Hi Kelly. That all sounds simple enough, the only problem being that the Allen Brain API does not specify where the bregma and lambda are (as per this official explanation). Given this, what did you estimate as the position of bregma and lambda in the CCF coordinates?
I wish I could capture each mouse’s 2P tomography volume and register to the CCF as per this recent work. Unfortunately, we lack the necessary hardware.
EDIT: Based on the Paxinos and Franklin atlas (2012) as well as Allen’s older atlas (2008) which does come with stereotaxic coordinates, I estimated that lambda is at y = 206, bregma is at y = 370, and 1 mm lateral is at z = 195 in the 25 micron volume. Is this close to what you have? This is not a rigorous estimate but combined with a sensory response assay (e.g. visual, somatosensory) may be good enough for delineating large cortical areas.