A method and system for detecting and counting mitotic figures in an image of a biopsy sample stained with at least one dye, includes color filtering the image in a computer process to identify pixels in the image that have a color which is indicative a mitotic figure; extracting the mitotic pixels in the image that are connected to one another in a computer process, thereby producing blobs of mitotic pixels; shape-filtering and clustering the blobs of mitotic pixels in a computer process to produce mitotic figure candidates; extracting sub-images of mitotic figures by cropping the biopsy sample image at the location of the blobs; extracting two sets of features from the mitotic figure candidates in two separate computer processes; determining which of the mitotic figure candidates are mitotic figures in a computer classification process based on the extracted sets of features; and counting the number of mitotic figures per square unit of biopsy sample tissue.