Expression of human A/342 peptide in the Drosophila brain induces pathological phenotypes resembling Alzheimer's disease (PNAS 101, 6623-6628). Three-dimensional confocal imaging reveals extensive vacuoles caused by neurodegeneration in the brain of aged but not young A β 42 flies. Here, we report a three-dimensional computation algorism allowing semi-automatic measurement of numbers and volumes of brain vacuoles. The method employed matched filters, α -shape, and the active-contour techniques. Using this method, a good result depicting the contours of the vacuoles can be obtained. A more accurate algorithm is still under development. Accurate evaluation of brain pathology in Alzheimer's flies may facilitate the understanding of molecular mechanisms underlying A β. toxicity and the discovery of novel therapeutic targets for Alzheimer's disease.