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arXiv · 1909.03108

High Resolution Medical Image Analysis with Spatial Partitioning

Le Hou·Youlong Cheng·Noam Shazeer·Niki Parmar·Yeqing Li·Panagiotis Korfiatis·Travis M. Drucker·Daniel J. Blezek·Xiaodan Song
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Abstract

Medical images such as 3D computerized tomography (CT) scans and pathology images, have hundreds of millions or billions of voxels/pixels. It is infeasible to train CNN models directly on such high resolution images, because neural activations of a single image do not fit in the memory of a single GPU/TPU, and naive data and model parallelism approaches do not work. Existing image analysis approaches alleviate this problem by cropping or down-sampling input images, which leads to complicated implementation and sub-optimal performance due to information loss. In this paper, we implement spatial partitioning, which internally distributes the input and output of convolutional layers across GPUs/TPUs. Our implementation is based on the Mesh-TensorFlow framework and the computation distribution is transparent to end users. With this technique, we train a 3D Unet on up to 512 by 512 by 512 resolution data. To the best of our knowledge, this is the first work for handling such high resolution images end-to-end.

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Le Hou, Youlong Cheng, Noam Shazeer, Niki Parmar, Yeqing Li, Panagiotis Korfiatis, Travis M. Drucker, Daniel J. Blezek, Xiaodan Song. 2019-09-06. High Resolution Medical Image Analysis with Spatial Partitioning. https://arxiv.org/abs/1909.03108

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