Absorbance imaging is applied to measure the 3D shape of liquid droplets in isotropically etched linear micro channels. The pressure drop due to the deformation of the droplet interfaces was derived directly from the geometrical properties of its three-dimensional shape and compared to models based on Brethertons theory for different channel cross sections, viscosity ratios and droplet velocities. Particularly with regard to a system modeling of droplet-based micro channel networks, this work contributes to an accurate droplet transport model which is crucial for optimal simulation results. The capabilities of the absorbance imaging approach are demonstrated and its straightforward application to droplet transport problems is shown.