An auto focus apparatus, comprising: a light source ; a splitter for splitting a light beam illuminated by the light source to a first portion of a light signal and a second portion of a light signal ; a fiber optic circulator having a first port, second port and a third port; wherein the light signal in the fiber optic circulator travels only from the first port to the second port and from the second port to the third port; wherein the fiber optic circulator couples to the second portion of the light signal at the first port; an optical collimator for directing a light output from the second port of the fiber optic circulator onto a sample placed on a substrate through a dichroic mirror and a microscope objective , wherein the separation between the sample and objective can be adjusted; wherein the sample with the substrate are placed on an adjustable microscopy stage; a balance detector comprising a first input port and a second input port, the balance detector being configured for receiving the first portion of the light signal at the first input port, and for converting a light signal, reflected off of the substrate that the sample is placed on, into an analog voltage signal, wherein the reflected light signal is captured by the microscope objective and sent to the second input port of the balance detector through the dichroic mirror , the optical collimator , and into the second port and out of the third port of the fiber optic circulator ; wherein the balance detector divides the reflected light signal by the first portion of the light signal , thereby cancelling out any change in the light source intensity over time; and a microprocessor for processing the analog voltage signal from the balance detector and for commanding a controller configured to move the adjustable microscopy stage to achieve a desired optical focus based on voltage signal peaks measured by the balance detector and position feedback received from the adjustable microscopy stage. a light source ; a splitter for splitting a light beam illuminated by the light source to a first portion of a light signal and a second portion of a light signal ; a fiber optic circulator having a first port, second port and a third port; wherein the light signal in the fiber optic circulator travels only from the first port to the second port and from the second port to the third port; wherein the fiber optic circulator couples to the second portion of the light signal at the first port; an optical collimator for directing a light output from the second port of the fiber optic circulator onto a sample placed on a substrate through a dichroic mirror and a microscope objective , wherein the separation between the sample and objective can be adjusted; wherein the sample with the substrate are placed on an adjustable microscopy stage; a balance detector comprising a first input port and a second input port, the balance detector being configured for receiving the first portion of the light signal at the first input port, and for converting a light signal, reflected off of the substrate that the sample is placed on, into an analog voltage signal, wherein the reflected light signal is captured by the microscope objective and sent to the second input port of the balance detector through the dichroic mirror , the optical collimator , and into the second port and out of the third port of the fiber optic circulator ; wherein the balance detector divides the reflected light signal by the first portion of the light signal , thereby cancelling out any change in the light source intensity over time; and a microprocessor for processing the analog voltage signal from the balance detector and for commanding a controller configured to move the adjustable microscopy stage to achieve a desired optical focus based on voltage signal peaks measured by the balance detector and position feedback received from the adjustable microscopy stage. <EOS>