A system and method for analyzing images using a non-transitory programmable device is disclosed. A user interface generator operating on the non-transitory programmable device receives specifications of a first image of a biological sample and a first image analysis step. A sequencer operating on the non-transitory programmable device applies the first image analysis step to the first image to develop annotated training data, and a machine learning system trainer operating on the non-transitory programmable device trains an untrained machine learning system to develop a trained machine learning system. When the trained machine learning system is presented with the first image as an input, the trained machine learning system develops a prediction of the annotated training data. In addition, the sequencer receives a specification of a workflow that comprises a second image analysis step that specifies operating the trained machine learning system and the sequencer undertakes the workflow on a second image to analyze the second image.