The invention provides a method for quantifying the number of target entities that were successfully encapsulated into a microfluidic compartment such as a microfluidic droplet. The invention is predicated upon a continuous quantifiable detectable signal corresponding to the quantity of entities encapsulated in a microfluidic compartment. The present invention is useful in the context of high throughput microfluidic screening approaches which require thorough signal normalization in order to reliably improve signal to noise ratio and to reliably identify screening hits.