1Artificial neural networks are being widely implemented for a range of different biomedical 2 imaging applications. Convolutional neural networks are by far the most popular type of deep 3 learning architecture, but often require very large datasets for robust training and evaluation. 4We introduce deep learning diffusion fingerprinting (DLDF), which we have used to classify 5 diffusion-weighted magnetic resonance imaging voxels in a mouse model of glioblastoma 6 (GL261 cell line), both prior to and in response to Temozolomide (TMZ) chemotherapy. We 7show that, even with limited training, DLDF can automatically segment brain tumours from 8 normal brain, can automatically distinguish between young and older (after 9 days of growth) 9 tumours and that DLDF can detect whether or not a tumour has been treated with 10 chemotherapy. Our results also suggest that DLDF can detect localised changes in the 11 underlying tumour microstructure, which are not evident using conventional measurements 12 of the apparent diffusion coefficient (ADC). Tissue category maps generated by DLDF 13 showed regions containing a mixture of normal brain and tumour cells, and in some cases 14 evidence of tumour invasion across the corpus callosum, which were broadly consistent with 15 histology. In conclusion, DLDF shows the potential for applying deep learning on a pixel-wise 16 level, which reduces the need for vast training datasets and could easily be applied to other 17 multi-dimensional imaging acquisitions. 18 19