Rapid Artificial Intelligence Solutions in a Pandemic - The COVID-19-20 Lung CT Lesion Segmentation Challenge.
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ABSTRACT:
SUBMITTER: Roth HR
PROVIDER: S-EPMC8183044 | biostudies-literature | 2021 Jun
REPOSITORIES: biostudies-literature
Publications
Rapid Artificial Intelligence Solutions in a Pandemic - The COVID-19-20 Lung CT Lesion Segmentation Challenge.
Roth Holger R HR Xu Ziyue Z Diez Carlos Tor CT Jacob Ramon Sanchez RS Zember Jonathan J Molto Jose J Li Wenqi W Xu Sheng S Turkbey Baris B Turkbey Evrim E Yang Dong D Harouni Ahmed A Rieke Nicola N Hu Shishuai S Isensee Fabian F Tang Claire C Yu Qinji Q Sölter Jan J Zheng Tong T Liauchuk Vitali V Zhou Ziqi Z Moltz Jan Hendrik JH Oliveira Bruno B Xia Yong Y Maier-Hein Klaus H KH Li Qikai Q Husch Andreas A Zhang Luyang L Kovalev Vassili V Kang Li L Hering Alessa A Vilaça João L JL Flores Mona M Xu Daguang D Wood Bradford B Linguraru Marius George MG
Research square 20210604
Artificial intelligence (AI) methods for the automatic detection and quantification of COVID-19 lesions in chest computed tomography (CT) might play an important role in the monitoring and management of the disease. We organized an international challenge and competition for the development and comparison of AI algorithms for this task, which we supported with public data and state-of-the-art benchmark methods. Board Certified Radiologists annotated 295 public images from two sources (A and B) f ...[more]
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Project description:Artificial intelligence (AI) methods for the automatic detection and quantification of COVID-19 lesions in chest computed tomography (CT) might play an important role in the monitoring and management of the disease. We organized an international challenge and competition for the development and comparison of AI algorithms for this task, which we supported with public data and state-of-the-art benchmark methods. Board Certified Radiologists annotated 295 public images from two sources (A and B) for algorithms training (n=199, source A), validation (n=50, source A) and testing (n=23, source A; n=23, source B). There were 1,096 registered teams of which 225 and 98 completed the validation and testing phases, respectively. The challenge showed that AI models could be rapidly designed by diverse teams with the potential to measure disease or facilitate timely and patient-specific interventions. This paper provides an overview and the major outcomes of the COVID-19 Lung CT Lesion Segmentation Challenge - 2020.
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Project description:Knowledge of gas volume, tissue mass and recruitability measured by the quantitative CT scan analysis (CT-qa) is important when setting the mechanical ventilation in acute respiratory distress syndrome (ARDS). Yet, the manual segmentation of the lung requires a considerable workload. Our goal was to provide an automatic, clinically applicable and reliable lung segmentation procedure. Therefore, a convolutional neural network (CNN) was used to train an artificial intelligence (AI) algorithm on 15 healthy subjects (1,302 slices), 100 ARDS patients (12,279 slices), and 20 COVID-19 (1,817 slices). Eighty percent of this populations was used for training, 20% for testing. The AI and manual segmentation at slice level were compared by intersection over union (IoU). The CT-qa variables were compared by regression and Bland Altman analysis. The AI-segmentation of a single patient required 5-10 s vs. 1-2 h of the manual. At slice level, the algorithm showed on the test set an IOU across all CT slices of 91.3 ± 10.0, 85.2 ± 13.9, and 84.7 ± 14.0%, and across all lung volumes of 96.3 ± 0.6, 88.9 ± 3.1, and 86.3 ± 6.5% for normal lungs, ARDS and COVID-19, respectively, with a U-shape in the performance: better in the lung middle region, worse at the apex and base. At patient level, on the test set, the total lung volume measured by AI and manual segmentation had a R 2 of 0.99 and a bias -9.8 ml [CI: +56.0/-75.7 ml]. The recruitability measured with manual and AI-segmentation, as change in non-aerated tissue fraction had a bias of +0.3% [CI: +6.2/-5.5%] and -0.5% [CI: +2.3/-3.3%] expressed as change in well-aerated tissue fraction. The AI-powered lung segmentation provided fast and clinically reliable results. It is able to segment the lungs of seriously ill ARDS patients fully automatically.
