TY - JOUR T1 - Holographic deep learning for rapid optical screening of anthrax spores JF - bioRxiv DO - 10.1101/109108 SP - 109108 AU - YoungJu Jo AU - Sangjin Park AU - JaeHwang Jung AU - Jonghee Yoon AU - Hosung Joo AU - Min-hyeok Kim AU - Suk-Jo Kang AU - Myung Chul Choi AU - Sang Yup Lee AU - YongKeun Park Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/02/16/109108.abstract N2 - Establishing early warning systems for anthrax attacks is crucial in biodefense. Here we present an optical method for rapid screening of Bacillus anthracis spores through the synergistic application of holographic microscopy and deep learning. A deep convolutional neural network is designed to classify holographic images of unlabeled living cells. After training, the network outperforms previous techniques in all accuracy measures, achieving single-spore sensitivity and sub-genus specificity. The unique ‘representation learning’ capability of deep learning enables direct training from raw images instead of manually extracted features. The method automatically recognizes key biological traits encoded in the images and exploits them as fingerprints. This remarkable learning ability makes the proposed method readily applicable to classifying various single cells in addition to B. anthracis, as demonstrated for the diagnosis of Listeria monocytogenes, without any modification. We believe that our strategy will make holographic microscopy more accessible to medical doctors and biomedical scientists for easy, rapid, and accurate diagnosis of pathogens, and facilitate exciting new applications. ER -