A method for differentiating two groups of microorganisms, the method comprising: using an imaging device of a biological scanning system, to produce a first image of a thin film culture device, the culture device having a front side having a transparent film cover sheet and a back side having a translucent substrate, wherein the first image is produced while providing illumination to the front side of the culture device, wherein the culture device comprises first and second indicator compounds, wherein the first indicator compound is converted by microorganisms in a first group of microorganisms and microorganisms in a second group of microorganisms to a non-water diffusible first product having a first color, wherein the second indicator compound is converted by the microorganisms in the second group of microorganisms to a water-diffusible second product that forms a second color, and wherein the first image is produced while illuminating the culture device with a first ratio of front-side illumination to back-side illumination; using the imaging device to produce a second image of the culture device, wherein the second image is produced while providing illumination to the back side of the culture device, wherein the second image is produced while illuminating the culture device with a second ratio of front-side illumination to back-side illumination that is lower than the first ratio; analyzing, by a processor, the first and second images to identify microorganism colonies in each of the first image and the second image; analyzing, by the processor, the first image to calculate a first value of a size parameter for a colony at a particular location in the culture device; analyzing, by the processor, the second image to calculate a second value of the size parameter at the particular location in the culture device; comparing, by the processor, the first value to the second value; and counting, by the processor, the colony, wherein the processor counts the colony as being in the first group of microorganisms based on the first value and the second value being the same, wherein the processor counts the colony as being in the second group of microorganisms based on the first value and the second value being different, wherein the first value and the second value are considered the same if the first value and the second value are within a predetermined range. using an imaging device of a biological scanning system, to produce a first image of a thin film culture device, the culture device having a front side having a transparent film cover sheet and a back side having a translucent substrate, wherein the first image is produced while providing illumination to the front side of the culture device, wherein the culture device comprises first and second indicator compounds, wherein the first indicator compound is converted by microorganisms in a first group of microorganisms and microorganisms in a second group of microorganisms to a non-water diffusible first product having a first color, wherein the second indicator compound is converted by the microorganisms in the second group of microorganisms to a water-diffusible second product that forms a second color, and wherein the first image is produced while illuminating the culture device with a first ratio of front-side illumination to back-side illumination; using the imaging device to produce a second image of the culture device, wherein the second image is produced while providing illumination to the back side of the culture device, wherein the second image is produced while illuminating the culture device with a second ratio of front-side illumination to back-side illumination that is lower than the first ratio; analyzing, by a processor, the first and second images to identify microorganism colonies in each of the first image and the second image; analyzing, by the processor, the first image to calculate a first value of a size parameter for a colony at a particular location in the culture device; analyzing, by the processor, the second image to calculate a second value of the size parameter at the particular location in the culture device; comparing, by the processor, the first value to the second value; and counting, by the processor, the colony, wherein the processor counts the colony as being in the first group of microorganisms based on the first value and the second value being the same, wherein the processor counts the colony as being in the second group of microorganisms based on the first value and the second value being different, wherein the first value and the second value are considered the same if the first value and the second value are within a predetermined range.