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Project description:Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multimodality cell segmentation benchmark, comprising more than 1,500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.
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Project description:BackgroundPneumonia can be anatomically classified into lobar, lobular, and interstitial types, with each type associated with different pathogens. Utilizing artificial intelligence (AI) to determine the anatomical classifications of pneumonia and assist in refining the differential diagnosis may offer a more viable and clinically relevant solution. This study aimed to develop a multi-classification model capable of identifying the occurrence of pneumonia in patients by utilizing case-specific computed tomography (CT) information, categorizing the pneumonia type (lobar, lobular, and interstitial pneumonia), and performing segmentation of the associated lesions.MethodsA total of 61 lobar pneumonia patients, 60 lobular pneumonia patients, and 60 interstitial pneumonia patients were consecutively enrolled at our local hospital from June 2020 and May 2022. All selected cases were divided into a training cohort (n=135) and an independent testing cohort (n=46). To generate the ground truth labels for the training process, manual segmentation and labeling were performed by three junior radiologists. Subsequently, the segmentations were manually reviewed and edited by a senior radiologist. AI models were developed to automatically segment the infected lung regions and classify the pneumonia. The accuracy of pneumonia lesion segmentation was analyzed and evaluated using the Dice coefficient. Receiver operating characteristic curves were plotted, and the area under the curve (AUC), accuracy, precision, sensitivity, and specificity were calculated to assess the efficacy of pneumonia classification.ResultsOur AI model achieved a Dice coefficient of 0.743 [95% confidence interval (CI): 0.657-0.826] for lesion segmentation in the training set and 0.723 (95% CI: 0.602-0.845) in the test set. In the test set, our model achieved an accuracy of 0.927 (95% CI: 0.876-0.978), precision of 0.889 (95% CI: 0.827-0.951), sensitivity of 0.889 (95% CI: 0.827-0.951), specificity of 0.946 (95% CI: 0.902-0.990), and AUC of 0.989 (95% CI: 0.969-1.000) for pneumonia classification. We trained the model using labels annotated by senior physicians and compared it to a model trained using labels annotated by junior physicians. The Dice coefficient of the model's segmentation improved by 0.014, increasing from 0.709 (95% CI: 0.589-0.830) to 0.723 (95% CI: 0.602-0.845), and the AUC improved by 0.042, rising from 0.947 to 0.989.ConclusionsOur study presents a robust multi-task learning model with substantial promise in enhancing the segmentation and classification of pneumonia in medical imaging.
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Project description:Background: Diagnostic reports contribute not only to the particular patient, but also to constructing massive training dataset in the era of artificial intelligence (AI). The maximum standardized uptake value (SUVmax) is often described in daily diagnostic reports of [18F] fluorodeoxyglucose (FDG) positron emission tomography (PET) - computed tomography (CT). If SUVmax can be used as an identifier of lesion, that would greatly help AI interpret diagnostic reports. We aimed to clarify whether the lesion can be localized using SUVmax strings. Methods: The institutional review board approved this retrospective study. We investigated a total of 112 lesions from 30 FDG PET-CT images acquired with 3 different scanners. SUVmax was calculated from DICOM files based on the latest Quantitative Imaging Biomarkers Alliance (QIBA) publication. The voxels showing the given SUVmax were exhaustively searched in the whole-body images and counted. SUVmax was provided with 5 different degrees of precision: integer (e.g., 3), 1st decimal places (DP) (3.1), 2nd DP (3.14), 3rd DP (3.142), and 4th DP (3.1416). For instance, when SUVmax = 3.14 was given, the voxels with 3.135 ≤ SUVmax < 3.145 were extracted. We also evaluated whether local maximum restriction could improve the identifying performance, where only the voxels showing the highest intensity within some neighborhood were considered. We defined that "identical detection" was achieved when only single voxel satisfied the criterion. Results: A total of 112 lesions from 30 FDG PET-CT images were investigated. SUVmax ranged from 1.3 to 49.1 (median = 5.6). Generally, when larger and more precise SUVmax values were given, fewer voxels satisfied the criterion. The local maximum restriction was very effective. When SUVmax was determined to 4 decimal places (e.g., 3.1416) and the local maximum restriction was applied, identical detection was achieved in 33.3% (lesions with SUVmax < 2), 79.5% (2 ≤ SUVmax < 5), and 97.8% (5 ≤ SUVmax) of lesions. Conclusion: In this preliminary study, SUVmax of FDG PET-CT could be used as an identifier to localize the lesion if precise SUVmax is provided and local maximum restriction was applied, although the lesions showing SUVmax < 2 were difficult to identify. The proposed method may have potential to make use of diagnostic reports retrospectively for constructing training datasets for AI.
