Capturing aerial images by Unmanned Aerial Vehicles (UAV) allows gathering a general view of an agricultural site together with a detailed exploration of its relevant aspects for operational actions. Here we explore the challenging task of detecting cirsium arvense, a thistle-weed species, from aerial images of barley-cereal crops taken from 50 m above the ground, with the purpose of applying herbicide for site-specific weed treatment. The methods for automatic detection are based on object-based annotations, pointing out the RGB attributes of the Weed or Cereal classes for an entire group of pixels, referring to a crop area which will have to be treated if it is classified as being of the Weed class. In this way, an annotation belongs to the Weed class if more than half of its area is known to be covered by thistle weeds. Hence, based on object and pixel-level analysis, we compare the use of k-Nearest Neighbours (k-NN) and (feed-forward, one-hidden layer) neural networks, obtaining the best results for weed detection based on pixel-level analysis, based on a soft measure given by the proportion of predicted weed pixels per object, with a global accuracy of over 98%.