This is the final version of the article. Available from the publisher via the DOI in this record. ; Gap genes are involved in segment determination during early development in dipteran insects (flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis of the gap gene network across different dipteran species. Our work provides mechanistic insights into the evolution of this pattern-forming network. As a central component of our project, we created a high-resolution quantitative spatio-temporal data set of gap and maternal co-ordinate gene expression in the blastoderm embryo of the non-drosophilid scuttle fly, Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated embryos. The data-covering 10 genes, 10 time points, and over 1,000 individual embryos-consist of original embryo images, quantified expression profiles, extracted positions of expression boundaries, and integrated expression patterns, plus metadata and intermediate processing steps. These data provide a valuable resource for researchers interested in the comparative study of gene regulatory networks and pattern formation, an essential step towards a more quantitative and mechanistic understanding of developmental evolution. ; This work was funded by the MEC-EMBL agreement for the EMBL/ CRG Research Unit in Systems Biology, by European Commission grant FP7-KBBE-2011-5/289434 (BioPreDyn), by Grant 153 (MOPDEV) of the ERANet: ComplexityNET programme, by AGAUR SGR Grant 406, as well as grants BFU2009-10184 and BFU2012-33775 from the Spanish Ministry of the Economy and Competitiveness (MINECO, formerly MICINN). The Centre for Genomic Regulation (CRG) acknowledges support from MINECO, 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012-0208.