Whole-Brain Axonal Projection Quantification Using ABBA and QuPath v1

This protocol describes whole-brain quantification of axonal projections using atlas-based registration with ABBA [51] followed by fluorescence intensity measurement in QuPath [52]. Brain sections are first aligned to the Allen Mouse Brain Atlas using ABBA to obtain standardized anatomical region boundaries. Fluorescence intensity is then quantified in QuPath and background-corrected. Data are aggregated per animal to avoid pseudoreplication.