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Register a new userAlignShift: Bridging the Gap of Imaging Thickness in 3D Anisotropic Volumes
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Jiancheng Yang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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This paper addresses a fundamental challenge in 3D medical image processing: how to deal with imaging thickness. For anisotropic medical volumes, there is a significant performance gap between thin-slice (mostly 1mm) and thick-slice (mostly 5mm) volumes. Prior arts tend to use 3D approaches for the thin-slice and 2D approaches for the thick-slice, respectively. We aim at a unified approach for both thin- and thick-slice medical volumes. Inspired by recent advances in video analysis, we propose AlignShift, a novel parameter-free operator to convert theoretically any 2D pretrained network into thickness-aware 3D network. Remarkably, the converted networks behave like 3D for the thin-slice, nevertheless degenerate to 2D for the thick-slice adaptively. The unified thickness-aware representation learning is achieved by shifting and fusing aligned virtual slices as per the input imaging thickness. Extensive experiments on public large-scale DeepLesion benchmark, consisting of 32K lesions for universal lesion detection, validate the effectiveness of our method, which outperforms previous state of the art by considerable margins without whistles and bells. More importantly, to our knowledge, this is the first method that bridges the performance gap between thin- and thick-slice volumes by a unified framework. To improve research reproducibility, our code in PyTorch is open source at https://github.com/M3DV/AlignShift.
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While deep convolutional neural networks (CNN) have been successfully applied for 2D image analysis, it is still challenging to apply them to 3D anisotropic volumes, especially when the within-slice resolution is much higher than the between-slice resolution and when the amount of 3D volumes is relatively small. On one hand, direct learning of CNN with 3D convolution kernels suffers from the lack of data and likely ends up with poor generalization; insufficient GPU memory limits the model size or representational power. On the other hand, applying 2D CNN with generalizable features to 2D slices ignores between-slice information. Coupling 2D network with LSTM to further handle the between-slice information is not optimal due to the difficulty in LSTM learning. To overcome the above challenges, we propose a 3D Anisotropic Hybrid Network (AH-Net) that transfers convolutional features learned from 2D images to 3D anisotropic volumes. Such a transfer inherits the desired strong generalization capability for within-slice information while naturally exploiting between-slice information for more effective modelling. The focal loss is further utilized for more effective end-to-end learning. We experiment with the proposed 3D AH-Net on two different medical image analysis tasks, namely lesion detection from a Digital Breast Tomosynthesis volume, and liver and liver tumor segmentation from a Computed Tomography volume and obtain the state-of-the-art results.
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