Hi Luc,
-
mouse_ccf/ara_nissl is the Nissl volume after it has been registered and rewarped to mouse_ccf/average_template
-
mouse_ccf/annotation/mouse_2011 is the “CCFv2 annotation based on the Nissl” rewarped in the same way as mouse_ccf/ara_nissl
-
mouse_ccf/annotation/ccf_2017 is the “CCFv3 annotation based on the average template” and as described in the whitepaper
There will be discrepancy between mouse_2011 and ccf_2017 due to multiple factors including:
-
Difference parcellation strategy of the original Allen Reference Atlas versus the 3D multi-modal approach of the CCFv3 including the use of registered data to ground the paracellation
-
Registration error between the Nissl volume and the average template
-
Limitation in the 3D reconstructed Nissl cause by deformation and tissue damage of the Nissl section