Find DeepSlice here.

  • DeepSlice performes automated linear registration to the Allen Mouse Brain Atlas CCF version using deep convolutional neural networks. There is also a beta-version for the Waxholm atlas of the Sprague Dawley rat.

  • At present DeepSlice only works for adult mouse brain sections cut in the coronal plane, although future versions will be compatible with sagittal and horizontal sections.

  • It can be used to automate and speed up steps 1 and 2 of the QuickNII registration process for coronal mouse brain sections.

  • DeepSlice generates an XML or JSON file that can be opened with the QuickNII software to validate the registration. Nonlinear refinements can be applied with VisuAlign.

  • It is recommended to inspect the outputs in QuickNII and make small adjustments to the position.