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Project description:There is a dearth of literature that provides a bibliometric analysis concerning the role of Artificial Intelligence (AI) in sustainable agriculture therefore this study attempts to fill this research gap and provides evidence from the studies conducted between 2000-2021 in this field of research. The study is a systematic bibliographic analysis of the 465 previous articles and reviews done between 2000-2021 in relation to the utilization of AI in sustainable methods of agriculture. The results of the study have been visualized and presented using the VOSviewer and Biblioshiny visualizer software. The results obtained post analysis indicate that, the amount of academic works published in the field of AI's role in enabling sustainable agriculture increased significantly from 2018. Therefore, there is conclusive evidence that the growth trajectory shows a significant climb upwards. Geographically analysed, the country collaboration network highlights that most number of studies in the realm of this study originate from China, USA, India, Iran, France. The co-author network analysis results represent that there are multi-disciplinary collaborations and interactions between prominent authors from United States of America, China, United Kingdom and Germany. The final framework provided from this bibliometric study will help future researchers identify the key areas of interest in research of AI and sustainable agriculture and narrow down on the countries where prominent academic work is published to explore co-authorship opportunities.
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Project description:BackgroundData-driven gating (DDG) can improve PET quantitation and alleviate many issues with patient motion. However, misregistration between DDG-PET and CT may occur due to the distinct temporal resolutions of PET and CT and can be mitigated by DDG-CT. Here, the effects of misregistration and respiratory motion on PET quantitation and lesion segmentation were assessed with a new DDG-PET/CT method.MethodsA low-dose cine-CT was acquired in misregistered regions to enable both average CT (ACT) and DDG-CT. The following were compared: (1) baseline PET/CT, (2) PET/ACT (attenuation correction, AC = ACT), (3) DDG-PET (AC = helical CT), and (4) DDG-PET/CT (AC = DDG-CT). For DDG-PET, end-expiration (EE) data were derived from 50% of the total PET data at 30% from end-inspiration. For DDG-CT, EE phase CT data were extracted from cine-CT data by lung Hounsfield unit (HU) value and body contour. A total of 91 lesions from 16 consecutive patients were assessed for changes in standard uptake value (SUV), lesion glycolysis (LG), lesion volume, centroid-to-centroid distance (CCD), and DICE coefficients.ResultsRelative to baseline PET/CT, median changes in SUVmax ± σ for all 91 lesions were 20 ± 43%, 26 ± 23%, and 66 ± 66%, respectively, for PET/ACT, DDG-PET, and DDG-PET/CT. Median changes in lesion volume were 0 ± 58%, - 36 ± 26%, and - 26 ± 40%. LG for individual lesions increased for PET/ACT and decreased for DDG-PET, but was not different for DDG-PET/CT. Changes in mean HU from baseline PET/CT were dramatic for most lesions in both PET/ACT and DDG-PET/CT, especially for lesions with mean HU < 0 at baseline. CCD and DICE were both affected more by motion correction with DDG-PET than improved registration with ACT or DDG-CT.ConclusionAs misregistration becomes more prominent, the impact of motion correction with DDG-PET is diminished. The potential benefits of DDG-PET toward accurate lesion segmentation and quantitation could only be fully realized when combined with DDG-CT. These results impress upon the necessity of ensuring both misregistration and motion correction are accounted for together to optimize the clinical utility of PET/CT.
