A three-dimensional (3D) metrology based on light field imaging is developed to study the behavior of rising bubbles in a cylindrical column. A multi-focus plenoptic camera is used to obtain the depth location of bubbles and their size. The all-in-focus images obtained from the light field have a different magnification along the x or y axis due to the astigmatism of the cylinder's window. This phenomenon also affects depth estimation and makes the measured depth dependent on the orientation of the bubble image's interface. We developed a new 3D calibration that takes into account these dependencies. We tested our method for two configurations and two regimes by changing the gaseous Reynolds number. Results show that the far configuration is more adapted as it provides a larger depth of field and field of view at the cost of a lower spatial resolution. We were able to obtain the 3D location and size distribution of bubbles for the studied regimes. Results show that light field imaging can be adapted to in-cylinder flow visualization.