Papers › High Resolution Medical Image Analysis with Spatial Partitioning

High Resolution Medical Image Analysis with Spatial Partitioning

6 Sep 2019arXiv:1909.03108archive 2025-07-28

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

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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