Keywords: Data augmentation, style transfer, disentanglement, nuclei segmentation
TL;DR: Data augmentation technique based on a multi-modality style transfer GAN using disentangled representations for nuclei segmentation.
Abstract: Annotating microscopy images for nuclei segmentation is laborious and time-consuming. To leverage the few existing annotations, also across multiple modalities, we propose a microscopy-style augmentation technique based on a generative adversarial network (GAN). Unlike other style transfer methods, it can not only deal with different cell assay types and lighting conditions but also with different imaging modalities, such as bright-field and fluorescence microscopy. Using disentangled representations for content and style, we can preserve the structure of the original image while altering its style during augmentation. We evaluate our data augmentation on the 2018 Data Science Bowl dataset, consisting of various cell assays, lighting conditions, and imaging modalities. With our style augmentation, the segmentation accuracy of the two top-ranked Mask R-CNN-based nuclei segmentation algorithms in the competition increases significantly. Thus, our augmentation technique renders the downstream task more robust to the test data heterogeneity and helps counteract class imbalance without resampling of minority classes.
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Paper Type: recently published or submitted journal contributions
Primary Subject Area: Image Synthesis
Secondary Subject Area: Segmentation
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