Segmenting lung lesions of COVID-19 from CT images via pyramid pooling improved Unet

Biomed Phys Eng Express. 2021 May 20;7(4). doi: 10.1088/2057-1976/ac008a.

Abstract

Segmenting lesion regions of Coronavirus Disease 2019 (COVID-19) from computed tomography (CT) images is a challenge owing to COVID-19 lesions characterized by high variation, low contrast between infection lesions and around normal tissues, and blurred boundaries of infections. Moreover, a shortage of available CT dataset hinders deep learning techniques applying to tackling COVID-19. To address these issues, we propose a deep learning-based approach known as PPM-Unet to segmenting COVID-19 lesions from CT images. Our method improves an Unet by adopting pyramid pooling modules instead of the conventional skip connection and then enhances the representation of the neural network by aiding the global attention mechanism. We first pre-train PPM-Unet on COVID-19 dataset of pseudo labels containing1600 samples producing a coarse model. Then we fine-tune the coarse PPM-Unet on the standard COVID-19 dataset consisting of 100 pairs of samples to achieve a fine PPM-Unet. Qualitative and quantitative results demonstrate that our method can accurately segment COVID-19 infection regions from CT images, and achieve higher performance than other state-of-the-art segmentation models in this study. It offers a promising tool to lay a foundation for quantitatively detecting COVID-19 lesions.

Keywords: COVID-19; computed tomography; deep learning; image segmentation; medical image.

MeSH terms

  • Algorithms
  • COVID-19 / complications*
  • COVID-19 / virology
  • Deep Learning*
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • Lung Diseases / diagnostic imaging
  • Lung Diseases / pathology*
  • Lung Diseases / virology
  • Neural Networks, Computer*
  • SARS-CoV-2 / isolation & purification*
  • Specimen Handling
  • Tomography, X-Ray Computed / methods*