Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for image segmentation and chemical analysis using machine learning. In some implementations, a system obtains a hyperspectral image that includes a representation of an object. The system segments the hyperspectral image to identify regions of a particular type on the object. The system generates a set of feature values derived from image data for different wavelength bands that is located in the hyperspectral image in the identified regions of the particular type. The system generates a prediction of a level of one or more chemicals in the object based on an output produced by a machine learning model in response to the set of feature values being provided as input to the machine learning model. The system provides data indicating the prediction of the level of the one or more chemicals in the object.