DeepSlice
Note
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.