3D image segmentation plays an important role in biomedical image analysis.
Many 2D and 3D deep learning models have achieved state-of-the-art segmentation
performance on 3D biomedical image datasets. Yet, 2D and 3D models have their
own strengths and weaknesses, and by unifying them together, one may be able to
achieve more accurate results. In this paper, we propose a new ensemble
learning framework for 3D biomedical image segmentation that combines the
merits of 2D and 3D models. First, we develop a fully convolutional network
based meta-learner to learn how to improve the results from 2D and 3D models
(base-learners). Then, to minimize over-fitting for our sophisticated
meta-learner, we devise a new training method that uses the results of the
base-learners as multiple versions of "ground truths". Furthermore, since our
new meta-learner training scheme does not depend on manual annotation, it can
utilize abundant unlabeled 3D image data to further improve the model.
Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset
and the mouse piriform cortex dataset) show that our approach is effective
under fully-supervised, semi-supervised, and transductive settings, and attains
superior performance over state-of-the-art image segmentation methods.