DeepSlice

Note

Find DeepSlice here for Allen CCF and WHS.

• DeepSlice performs automatic registration to the Allen CCF using Deep Convolutional Neural Networks (linear registration only). It generates a JSON file compatible with the QuickNII software, and can be used to automate steps 1 and 2 of the QuickNII atlas-registation process.

• After generating a Deepslice JSON, it is recommended to inspect the results in QuickNII and to make small positional adjustments as required.

• Use the VisuAlign software in a subsequent step to apply nonlinear refinements for a better fit of the atlas over the sections.

• There is a beta-version for the Waxholm atlas of the Sprague Dawley rat.

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

Tip

To convert an Allen CCF registration to the Kim Unified Mouse Brain Atlas use our converter.