ClassifyPixels performs per-pixel classification using the Ilastik application. Ilastik is now bundled with the CellProfiler distribution; it applies supervised machine learning techniques to images to learn their features. A user trains a classifier with Ilastik and then saves the classifier. The user then uses the ClassifyPixels module to classify the pixels in an image. ClassifyPixels produces an "image" consisting of probabilities that the pixel belongs to the chosen class.