Double Slit Experiment: How do scientists ensure that there's only one photon?

Quantum dots. nanoscale semiconductor materials that can confine photons in 3 dimensions and release them a measurable time after. Based on material used the decay time is known empirically. frequency is also known. the latter is sufficient to calculate the energy of one photon. The former is then sufficient to calculate the rate of photon re emission from the QD. If the peaks at the detector are further apart than the decay time and each peak is measurable to one photon's worth of energy then you know you have a beam of single photons.

In the double slit experiment, if you decrease the amplitude of the output light gradually, you will see a transition from continuous bright and dark fringe on the screen to a single dots at a time. If you can measure the dots very accurately, you always see there is one and only one dots there. It is the proof of the existence of the smallest unit of each measurement which is called single photon: You either get a single bright dot, or not.

So, probably you may ask why it is not a single photon composite of two "sub-photon", each of them passing through the slit separately and then interference with "itself" at the screen so that we only get one dot. However, the same thing occurs for three slits, four slits, etc... but the final results is still a single dot. It means that the photon must be able to split into infinitely many "sub-photon". If you get to this point, then congratulation, you basically discover the path-integral formalism of quantum mechanics.

The practical answer (which I also wrote in a comment on the linked question) is that you turn the intensity of the light source down until the expectation value for the number of photons on the optical path is low enough to suit you.

If $\bar{n} = 0.1$ then very few of the events that are recorded on the screen will come from events where more than one photon was present on the optical path and the data will be dominated by single photon event.

Not good enough for you? Turn it down until $\bar{n} = 0.01$. Or $0.001$ or whatever suits you.

At some point the exercise becomes silly.