Apparatus and methods are described for use with a cell sample that includes a plurality of cells disposed in a monolayer. A series of images associated with a series of depth levels of the cell sample are acquired, by performing a depth scan of cell sample with a microscope. One of the depth levels is identified as being an optimum focal plane for imaging one or more entities within the cell sample using the microscope, by identifying that a drop in image contrast occurs at the identified depth level relative to the image contrast of images acquired at depth levels within a given range of distances from the identified depth level. The cell sample is imaged using the microscope, by focusing the microscope at an investigative depth level that is based on the identified depth level. Other applications are also described.