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Deep learning for cellular image analysis


Recent advances in computer vision and machine learning underpin a collection of algorithms with an impressive ability to decipher the content of images. These deep learning algorithms are being applied to biological images and are transforming the analysis and interpretation of imaging data. These advances are positioned to render difficult analyses routine and to enable researchers to carry out new, previously impossible experiments. Here we review the intersection between deep learning and cellular image analysis and provide an overview of both the mathematical mechanics and the programming frameworks of deep learning that are pertinent to life scientists. We survey the field’s progress in four key applications: image classification, image segmentation, object tracking, and augmented microscopy. Last, we relay our labs’ experience with three key aspects of implementing deep learning in the laboratory: annotating training data, selecting and training a range of neural network architectures, and deploying solutions. We also highlight existing datasets and implementations for each surveyed application.

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Fig. 1: Software 2.0 combines data annotations with deep learning to produce intelligent software.
Fig. 2: Common mathematical components of deep learning models.
Fig. 3: Image classification applied to biological images.
Fig. 4: Image segmentation applied to biological images.
Fig. 5: Augmenting microscopy images with deep learning.

Data availability

Links to the data referred to in this Review can be found in Table 2.

Table 2 Available datasets


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We thank A. Anandkumar, M. Angelo, L. Cai, S. Cooper, M. Elowitz, K.C. Huang, G. Johnson, A. Karpathy, L. Keren, A. Raj, T. Vora, and R. Wollman for helpful discussions and comments. This work was supported by several funding sources, including the Allen Discovery Center (award supporting W.G.; award supporting T.K., M.C., and D.V.V.), the Burroughs Wellcome Fund Postdoctoral Enrichment Program, a Figure Eight AI for Everyone award, and the NIH (subaward U24CA224309-01 to D.V.V.).

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E.M., D.B., T.K., W.G., M.C., and D.V.V. wrote the paper.

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Correspondence to David Van Valen.

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Moen, E., Bannon, D., Kudo, T. et al. Deep learning for cellular image analysis. Nat Methods 16, 1233–1246 (2019).

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