pattern images. In this talk, I will review four projects on image mining of fruitfly embryo gene expression patterns. (a) Gaussian mixture model based embryonic expression pattern extraction and comparison, (b) Gene expression pattern clustering using novel MSTCUT and probabilistic ensemble clustering techniques, (c) Surface/volume models for 3D modeling and registration of early embryos, and (d) A manifold learning method for spatio-temporal registration of 3D gene expression patterns and reconstruction of the embryonic developmental time series. For more information, see http://hpeng.net/. (This talk is based on several pieces of joint work with Gene Myers, Michael Eisen, Mark Biggin, David Knowles, and other BDTNP members.)