AD is characterized immunohistologically by the presence of extracellular amyloid plaque deposits and associated neuroinflammation throughout the cerebral cortex and hippocampus. Amyloid plaques are aggregates of amyloid beta (Aβ) peptides that are released by successive cleavages of full length APP. Our lab has developed a novel CRISPR-based, APP-editing approach that effectively deletes the YENPTY endocytic domain at the C-terminus of APP, thus attenuating pathologic beta-cleavage and up-regulating neuroprotective alpha-cleavage. In order to assess the efficacy of our approach in vivo, we used CRISPRs to generate germ-line and somatic edits in an APP knock in (APP NL/G/F) mouse model of AD. 

Immunohistochemistry (IHC): Tissues from appropriately aged control and CRISPR-edited APP NL/G/F mice were immunostained for Aβ plaques (6E10 antibodies), astrocytes (anti-GFAP antibodies) and microglia (anti-Iba1 antibodies).

MATLAB analyses: After images were optimally contrasted, a color-channel filter was applied to isolate cells and plaques from the background. Our MATLAB program was then able to segment individual cells/plaques and measure their area, distance to nearby cells/plaques, and percentage of overlap. Activated microglia were defined as those with an area of 25 μm² or greater.

Our MATLAB toolkit can reliably quantify common neuropathological IHC markers and may be useful for evaluating the efficacy of neurotherapeutics.