We developed a deep learning network that can generate new tissue contrasts from MRI data to match the contrasts of several histological methods. The network was trained using the carefully curated histological data from the Allen Institute mouse brain atlas and co-registered MRI data. In our tests, the new contrasts, which resembled Nissl, neurofilament, and myelin-basic-protein stained histology, demonstrated higher sensitivity and specificity than commonly used diffusion MRI markers to characterize neuronal, axonal, and myelin structures in the mouse brain. The contrasts were further validated using two mouse models with abnormal neuronal structures and dysmyelination.
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