Segmentation of distinct bones plays a crucial role in diagnosis, planning, navigation, and the assessment of bone metastasis. It supplies semantic knowledge to visualisation tools for the planning of surgical interventions and the education of health professionals. Fully supervised segmentation of 3D data using Deep Learning methods has been extensively studied for many tasks but is usually restricted to distinguishing only a handful of classes. With 125 distinct bones, our case includes many more labels than typical 3D segmentation tasks. For this reason, the direct adaptation of most established methods is not possible. This paper discusses the intricacies of training a 3D segmentation network in a many-label setting and shows necessary modifications in network architecture, loss function, and data augmentation. As a result, we demonstrate the robustness of our method by automatically segmenting over one hundred distinct bones simultaneously in an end-to-end learnt fashion from a CT-scan.
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