Metaphase is the best time to count and study the number and morphology of chromosomes. The distinctly visible chromosome arrange themselves at the equatorial or metaphasic plate. The centromeres lie at the equatorial plate while the limbs are placed variously according to their size and spiral arrangement. At prophase the chromosomes appear thin and filamentous, forming a network.

So they are not very clearly visible. At telophase the chromosomes uncoil and lengthen and therefore are not clearly seen. Anaphase also shows chromosomes distinctly and they can be counted. But during anaphase chromatids seperate and start moving towards opposite pole. So for counting metaphase is the best stage.