Dataset Information

The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 challenge.

ABSTRACT: There is a large body of literature linking anatomic and geometric characteristics of kidney tumors to perioperative and oncologic outcomes. Semantic segmentation of these tumors and their host kidneys is a promising tool for quantitatively characterizing these lesions, but its adoption is limited due to the manual effort required to produce high-quality 3D segmentations of these structures. Recently, methods based on deep learning have shown excellent results in automatic 3D segmentation, but they require large datasets for training, and there remains little consensus on which methods perform best. The 2019 Kidney and Kidney Tumor Segmentation challenge (KiTS19) was a competition held in conjunction with the 2019 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) which sought to address these issues and stimulate progress on this automatic segmentation problem. A training set of 210 cross sectional CT images with kidney tumors was publicly released with corresponding semantic segmentation masks. 106 teams from five continents used this data to develop automated systems to predict the true segmentation masks on a test set of 90 CT images for which the corresponding ground truth segmentations were kept private. These predictions were scored and ranked according to their average Sørensen-Dice coefficient between the kidney and tumor across all 90 cases. The winning team achieved a Dice of 0.974 for kidney and 0.851 for tumor, approaching the inter-annotator performance on kidney (0.983) but falling short on tumor (0.923). This challenge has now entered an "open leaderboard" phase where it serves as a challenging benchmark in 3D semantic segmentation.

SUBMITTER: Heller N

PROVIDER: S-EPMC7734203 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 challenge.

Heller Nicholas N Isensee Fabian F Maier-Hein Klaus H KH Hou Xiaoshuai X Xie Chunmei C Li Fengyi F Nan Yang Y Mu Guangrui G Lin Zhiyong Z Han Miofei M Yao Guang G Gao Yaozong Y Zhang Yao Y Wang Yixin Y Hou Feng F Yang Jiawei J Xiong Guangwei G Tian Jiang J Zhong Cheng C Ma Jun J Rickman Jack J Dean Joshua J Stai Bethany B Tejpaul Resha R Oestreich Makinna M Blake Paul P Kaluzniak Heather H Raza Shaneabbas S Rosenberg Joel J Moore Keenan K Walczak Edward E Rengel Zachary Z Edgerton Zach Z Vasdev Ranveer R Peterson Matthew M McSweeney Sean S Peterson Sarah S Kalapara Arveen A Sathianathen Niranjan N Papanikolopoulos Nikolaos N Weight Christopher C

Medical image analysis 20201002

There is a large body of literature linking anatomic and geometric characteristics of kidney tumors to perioperative and oncologic outcomes. Semantic segmentation of these tumors and their host kidneys is a promising tool for quantitatively characterizing these lesions, but its adoption is limited due to the manual effort required to produce high-quality 3D segmentations of these structures. Recently, methods based on deep learning have shown excellent results in automatic 3D segmentation, but t ...[more]

PMID: 33049579

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Project description:ObjectivesAccurate kidney and tumor segmentation of computed tomography (CT) scans is vital for diagnosis and treatment, but manual methods are time-consuming and inconsistent, highlighting the value of AI automation. This study develops a fully automated AI model using vision transformers (ViTs) and convolutional neural networks (CNNs) to detect and segment kidneys and kidney tumors in Contrast-Enhanced (CECT) scans, with a focus on improving sensitivity for small, indistinct tumors.MethodsThe segmentation framework employs a ViT-based model for the kidney organ, followed by a 3D UNet model with enhanced connections and attention mechanisms for tumor detection and segmentation. Two CECT datasets were used: a public dataset (KiTS23: 489 scans) and a private institutional dataset (Private: 592 scans). The AI model was trained on 389 public scans, with validation performed on the remaining 100 scans and external validation performed on all 592 private scans. Tumors were categorized by TNM staging as small (≤4 cm) (KiTS23: 54%, Private: 41%), medium (>4 cm to ≤7 cm) (KiTS23: 24%, Private: 35%), and large (>7 cm) (KiTS23: 22%, Private: 24%) for detailed evaluation.ResultsKidney and kidney tumor segmentations were evaluated against manual annotations as the reference standard. The model achieved a Dice score of 0.97 ± 0.02 for kidney organ segmentation. For tumor detection and segmentation on the KiTS23 dataset, the sensitivities and average false-positive rates per patient were as follows: 0.90 and 0.23 for small tumors, 1.0 and 0.08 for medium tumors, and 0.96 and 0.04 for large tumors. The corresponding Dice scores were 0.84 ± 0.11, 0.89 ± 0.07, and 0.91 ± 0.06, respectively. External validation on the private data confirmed the model's effectiveness, achieving the following sensitivities and average false-positive rates per patient: 0.89 and 0.15 for small tumors, 0.99 and 0.03 for medium tumors, and 1.0 and 0.01 for large tumors. The corresponding Dice scores were 0.84 ± 0.08, 0.89 ± 0.08, and 0.92 ± 0.06.ConclusionsThe proposed model demonstrates consistent and robust performance in segmenting kidneys and kidney tumors of various sizes, with effective generalization to unseen data. This underscores the model's significant potential for clinical integration, offering enhanced diagnostic precision and reliability in radiological assessments.

Project description:BackgroundSolitary pulmonary nodules (SPNs) measuring 8 to 30 mm in diameter require further workup to determine the likelihood of malignancy.Research questionWhat is the diagnostic performance of a lung cancer prediction convolutional neural network (LCP-CNN) in SPNs using unenhanced and contrast-enhanced CT imaging compared with the current clinical workup?Study design and methodsThis was a post hoc analysis of the Single Pulmonary Nodule Investigation: Accuracy and Cost-Effectiveness of Dynamic Contrast Enhanced Computed Tomography in the Characterisation of Solitary Pulmonary Nodules trial, a prospective multicenter study comparing the diagnostic accuracy of dynamic contrast-enhanced (DCE) CT imaging with PET imaging in SPNs. The LCP-CNN was designed and validated in an external cohort. LCP-CNN-generated risk scores were created from the noncontrast and contrast-enhanced CT scan images from the DCE CT imaging. The gold standard was histologic analysis or 2 years of follow-up. The area under the receiver operating characteristic curves (AUC) were calculated using LCP-CNN score, maximum standardized uptake value, and DCE CT scan maximum enhancement and were compared using the DeLong test.ResultsTwo hundred seventy participants (mean ± SD age, 68.3 ± 8.8 years; 49% women) underwent PET with CT scan imaging and DCE CT imaging with CT scan data available centrally for LCP-CNN analysis. The accuracy of the LCP-CNN on the noncontrast images (AUC, 0.83; 95% CI, 0.79-0.88) was superior to that of DCE CT imaging (AUC, 0.76; 95% CI, 0.69-0.82; P = .03) and equal to that of PET with CT scan imaging (AUC, 0.86; 95% CI, 0.81-0.90; P = .35). The presence of contrast resulted in a small reduction in diagnostic accuracy, with the AUC falling from 0.83 (95% CI, 0.79-0.88) on the noncontrast images to 0.80 to 0.83 after contrast (P < .05 for 240 s after contrast only).InterpretationAn LCP-CNN algorithm provides an AUC equivalent to PET with CT scan imaging in the diagnosis of solitary pulmonary nodules.Trial registrationClinicalTrials.gov Identifier; No.: NCT02013063.

Dataset Information

The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 challenge.

Publications

The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 challenge.

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