Does CCFv3 include 3D atlas of AchE, NeuN, DAPI, SMI-99, and NF-160?

Hi community,

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?

Many thanks,

Hi @wangniannw The CCFv3 was only made up of registered image volumes from 1675 young adult C57BL/6J mice. In addition to that set of data, a series of histologically stained reference data were collected that have been registered to the CCF and can be mapped to the reference atlas. The Allen Brain Atlas API contains functions to do this.

Best regards,