No matter how powerful it is, every scanner relies on the computer to which it's connected for instructions on what and how to scan. These signals are supplied by driver software that runs on your computer and translates instructions into commands the scanner understands.
In the old days, scanner manufacturers provided a separate driver for each graphics or text scanning program. Now, most manufacturers rely on a common standard called TWAIN to control the interaction between different programs. Under TWAIN, applications send their scanning instructions in a standard format that any compatible driver software can understand. As a result, almost all TWAIN programs can work with any TWAIN-compatible scanner. Most programs even use the same menu choice for scanning (Acquire, in the File menu), so scanning from different applications doesn't require much study.
The biggest drawback to TWAIN is that some scanner manufacturers have implemented TWAIN drivers that are not terribly good. For instance, many of them do not support the full range of specified capabilities, which can potentially render some of your software's capabilities useless.