systems are widely used to convert synthesis gas to clean hydrocarbon fuel. However, surprisingly little is known about the morphology of the catalysts on the nanoscale. Here we show that scanning transmission electron tomography reveals their true 3-D morphology and provides direct evidence that the support controls the final morphology of the catalyst. Such direct local three-dimensional measurements provide unprecedented insight into catalysis, and can henceforth transform our understanding of these complex materials.