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In-flame soot sampling based on the thermophoresis of particles and subsequent transmission electron microscope (TEM) imaging has been conducted in a diesel engine to study size, shape and structure of soot particles within the reacting diesel jet. A direct TEM sampling is pursued, as opposed to exhaust sampling, to gain fundamental insight about the structure of soot during key formation and oxidation stages. The size and shape of soot particles aggregate structure with stretched chains of spherical-like primary particles is currently an unknown for engine soot modelling approaches. However, the in-flame sampling of soot particles in the engine poses significant challenges in order to extract meaningful data. In this paper, the engine modification to address the challenges of high-pressure sealing and avoiding interference with moving valves and piston are discussed in detail.