Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning.

Journal: G3 (Bethesda, Md.)
Published Date:

Abstract

High-throughput microscopy of many single cells generates high-dimensional data that are far from straightforward to analyze. One important problem is automatically detecting the cellular compartment where a fluorescently-tagged protein resides, a task relatively simple for an experienced human, but difficult to automate on a computer. Here, we train an 11-layer neural network on data from mapping thousands of yeast proteins, achieving per cell localization classification accuracy of 91%, and per protein accuracy of 99% on held-out images. We confirm that low-level network features correspond to basic image characteristics, while deeper layers separate localization classes. Using this network as a feature calculator, we train standard classifiers that assign proteins to previously unseen compartments after observing only a small number of training examples. Our results are the most accurate subcellular localization classifications to date, and demonstrate the usefulness of deep learning for high-throughput microscopy.

Authors

  • Tanel Pärnamaa
    Institute of Computer Science, University of Tartu, 50409, Estonia.
  • Leopold Parts
    Institute of Computer Science, University of Tartu, 50409, Estonia leopold.parts@sanger.ac.uk.