A method of determining a plurality of positions associated with a plurality of reaction chambers of a microfluidic device includes a) providing a baseline image; b) providing a template image of a reaction chamber; and c) selecting a region of the baseline image. The method also includes d) performing a matching process including matching the template image to one or more portions of the region of the baseline image; e) determining a position of a first chamber; and f) predicting a position of a second chamber. The method further includes g) repeating steps c) through f) for subsequent chambers.