Multisection CCFv3-aligned atlas of cFos, Arc and NPAS4 following contextual fear conditioning (v1)

The data presented in this dataset consist of a representative set of whole-brain imaging raw-data as well as the image analysis outputs of all the brains analysed in Chiarrutini, Castoldi et al 2024. Brains derive from animals subjected to three different behavioural conditions characterized by increasing salience (i.e., mice in their home cage [N=5], mice exposed to a novel context [N=6] and mice exposed to a salient associative learning paradigm [N=6]). Each mouse was transcardially perfused 90 min following behavioral testing, brains were cut at 40µm and 1 every 4 slices was stained with DAPI, and IHC for cFos (channel AF568) and Arc (channel AF647), while another 1 every 4 slices was stained with DAPI, and IHC cFos (channel AF594) and NPAS4 (channel AF647). Both brain section samples were acquired with a slide scanner, aligned to Allen Institute’s atlas with ABBA and QuPath, and quantified with BraiAn.
Due to storage limitation, the current dataset only presents the raw-images datasets of 2 animals per brain section sample.