Glaucoma is a multifactorial optic neuropathy characterized by the damage and death of the retinal gan-glion cells. This disease results in vision loss and blindness. Any vision loss resulting from the disease cannot be restored and nowadays there is no available cure for glaucoma;however an early detection and treatment, could offer neuronal protection and avoid later serious damages to the visual function. A full understanding of the etiology of the disease will still require the contribution of many scientiifc efforts. Glial activation has been observed in glaucoma, being microglial proliferation a hallmark in this neuro-degenerative disease. A typical project studying these cellular changes involved in glaucoma often needs thousands of images-from several animals-covering different layers and regions of the retina. The gold standard to evaluate them is the manual count. This method requires a large amount of time from special-ized personnel. It is a tedious process and prone to human error. We present here a new method to count microglial cells by using a computer algorithm. It counts in one hour the same number of images that a researcher counts in four weeks, with no loss of reliability.