Automatic recognition and annotation of gene expression patterns of fly embryos

Motivation: Gene expression patterns obtained by in situ mRNA hybridization provide important information about different genes during Drosophila embryogenesis. So far, annotations of these images are done by manually assigning a subset of anatomy ontology terms to an image. This time-consuming process depends heavily on the consistency of experts. Results: We develop a system to automatically annotate a fruitfly's embryonic tissue in which a gene has expression. We formulate the task as an image pattern recognition problem. For a new fly embryo image, our system answers two questions: ( 1) Which stage range does an image belong to? ( 2) Which annotations should be assigned to an image? We propose to identify the wavelet embryo features by multi-resolution 2D wavelet discrete transform, followed by min-redundancy max-relevance feature selection, which yields optimal distinguishing features for an annotation. We then construct a series of parallel bi-class predictors to solve the multi-objective annotation problem since each image may correspond to multiple annotations. Supplementary information: The complete annotation prediction results are available at: http://www.cs.niu.edu/similar to jzhou/papers/fruitfly and http://research.janelia.org/peng/proj/fly_embryo_annotation/. The datasets used in experiments will be available upon request to the correspondence author. Contact: jzhou@cs.niu.edu and pengh@janelia.hhmi.org.