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To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-13-107","type":"journal-article","created":{"date-parts":[[2012,5,31]],"date-time":"2012-05-31T15:42:59Z","timestamp":1338478979000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval"],"prefix":"10.1186","volume":"13","author":[{"given":"Lei","family":"Yuan","sequence":"first","affiliation":[]},{"given":"Alexander","family":"Woodard","sequence":"additional","affiliation":[]},{"given":"Shuiwang","family":"Ji","sequence":"additional","affiliation":[]},{"given":"Yuan","family":"Jiang","sequence":"additional","affiliation":[]},{"given":"Zhi-Hua","family":"Zhou","sequence":"additional","affiliation":[]},{"given":"Sudhir","family":"Kumar","sequence":"additional","affiliation":[]},{"given":"Jieping","family":"Ye","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,5,23]]},"reference":[{"issue":"12","key":"5313_CR1","doi-asserted-by":"publisher","first-page":"0088.1","DOI":"10.1186\/gb-2002-3-12-research0088","volume":"3","author":"P Tomancak","year":"2002","unstructured":"Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, Lewis SE, Richards S, Ashburner M, Hartenstein V, Celniker SE, Rubin GM: Systematic determination of patterns of gene expression during Drosophila embryogenesis. 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