aMAP stands for automated mouse atlas propagation. It is both, the name and underlying method of our pipeline for rapid and accurate automated segmentation of 3D fluorescence mouse brain data


aMAPs is based on the NiftyReg MRI segmentation toolkit and its accuracy on serial two-photon data has been validated against that of human raters in an open access paper in Nature Communications.

The software is completely open source and documentation, supplementary data, code and binaries for Linux and MacOS are available on Github.