Papers › U-Net-and-a-half: Convolutional network for biomedical image segmentation using...
U-Net-and-a-half: Convolutional network for biomedical image segmentation using multiple expert-driven annotations
Yichi Zhang, Jesper Kers, Clarissa A. Cassol, Joris J. Roelofs, Najia Idrees, Alik Farber, Samir Haroon, Kevin P. Daly, Suvranu Ganguli, Vipul C. Chitalia, Vijaya B. Kolachalama
Development of deep learning systems for biomedical segmentation often requires access to expert-driven, manually annotated datasets. If more than a single expert is involved in the annotation of the same images, then the inter-expert agreement is not necessarily perfect, and no single expert annotation can precisely capture the so-called ground truth of the regions of interest on all images. Also, it is not trivial to generate a reference estimate using annotations from multiple experts. Here we present a deep neural network, defined as U-Net-and-a-half, which can simultaneously learn from annotations performed by multiple experts on the same set of images. U-Net-and-a-half contains a convolutional encoder to generate features from the input images, multiple decoders that allow simultaneous learning from image masks obtained from annotations that were independently generated by multiple experts, and a shared low-dimensional feature space. To demonstrate the applicability of our framework, we used two distinct datasets from digital pathology and radiology, respectively. Specifically, we trained two separate models using pathologist-driven annotations of glomeruli on whole slide images of human kidney biopsies (10 patients), and radiologist-driven annotations of lumen cross-sections of human arteriovenous fistulae obtained from intravascular ultrasound images (10 patients), respectively. The models based on U-Net-and-a-half exceeded the performance of the traditional U-Net models trained on single expert annotations alone, thus expanding the scope of multitask learning in the context of biomedical image segmentation.
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