A method for determining the concentration of a single stranded target nucleic acid sequence in a sample comprising the steps of: (a) combining in a reaction mixture (i) a sample suspected of containing a single stranded target nucleic acid sequence, (ii) a single stranded capture nucleic acid sequence attached to a microparticle that is complementary to the single stranded target nucleic acid sequence, and (iii) a fluorescently labeled single stranded nucleic acid sequence that is identical to the single stranded target nucleic acid sequence, and allowing formation of a complex comprising the microparticle attached to the single stranded capture nucleic acid sequence, the single stranded target nucleic acid sequence, and the fluorescently labeled single stranded nucleic acid sequence; (b) acquiring a white light image of the reaction mixture in order to determine the location of the microparticle in the reaction of step (a) and a fluorescence image of the reaction mixture in order to determine the location of the fluorescently labeled single stranded nucleic acid sequence in the reaction of step (a); (c) selecting at least one region of interest from the images acquired in step (b), wherein the at least one region of interest is a region from which light signals emanate from the complex formed in step (a); (d) selecting pixels in the at least one region of interest for analysis; (e) calculating and recording the average and variance of the counts per pixel for the pixels selected in step (d), wherein the counts per pixel is the number of photons counted per pixel per unit of time; (f) omitting pixels that have counts greater or less than a specified variance; (g) calculating average counts per pixel of the remaining pixels; and (h) determining the concentration of the single stranded target nucleic acid sequence from the data in step (g). (a) combining in a reaction mixture (i) a sample suspected of containing a single stranded target nucleic acid sequence, (ii) a single stranded capture nucleic acid sequence attached to a microparticle that is complementary to the single stranded target nucleic acid sequence, and (iii) a fluorescently labeled single stranded nucleic acid sequence that is identical to the single stranded target nucleic acid sequence, and allowing formation of a complex comprising the microparticle attached to the single stranded capture nucleic acid sequence, the single stranded target nucleic acid sequence, and the fluorescently labeled single stranded nucleic acid sequence; (b) acquiring a white light image of the reaction mixture in order to determine the location of the microparticle in the reaction of step (a) and a fluorescence image of the reaction mixture in order to determine the location of the fluorescently labeled single stranded nucleic acid sequence in the reaction of step (a); (c) selecting at least one region of interest from the images acquired in step (b), wherein the at least one region of interest is a region from which light signals emanate from the complex formed in step (a); (d) selecting pixels in the at least one region of interest for analysis; (e) calculating and recording the average and variance of the counts per pixel for the pixels selected in step (d), wherein the counts per pixel is the number of photons counted per pixel per unit of time; (f) omitting pixels that have counts greater or less than a specified variance; (g) calculating average counts per pixel of the remaining pixels; and (h) determining the concentration of the single stranded target nucleic acid sequence from the data in step (g).