tetano
Editor, Senior Moderator
BMC Med Imaging
. 2021 Mar 23;21(1):57.
doi: 10.1186/s12880-021-00588-2.
Computing infection distributions and longitudinal evolution patterns in lung CT images
Dongdong Gu[SUP] #[/SUP][SUP] 1 2 [/SUP], Liyun Chen[SUP] #[/SUP][SUP] 3 2 [/SUP], Fei Shan[SUP] 4 [/SUP], Liming Xia[SUP] 5 [/SUP], Jun Liu[SUP] 6 [/SUP], Zhanhao Mo[SUP] 7 [/SUP], Fuhua Yan[SUP] 8 [/SUP], Bin Song[SUP] 9 [/SUP], Yaozong Gao[SUP] 2 [/SUP], Xiaohuan Cao[SUP] 2 [/SUP], Yanbo Chen[SUP] 2 [/SUP], Ying Shao[SUP] 2 [/SUP], Miaofei Han[SUP] 2 [/SUP], Bin Wang[SUP] 2 [/SUP], Guocai Liu[SUP] 1 [/SUP], Qian Wang[SUP] 3 [/SUP], Feng Shi[SUP] 2 [/SUP], Dinggang Shen[SUP] 2 [/SUP], Zhong Xue[SUP] 10 [/SUP]
Affiliations
Abstract
Background: Spatial and temporal lung infection distributions of coronavirus disease 2019 (COVID-19) and their changes could reveal important patterns to better understand the disease and its time course. This paper presents a pipeline to analyze statistically these patterns by automatically segmenting the infection regions and registering them onto a common template.
Methods: A VB-Net is designed to automatically segment infection regions in CT images. After training and validating the model, we segmented all the CT images in the study. The segmentation results are then warped onto a pre-defined template CT image using deformable registration based on lung fields. Then, the spatial distributions of infection regions and those during the course of the disease are calculated at the voxel level. Visualization and quantitative comparison can be performed between different groups. We compared the distribution maps between COVID-19 and community acquired pneumonia (CAP), between severe and critical COVID-19, and across the time course of the disease.
Results: For the performance of infection segmentation, comparing the segmentation results with manually annotated ground-truth, the average Dice is 91.6% ? 10.0%, which is close to the inter-rater difference between two radiologists (the Dice is 96.1% ? 3.5%). The distribution map of infection regions shows that high probability regions are in the peripheral subpleural (up to 35.1% in probability). COVID-19 GGO lesions are more widely spread than consolidations, and the latter are located more peripherally. Onset images of severe COVID-19 (inpatients) show similar lesion distributions but with smaller areas of significant difference in the right lower lobe compared to critical COVID-19 (intensive care unit patients). About the disease course, critical COVID-19 patients showed four subsequent patterns (progression, absorption, enlargement, and further absorption) in our collected dataset, with remarkable concurrent HU patterns for GGO and consolidations.
Conclusions: By segmenting the infection regions with a VB-Net and registering all the CT images and the segmentation results onto a template, spatial distribution patterns of infections can be computed automatically. The algorithm provides an effective tool to visualize and quantify the spatial patterns of lung infection diseases and their changes during the disease course. Our results demonstrate different patterns between COVID-19 and CAP, between severe and critical COVID-19, as well as four subsequent disease course patterns of the severe COVID-19 patients studied, with remarkable concurrent HU patterns for GGO and consolidations.
Keywords: COVID-19; Coronavirus infections; Lung; Probability; Registration; Segmentation.
. 2021 Mar 23;21(1):57.
doi: 10.1186/s12880-021-00588-2.
Computing infection distributions and longitudinal evolution patterns in lung CT images
Dongdong Gu[SUP] #[/SUP][SUP] 1 2 [/SUP], Liyun Chen[SUP] #[/SUP][SUP] 3 2 [/SUP], Fei Shan[SUP] 4 [/SUP], Liming Xia[SUP] 5 [/SUP], Jun Liu[SUP] 6 [/SUP], Zhanhao Mo[SUP] 7 [/SUP], Fuhua Yan[SUP] 8 [/SUP], Bin Song[SUP] 9 [/SUP], Yaozong Gao[SUP] 2 [/SUP], Xiaohuan Cao[SUP] 2 [/SUP], Yanbo Chen[SUP] 2 [/SUP], Ying Shao[SUP] 2 [/SUP], Miaofei Han[SUP] 2 [/SUP], Bin Wang[SUP] 2 [/SUP], Guocai Liu[SUP] 1 [/SUP], Qian Wang[SUP] 3 [/SUP], Feng Shi[SUP] 2 [/SUP], Dinggang Shen[SUP] 2 [/SUP], Zhong Xue[SUP] 10 [/SUP]
Affiliations
- PMID: 33757431
- DOI: 10.1186/s12880-021-00588-2
Abstract
Background: Spatial and temporal lung infection distributions of coronavirus disease 2019 (COVID-19) and their changes could reveal important patterns to better understand the disease and its time course. This paper presents a pipeline to analyze statistically these patterns by automatically segmenting the infection regions and registering them onto a common template.
Methods: A VB-Net is designed to automatically segment infection regions in CT images. After training and validating the model, we segmented all the CT images in the study. The segmentation results are then warped onto a pre-defined template CT image using deformable registration based on lung fields. Then, the spatial distributions of infection regions and those during the course of the disease are calculated at the voxel level. Visualization and quantitative comparison can be performed between different groups. We compared the distribution maps between COVID-19 and community acquired pneumonia (CAP), between severe and critical COVID-19, and across the time course of the disease.
Results: For the performance of infection segmentation, comparing the segmentation results with manually annotated ground-truth, the average Dice is 91.6% ? 10.0%, which is close to the inter-rater difference between two radiologists (the Dice is 96.1% ? 3.5%). The distribution map of infection regions shows that high probability regions are in the peripheral subpleural (up to 35.1% in probability). COVID-19 GGO lesions are more widely spread than consolidations, and the latter are located more peripherally. Onset images of severe COVID-19 (inpatients) show similar lesion distributions but with smaller areas of significant difference in the right lower lobe compared to critical COVID-19 (intensive care unit patients). About the disease course, critical COVID-19 patients showed four subsequent patterns (progression, absorption, enlargement, and further absorption) in our collected dataset, with remarkable concurrent HU patterns for GGO and consolidations.
Conclusions: By segmenting the infection regions with a VB-Net and registering all the CT images and the segmentation results onto a template, spatial distribution patterns of infections can be computed automatically. The algorithm provides an effective tool to visualize and quantify the spatial patterns of lung infection diseases and their changes during the disease course. Our results demonstrate different patterns between COVID-19 and CAP, between severe and critical COVID-19, as well as four subsequent disease course patterns of the severe COVID-19 patients studied, with remarkable concurrent HU patterns for GGO and consolidations.
Keywords: COVID-19; Coronavirus infections; Lung; Probability; Registration; Segmentation.