DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas

Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.

Automated summary

Registration of data to a common frame of reference is crucial in analyzing and integrating diverse neuroscientific data. The traditional methods for registration are time-consuming and rely on expertise. However, using the neural network DeepSlice, we were able to significantly improve the speed while maintaining the accuracy of registering mouse brain histological images to the Allen Brain Common Coordinate Framework.