Image noise reduction
Maybe some of the following steps might help:

Desaturate the image using any method your prefer (either a color register, luminance or lightness). It is much easier to perform the next steps if the image is only 1 dimensional
possibly apply some non-linear function over the pixels gray value. This might increase the visual color difference between light pixels and dark pixels. Additionally, it will reduce the color difference between dark pixels and very light pixels. you could consider it as a smooth threshold function.
As the roots have a light color and the ground is overall dark, we should look for 2 aspects: a pixel with a light value and to which the neighboring pixels have a dark value. To enhance this second aspect, you could add a Laplace-edge detect filter to the image (so the resulting value will be the current value and the value of the laplace filter).
At this point, if properly done, the roots should already somewhat pop out the image. One could follow this up with some Dilate - Erode filters (you can stack those) to even out background color differences.

Hope this helped a bit.