Abstract: The subject invention provides a method for detecting and analyzing the hair follicles on a scalp to assist with hair follicle transplantation. The methods of the subject invention are able to count the number of hair follicle groups and the number of follicles within each group based upon a microscopic image of a sample from a human scalp. An algorithm is then used to cluster the follicles and generate a neighboring connected graph to calculate the inter object distances. A report can then be generated that provides information regarding the density, placement, and percentage of hair follicle type in different areas of the scalp. This report can be used to generate a hair follicle transplant strategy to assist a physician or robotic system.