For this work, we used our fully-automated platform for microenvironment analysis. This pipeline for multiplex immunofluorescence (IF) images measures stain density, detects and classifies microglia, segments amyloid-β plaques, and analyzes the environment around these plaques. For more information about this pipeline, please see Amyloid-β & the Inflammatory Microenvironment in an APP/PS1 Mouse Model of Alzheimer's Disease. We have extended this pipeline by adding an astrocyte detection and classification stage.