The Ct (Cycle threshold) – or more correctly – Cq (Cycle quantification) – value  is per definitionem being used to determine the gene expression via the fluorescence. Basically, one determines mathematically (commonly used is the 2nd derivative-method) the value where the fluorescence does not increase any more which indicates that the exponential phase of the amplification has ended. This happens in a certain cycle which is then called the “quantification cycle” (Cq).

However, there are many more mathematical methods to determine the Cq-value (see literature below). Most important is that you always use the same calculation method within one experiment.

Ruijter, J. M., Zhao, S., Spiess, A. N., Boggy, G., Blom, J., Rutledge, R. G., … Vandesompele, J. (2013). Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications. Methods, 59(1), 32–46.