Abstract: Methods and systems described herein may allow for the classification of microglial morphology at single cell resolution. Microglial cell states may be determined, and a biological sample from which the microglial cells are obtained may be classified based on the microglial cell states. Classifying microglial cells may involving segmenting microglia cells into soma and processes in immunofluorescence microscopy images. Additionally, a feature bank may be generated. Values of the features in the feature bank may be measured for an image. Cells may be clustered using the values of the features in the feature bank. The cells in a cluster may be compared to a reference cell with a known state and having known morphological properties. The cluster in the cell may then be assigned the same state as a reference cell. The amount of cells having the state may then be used to determine properties of the biological sample.