A system and method are provided for tracking magnetically-labeled substances, such as transplanted cells, in subjects using magnetic resonance imaging (MRI). The method includes obtaining a quantity of a substance that comprises an MRI contrast compound or is otherwise magnetically-labeled for purposes of an MRI scan, administering the substance into a region of interest of a subject, performing an imaging scan of a portion of the subject comprising the region of interest, obtaining an imaging data set from the scan, reducing the dataset into pixel groupings based on intensity profiles, where the pixel groupings have a pixel size larger than the expected pixel size of a unit of the MRI contrast compound or magnetically-labeled substance, extracting candidate pixel matrices from the imaging data, training a machine learning (ML) module by using the candidate pixel matrices, quantifying the presence, number and/or location of units of the substance within the subject by using the ML module, and displaying a visual representation of an identification of the substances within the subject as a result of using the ML module.