Using a scanner is the best way to have picture with a high contrast and resolution. However, the speed of the acquisition is rather slow compared to a camera, specially if the resolution is high.
Scanning can be used with large root system as it is possible to separate the different root on scanner surface. It is important to carefully spread the root in order to avoid overlaps and crossing as much as possible. They are a nightmare for most of the root image analysis softwares.
An easy way to separate the different root is to place the root system in a thin film of water. The roots will tend to recover their initial shape and they are easier to untangle as they float. This might require modify the scanner and to mount it on a specially design box (see image below).In order to avoid shadow around the roots floating in the water, a simple trick is to put a sheet of transparent paper on the spread roots.
Before scanning the image most scanning software (if not, then it is a bad one) let you choose the resolution you want for your image. This resolution is often given in DPI, which stands for Dots Per Inch (even in countries using the metric system). In other words, a resolution of 300 DPI means that an inch on the image is represented by 300 pixels (or 118 pixels per centimeters). If you know the diameter of the roots you plan to scan you can therefore adapt the resolution of the scanner to your needs. For instance, if the smaller roots on your root system has a diameter of 0.1 mm and you scan it at 300 DPI, the diameter of these roots will be represented by 1-2 pixels, which is not enough for most image analysis software. You would need to increase the scanner resolution to have a image suitable for analysis.