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Not in primary school. My DS2 is currently in year 10. Last year they implemented a finger print system for the canteen - parents pay money to a lunch account and the child spends it using their thumb print.
Our prep school uses fingerprints for the library so children can take out books even when the librarian isn't there. Works well and the DC love the fact that they are given the responsibility of checking out their own books
Do note that this technology isn't about 'fingerprints' - no actual fingerprints are stored. The prints are converted into numbers, and the technology uses these numbers to read the scans. Any system used in secondary schools (that's all I've looked into - I didn't know primary schools used it) have an opt out option, or should have. The system can bet set to use both fobs and scans. In most cases there's only a very few parents who take the alternative. It is so much easier for children to just scan a thumb print than have to remember to take a fob in every day.
two things. Firstly there is legislation coming in sometime within the next year, I believe, which means that all the so-called fingerprint systems (and there is an argument whether it or is not a finger print) will have to have parental agreement for it to be used. Secondly I have seen a system that works well in primary that is based on pupils faces, so the pupil presses the screen with there face and that then debits the account. There are obvious advantages to this where we are talking about infant children, as long as there is someone observing to make sure they press the right face!
My DD has the fingerprint system in place at her high school for the library and the dinners. Permission is sought, or they opt out and go for a pin number instead. Parents are assured that the fingerprints are stored in a digital information way rather than pictorially. So noone can access what their fingerprint actually looks like through the data.