myFX: Turn-key software for laboratory desktops that analyzes spatial patterns of gene expression in Drosophila embryos. Sudhir Kumar^1,2, Ivan Montiel¹, Qian Sun^1,3, Michael McCutchan¹, Bremen Braun¹, Adam Orr¹, Stuart Newfeld^1,2, Jieping Ye^1,3. 1) Center for Evolutionary Medicine and Informatics, Arizona State Univ, Tempe, AZ; 2) School of Life Sciences, Arizona State Univ, Tempe, AZ; 3) School of Computing, Informatics, and Decision Systems Engineering, Arizona State Univ, Tempe, AZ.

   Practical bioinformatics tools for data-driven analysis of images containing spatial patterns of gene expression are needed to effectively harness the power of existing knowledge when analyzing one's own data. We present a biologist-centric, turn-key software platform (myFX) for use in experimental laboratories actively collecting such data. It accepts images in multiple formats and contains new computational methods to automatically process images and standardize and align them. Among the new computational methods are programs that semi-automatically annotate anatomical view (e.g., lateral or dorsal) and asses developmental stage for embryos, information required for biologically meaningful image comparisons. myFX also provides approaches for creating digital descriptions of spatial expression patterns in images that enable measurements of gene pattern similarity and synthesis across images from one or genes. myFX contains facilities to generate Genomewide-Expression-Maps (GEMs) for new images acquired in the investigator's laboratory that illuminate transcriptionally active regions of the embryo by capturing the spatial expanse of expression in all embryos within a given set of images with similar stage and anatomical view. Using GEMs and direct image comparison, users can identify all images (and, thus, genes or genetic constructs) showing similar patterns of expression in their own dataset. myFX is programmed to interact directly with FlyExpress, which enables searching for images with similar patterns of expression in the wealth of community-generated data captured in FlyExpress. myFX is a cross-platform application with a user-friendly interface, optimized for use on laboratory desktops that provides a multi-user environment with an integrated image management system, and is available free of charge (http://www.flyexpress.net).