The planarian flatworm is a fascinating model organism which is not only able to adapt its body size to food conditions to but also to regenerate in its entirety even when chopped into tiny pieces. It naturally features a cell polarity along the anterior-posterior axis and is able to reorient it during the regeneration process such that the new head and tail coordinates with the original polarity.
In order to quantify this reorientation robustly, one has to visualize the tissue polarity as well as to process the images in an efficient way. In our lab, we developed a method, which automatically extracts the first layer of epithelia and corrects for uneven illumination within the images. Afterwards, the cell boundaries are inferred and used to compute the polarity of each cell.