PolarBean / DeepSlice

What it does

DeepSlice is a python library which automatically aligns mouse histology with the allen brain atlas common coordinate framework (and now rat brain histology to the Waxholm rat brain atlas, though this is in beta). The alignments are viewable, and refinable, using the QuickNII software package. DeepSlice requires no preprocessing and works on any stain, however we have found it performs best on brightfield images. At present one limitation is that it only works on Coronally cut sections, we will release an update in the future for sagittal and horizontally cut histology.