AFAIU, there are two ways to do scanning:
1. Server side - something like Trade-Ideas.
Pro: you can scan the whole universe of stocks.
Con: you can only run the scans that the server has pre-programmed (and probably combine such scans). So cannot do full customization.
2. Client side - like Medved Trader.
Pro: you can customize the scan as much as you want, it is just (in case of MT - C#) code, using any built-in indicators with any parameters you want, any timeframe, any candle frequency, etc.
Con: you only are running the scan on the data that is being streamed into the program. Granted, some data sources allow for quite a lot of tickers to be streamed (like 1500) but still.
I don't think there is a way for a third way that combines the pros of the two methods above. I was musing for a while about making a service like that where you would be able to upload a fully customized scanner and run it on the full universe of stocks, but I think the cost would be too much and not enough demand for it to justify it.