Esophageal Tumor Segmentation in CT Images using a Dilated Dense Attention Unet (DDAUnet)

Yousefi, Sahar; Sokooti, Hessam; Elmahdy, Mohamed S.; Lips, Irene M.; Shalmani, Mohammad T.Manzuri; Zinkstok, Roel T.; Dankers, Frank J.W.M.; Staring, M.

doi:10.1109/ACCESS.2021.3096270

Esophageal Tumor Segmentation in CT Images using a Dilated Dense Attention Unet (DDAUnet)

Title

Esophageal Tumor Segmentation in CT Images using a Dilated Dense Attention Unet (DDAUnet)

Author

Yousefi, Sahar (Leiden University Medical Center)
Sokooti, Hessam (Leiden University Medical Center)
Elmahdy, Mohamed S. (Leiden University Medical Center)
Lips, Irene M. (Leiden University Medical Center)
Shalmani, Mohammad T.Manzuri (Sharif University of Technology)
Zinkstok, Roel T. (Leiden University Medical Center)
Dankers, Frank J.W.M. (Leiden University Medical Center)
Staring, M. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center)

Date

2021

Abstract

Manual or automatic delineation of the esophageal tumor in CT images is known to be very challenging. This is due to the low contrast between the tumor and adjacent tissues, the anatomical variation of the esophagus, as well as the occasional presence of foreign bodies (e.g. feeding tubes). Physicians therefore usually exploit additional knowledge such as endoscopic findings, clinical history, additional imaging modalities like PET scans. Achieving his additional information is time-consuming, while the results are error-prone and might lead to non-deterministic results. In this paper we aim to investigate if and to what extent a simplified clinical workflow based on CT alone, allows one to automatically segment the esophageal tumor with sufficient quality. For this purpose, we present a fully automatic end-to-end esophageal tumor segmentation method based on convolutional neural networks (CNNs). The proposed network, called Dilated Dense Attention Unet (DDAUnet), leverages spatial and channel attention gates in each dense block to selectively concentrate on determinant feature maps and regions. Dilated convolutional layers are used to manage GPU memory and increase the network receptive field. We collected a dataset of 792 scans from 288 distinct patients including varying anatomies with air pockets, feeding tubes and proximal tumors. Repeatability and reproducibility studies were conducted for three distinct splits of training and validation sets. The proposed network achieved a DSC value of 0.79 ± 0.20, a mean surface distance of 5.4 ± 20.2mm and 95% Hausdorff distance of 14.7 ± 25.0mm for 287 test scans, demonstrating promising results with a simplified clinical workflow based on CT alone. Our code is publicly available via https://github.com/yousefis/DenseUnet_Esophagus_Segmentation.

Subject

attention gate
Computed tomography
CT images
densely connected pattern
dilated convolutional layer
Esophageal tumor segmentation
Esophagus
Image segmentation
Shape
Three-dimensional displays
Training
Tumors
UNet