The CCFv3 has the two-photon tomography images from 1,675 young adult C57BL/6J mice as well as the 3D Nissl images. I also found there are reference data of AchE, Pvalb, SMI-32, SMI-99, NeuN, NF-160 etc in the website (Reference Data :: Allen Brain Atlas: Mouse Connectivity) and these images are in 2D format. I’m wondering whether these datasets have been converted to 3D in CCFv3 space? I’m curious to quantitatively compare the histological staining/immuhistochemistry data to other image results. If not, is there anyway we can convert them to 3D and minimize the intensity inconsistencies between slices?