FlyCircuit is the world's first 3D single neuron image database. It is a public database for online archiving, cell type inventory, browsing, searching and 3D visualization of individual neurons in the Drosophila brain. FlyCircuit provides tools for analyzing neural connections and for similarity comparisons. These tools are accessible to researchers around the world. 3D image data is converted and stored in the database as one-dimensional sequences. This speeds up calculations, reduces analysis time and makes analyzing tools more efficient. FlyCircuit will continue to have images added to it until the database has about 130,000 images. These images then will be used to construct the Drosophila brain connectome. Gene expression data, which has already been integrated into the database, will provide researchers with a way to target specific genes and manipulate neuronal function. This database was created in cooperation with the National Center for High-performance Computing in Taiwan.