Despite being a powerful model organism for biology and the study of transcriptional enhancers, the tissue specific activity of less than 5% of the estimated 50,000 transcriptional enhancers in Drosophila melanogaster have been discovered. Over the past decade, the main method for detection of tissue- or cell-type specific activities of enhancers in Drosophila melanogaster was to test candidate enhancers by traditional reporter assays, which are low-throughput and costly. Over the past few years, even though enhancer discovery has been improved and other parallel reporter assays have been developed, none so far allowed the direct identification of enhancer activity in a genomic context in cell types of interest in a whole embryo.