We applied in vivo confocal microscopy of GFP-transgenic zebrafish in combination with 3D image analyses to study the asymmetric morphogenesis of the diencephalic parapineal organ on a supra-cellular, cellular, and sub-cellular level. Following a rough manual segmentation of the respective regions of interest (ROIs), the morphology of generated surface meshes was refined by an active surface model which iteratively adjusts the mesh towards the morphology of the cellular structures. This procedure is essential for a precise morpho-topological analysis, mostly because of the adversarial diffraction limited resolution in the z-dimension of confocal image stacks. 3D Morphology and topology of the reconstructed cellular and supra-cellular structures during morphogenesis was quantified by principal axis transformations and 3D moment invariants. Our data indicates that migration of the parapineal organ is accompanied by a rapid transition between predominantly parallel cell orientations towards predominantly perpendicular orientations, a phenomenon which requires a precise control of cell shape and polarity. The orientational transition is followed by a phase of polarized cell motility in which membrane protrusions in the form of blebs and filopodia become oriented in the direction of the asymmetric migration. The morpho-topological descriptors unveil information that is not perceptible for a direct visual analysis of the microscopical data sets. This approach becomes essential to access morphogenetic mechanisms which control asymmetry and migration.