A method of misregistration correction in a line scanning imaging system includes: generating a model of scan motion over a focal plane of the imaging system, using a coupled system of scan equations with constant coefficients; estimating programmed motion positions across a plurality of detector junction overlap regions via a state transition matrix solution to the scan equations; at each detector junction overlap region, measuring actual motion positions via image correlation of overlapping detectors; generating differences between the actual motion positions and the estimated programmed motion positions; estimating updates to the constant coefficients based on the generated differences; generating corrections from the estimated updates to remove unwanted motion; and applying the updates to the constant coefficients.