There is described a system and a method for analyzing spots in a micro-array, the spots containing targeted specimen, the method comprising the steps of: providing a slide with a micro-array of the spots thereon; illuminating at least one of the spots; directing the light onto the at least one spot; collecting light emitted from the at least one spot; forming an image of the at least one spot using the collected light; and analyzing the image to distinguish at least one unit of the targeted specimen located within the at least one spot from any undesired material. The analysis results are aimed at the detection, classification and quantification of optically resolvable specimen such as micro-organisms or cells.