Abstract: The present invention relates generally to the field of computer-based image recognition. More particularly, the invention relates to methods and systems for the identification, and optionally the quantitation of, discrete objects of biological origin such as cells, cytoplasmic structures, parasites, parasite ova, and the like which are typically the subject of microscopic analysis. The invention may be embodied in the form of a method for training a computer to identify a target biological material in a sample. The method may include accessing a plurality of training images, the training images being obtained by light microscopy of one or more samples containing a target biological material and optionally a non-target biological material. The training images are cropped by a human or a computer to produce cropped images, each of which shows predominantly the target biological material.