Atlas-based imaging data analysis tool for quantitative mouse brain histology (AIDAhisto)
AIDAhisto features a simple protocol for landmark-correspondence registration using ImageJ/Fiji for whole-brain slice microscopy with the Allen Mouse Bran Atlas, ARA, (Lein et al., 2006, Oh et al., 2014) and a two-step cell detection algorithm using the cell nuclei segmentation as a seed for cell counting. For the cell detection, we advanced previous implementations of kernel-based cell nuclei detection adding the Schmid Filter Bank and the Leung–Malik Filter Bank. Both filter banks are rotationally invariant and enable the identification of more complex non-circular geometries. AIDAhisto was developed as an open-source script for Python and Matlab and tested against other tools for the detection of cell nuclei and immunostainings of astrocytes and immune cells.