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Project description:A deep learning (DL) network for 2D-based breast mass segmentation in unenhanced dedicated breast CT images was developed and validated, and its robustness in radiomic feature stability and diagnostic performance compared to manual annotations of multiple radiologists was investigated. 93 mass-like lesions were extensively augmented and used to train the network (n = 58 masses), which was then tested (n = 35 masses) against manual ground truth of a qualified breast radiologist with experience in breast CT imaging using the Conformity coefficient (with a value equal to 1 indicating a perfect performance). Stability and diagnostic power of 672 radiomic descriptors were investigated between the computerized segmentation, and 4 radiologists' annotations for the 35 test set cases. Feature stability and diagnostic performance in the discrimination between benign and malignant cases were quantified using intraclass correlation (ICC) and multivariate analysis of variance (MANOVA), performed for each segmentation case (4 radiologists and DL algorithm). DL-based segmentation resulted in a Conformity of 0.85 ± 0.06 against the annotated ground truth. For the stability analysis, although modest agreement was found among the four annotations performed by radiologists (Conformity 0.78 ± 0.03), over 90% of all radiomic features were found to be stable (ICC>0.75) across multiple segmentations. All MANOVA analyses were statistically significant (p ≤ 0.05), with all dimensions equal to 1, and Wilks' lambda ≤0.35. In conclusion, DL-based mass segmentation in dedicated breast CT images can achieve high segmentation performance, and demonstrated to provide stable radiomic descriptors with comparable discriminative power in the classification of benign and malignant tumors to expert radiologist annotation.
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Project description:This study aims to evaluate an AI model designed to automatically classify skull fractures and visualize segmentation on emergent CT scans. The model's goal is to boost diagnostic accuracy, alleviate radiologists' workload, and hasten diagnosis, thereby enhancing patient outcomes. Unique to this research, both pediatric and post-operative patients were not excluded, and diagnostic durations were analyzed. Our testing dataset for the observer studies involved 671 patients, with a mean age of 58.88 years and fairly balanced gender representation. Model 1 of our AI algorithm, trained with 1499 fracture-positive cases, showed a sensitivity of 0.94 and specificity of 0.87, with a DICE score of 0.65. Implementing post-processing rules (specifically Rule B) improved the model's performance, resulting in a sensitivity of 0.94, specificity of 0.99, and a DICE score of 0.63. AI-assisted diagnosis resulted in significantly enhanced performance for all participants, with sensitivity almost doubling for junior radiology residents and other specialists. Additionally, diagnostic durations were significantly reduced (p < 0.01) with AI assistance across all participant categories. Our skull fracture detection model, employing a segmentation approach, demonstrated high performance, enhancing diagnostic accuracy and efficiency for radiologists and clinical physicians. This underlines the potential of AI integration in medical imaging analysis to improve patient care.
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Project description:We introduce multiple-organ objective segmentation (MOOSE) software that generates subject-specific, multiorgan segmentation using data-centric artificial intelligence principles to facilitate high-throughput systemic investigations of the human body via whole-body PET imaging. Methods: Image data from 2 PET/CT systems were used in training MOOSE. For noncerebral structures, 50 whole-body CT images were used, 30 of which were acquired from healthy controls (14 men and 16 women), and 20 datasets were acquired from oncology patients (14 men and 6 women). Noncerebral tissues consisted of 13 abdominal organs, 20 bone segments, subcutaneous fat, visceral fat, psoas muscle, and skeletal muscle. An expert panel manually segmented all noncerebral structures except for subcutaneous fat, visceral fat, and skeletal muscle, which were semiautomatically segmented using thresholding. A majority-voting algorithm was used to generate a reference-standard segmentation. From the 50 CT datasets, 40 were used for training and 10 for testing. For cerebral structures, 34 18F-FDG PET/MRI brain image volumes were used from 10 healthy controls (5 men and 5 women imaged twice) and 14 nonlesional epilepsy patients (7 men and 7 women). Only 18F-FDG PET images were considered for training: 24 and 10 of 34 volumes were used for training and testing, respectively. The Dice score coefficient (DSC) was used as the primary metric, and the average symmetric surface distance as a secondary metric, to evaluate the automated segmentation performance. Results: An excellent overlap between the reference labels and MOOSE-derived organ segmentations was observed: 92% of noncerebral tissues showed DSCs of more than 0.90, whereas a few organs exhibited lower DSCs (e.g., adrenal glands [0.72], pancreas [0.85], and bladder [0.86]). The median DSCs of brain subregions derived from PET images were lower. Only 29% of the brain segments had a median DSC of more than 0.90, whereas segmentation of 60% of regions yielded a median DSC of 0.80-0.89. The results of the average symmetric surface distance analysis demonstrated that the average distance between the reference standard and the automatically segmented tissue surfaces (organs, bones, and brain regions) lies within the size of image voxels (2 mm). Conclusion: The proposed segmentation pipeline allows automatic segmentation of 120 unique tissues from whole-body 18F-FDG PET/CT images with high accuracy.
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