Journal
NATURE METHODS
Volume 16, Issue 12, Pages 1254-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/s41592-019-0658-6
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Funding
- Knut and Alice Wallenberg Foundation [2016.0204]
- Swedish Research Council [2017-05327]
- Swedish Research Council [2017-05327] Funding Source: Swedish Research Council
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Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by similar to 20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.
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