Apparatus and methods are described for analyzing a bodily sample. One or more microscope images of the bodily sample are acquired. Using at least one computer processor at least one sample-informative feature that is indicative of a characteristic of the bodily sample is extracted from the images. Based upon the sample-informative feature, the computer processor determines that there is a defect associated with the bodily sample, and determines a source of the defect. Other applications are also described.