An inline vision-based system used for the inspection and processing of food material and associated imaging methods are disclosed. The system includes a conveyor belt, a transparent plate, and an imaging system, wherein the imaging system includes a light source and at least one camera. The imaging system produces image data from multiple views of light passing through an object on the transparent plate and captured by the camera. The image data corresponds to one of transmittance, interactance, or reflectance image data and is transmitted to a processor. The processor processes the data using machine learning to generate a three dimensional model of the geometry of a portion of material internal to the object so as to determine boundaries of the portion relative to the surrounding material.