The female Ae. aegypti reference brain was obtained from an LVPib12 mosquito 7 days after pupation. It was immunostained to label the synaptic protein Brp, and imaged using confocal microscopy. The images were then subjected to blind deconvolution to increase resolution. The female brain was manually annotated using the segmentation and 3D reconstruction software ITK-SNAP. This data is available to browse in our Brain Browser. 3D reconstructions of the segmented regions were exported for viewing using the data analysis and visualization software ParaView. The reference brain can be used as a template for brain warping and registration using the python program ClearMap, and we've provided a few examples of this. This application is being used to examine the expression patterns of newly generated driver lines in Ae. aegypti.