In this work we propose a system for automatic classification of Drosophila embryos into developmental stages. While the system is designed to solve an actual problem in biological research, we believe that the principle underlying it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time.In our biological setup, the information sources are the shape and the staining patterns of embryo images. We show experimentally that while neither of the methods can be used by itself to achieve satisfactory results, their combination achieves prediction quality comparable to human performance.