Volumetric (3d) images are acquired for many scientific and biomedical purposes using imaging methods such as serial section microscopy, CT scans, and MRI. A frequent step in the analysis and reconstruction of such data is the alignment and registration of images that were acquired in succession along a spatial or temporal dimension. For example, in serial section electron microscopy, individual 2d sections are imaged via electron microscopy and then must be aligned to one another in order to produce a coherent 3d volume. State of the art approaches find image correspondences derived from patch matching and invariant feature detectors, and then solve optimization problems that rigidly or elastically deform series of images into an aligned volume. Here we show how fully convolutional neural networks trained with an adversarial loss function can be used for two tasks: (1) synthesis of missing or damaged image data from adjacent sections, and (2) fine-scale alignment of block-face electron microscopy data. Finally, we show how these two capabilities can be combined in order to produce artificial isotropic volumes from anisotropic image volumes using a super-resolution adversarial alignment and interpolation approach.
Heinrich and colleagues recently introduced neural network architectures that produce impressive results on the task of generating isotropic 3d volumes from anisotropic source data @cite_12 , which is closely related to the experiments we pursue in Section 5. The novel training methods introduce in this work are likely to be complementary to general advances in neural network architectures for 3d image synthesis.
@cite_12
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Recent advances in convolutional neural networks have shown promising results in 3D shape completion. But due to GPU memory limitations, these methods can only produce low-resolution outputs. To inpaint 3D models with semantic plausibility and contextual details, we introduce a hybrid framework that combines a 3D Encoder-Decoder Generative Adversarial Network (3D-ED-GAN) and a Long-term Recurrent Convolutional Network (LRCN). The 3D-ED-GAN is a 3D convolutional neural network trained with a generative adversarial paradigm to fill missing 3D data in low-resolution. LRCN adopts a recurrent neural network architecture to minimize GPU memory usage and incorporates an Encoder-Decoder pair into a Long Short-term Memory Network. By handling the 3D model as a sequence of 2D slices, LRCN transforms a coarse 3D shape into a more complete and higher resolution volume. While 3D-ED-GAN captures global contextual structure of the 3D shape, LRCN localizes the fine-grained details. Experimental results on both real-world and synthetic data show reconstructions from corrupted models result in complete and high-resolution 3D objects.