In this thesis novel motion models have been developed and incorporated into an extended parameter estimation framework that allows to accurately estimate the parameters and regularize them if needed. The performance of this framework has been increased to real time and implemented on inexpensive graphics hardware. Confidence and situation measures have been designed to discard inaccurate estimates. A phase field approach was developed to estimate piecewise smooth motion while detecting object boundaries at the same time. These algorithmic improvements have been successfully applied to three areas of fluid dynamics: air-sea interaction, microfluidics and plant physiology. At the ocean surface, the fluxes of heat and momentum have been measured with thermographic techniques, both spatially and temporally highly resolved. These measurement techniques present milestones for research in air-sea interaction, where point measurements and particle based laboratory measurements represent the state-of-the art. Calculations were done with two models, both making complement assumptions. Still, results derived from both models agree remarkably well. Measurements were conducted in laboratory settings as well as in the field. Microfluidic flow was measured with a new approach to molecular tagging velocimetry that explicitly models Taylor dispersion. This has lead to an increase in accuracy and applicability. Inaccuracies and problems of previous approaches due to Taylor dispersion were successfully evaded. Ground truth test measurements have been conducted, proving the accuracy of this novel technique. For the first time, flow velocities were measured in the xylem of plant leaves with active thermography. This represents a technique for measuring these flows on extended leaf areas on free standing plants, minimizing the impact caused by the measurement. Ground truth measurements on perfused leafs were performed. Measurements were also conducted on free standing plants in a climatic chamber, to measure xylem flows and relate flow velocities to environmental parameter. With a cuvette, environmental factors were varied locally. These measurements underlined the sensitivity of the new approach. A linear relationship in between flow rates and xylem diameter was found
