Experimental Quality Control Induces Changes in Allen Mouse Brain Connectomes

This repository contains the original and rebuilt regionalized voxel model (RVM) and homogeneous model (HM) connectomes from "Experimental Quality Control Induces Changes in Allen Mouse Brain Connectomes" (Nathan et al., 2026; bioRxiv), as well as a conversion table of Allen region numbers to region names (    
allen_ccfv3_tree_wang_2020_s2.xlsx) to interpret these results (taken from Supplementary Data in Wang et al., 2020). For code to reproduce all analyses from Nathan et al., 2026 using these connectomes, see https://github.com/vik16nathan/allen_connectome_qc/).

The files with "knox" refer to the RVM, and the files with "oh" refer to the HM, based on the original formulation of each connectome in Knox et al., 2018 and Oh et al., 2014. Additionally, each connectome is built at the level of the 291 gray-matter regions from Knox et al. or the 211 regions from Oh et al. (out of the original 213 regions) that are still included in the most recent release of the Allen Institute's CCFv3 atlas. The connectomes with "ipsi" refer to regional connectivity ipsilateral to the injected region, whereas "contra" refers to connectivity contralateral to the injected region.