The importance of standardisation - COVID-19 CT & Radiograph Image Data Stock for deep learning purpose.
Ontology highlight
ABSTRACT:
SUBMITTER: Misztal K
PROVIDER: S-EPMC7591316 | biostudies-literature | 2020 Dec
REPOSITORIES: biostudies-literature
Publications
The importance of standardisation - COVID-19 CT & Radiograph Image Data Stock for deep learning purpose.
Misztal Krzysztof K Pocha Agnieszka A Durak-Kozica Martyna M Wątor Michał M Kubica-Misztal Aleksandra A Hartel Marcin M
Computers in biology and medicine 20201028
With the number of affected individuals still growing world-wide, the research on COVID-19 is continuously expanding. The deep learning community concentrates their efforts on exploring if neural networks can potentially support the diagnosis using CT and radiograph images of patients' lungs. The two most popular publicly available datasets for COVID-19 classification are COVID-CT and COVID-19 Image Data Collection. In this work, we propose a new dataset which we call COVID-19 CT & Radiograph Im ...[more]
Similar Datasets
Project description:We investigated the effect of deep learning-based image reconstruction (DLIR) compared to iterative reconstruction on image quality in CT pulmonary angiography (CTPA) for suspected pulmonary embolism (PE). For 220 patients with suspected PE, CTPA studies were reconstructed using filtered back projection (FBP), adaptive statistical iterative reconstruction (ASiR-V 30%, 60% and 90%) and DLIR (low, medium and high strength). Contrast-to-noise ratio (CNR) served as the primary parameter of objective image quality. Subgroup analyses were performed for normal weight, overweight and obese individuals. For patients with confirmed PE (n = 40), we further measured PE-specific CNR. Subjective image quality was assessed independently by two experienced radiologists. CNR was lowest for FBP and enhanced with increasing levels of ASiR-V and, even more with increasing strength of DLIR. High strength DLIR resulted in an additional improvement in CNR by 29-67% compared to ASiR-V 90% (p < 0.05). PE-specific CNR increased by 75% compared to ASiR-V 90% (p < 0.05). Subjective image quality was significantly higher for medium and high strength DLIR compared to all other image reconstructions (p < 0.05). In CT pulmonary angiography, DLIR significantly outperforms iterative reconstruction for increasing objective and subjective image quality. This may allow for further reductions in radiation exposure in suspected PE.
| S-EPMC10827738 | biostudies-literature
Project description:ObjectivesTo perform a comprehensive within-subject image quality analysis of abdominal CT examinations reconstructed with DLIR and to evaluate diagnostic accuracy compared to the routinely applied adaptive statistical iterative reconstruction (ASiR-V) algorithm.Materials and methodsOncologic patients were prospectively enrolled and underwent contrast-enhanced CT. Images were reconstructed with DLIR with three intensity levels of reconstruction (high, medium, and low) and ASiR-V at strength levels from 10 to 100% with a 10% interval. Three radiologists characterized the lesions and two readers assessed diagnostic accuracy and calculated signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), figure of merit (FOM), and subjective image quality, the latter with a 5-point Likert scale.ResultsFifty patients (mean age: 70 ± 10 years, 23 men) were enrolled and 130 liver lesions (105 benign lesions, 25 metastases) were identified. DLIR_H achieved the highest SNR and CNR, comparable to ASiR-V 100% (p ≥ .051). DLIR_M returned the highest subjective image quality (score: 5; IQR: 4-5; p ≤ .001) and significant median increase (29%) in FOM (p < .001). Differences in detection were identified only for lesions ≤ 0.5 cm: 32/33 lesions were detected with DLIR_M and 26 lesions were detected with ASiR-V 50% (p = .031). Lesion accuracy of was 93.8% (95% CI: 88.1, 97.3; 122 of 130 lesions) for DLIR and 87.7% (95% CI: 80.8, 92.8; 114 of 130 lesions) for ASiR-V 50%.ConclusionsDLIR yields superior image quality and provides higher diagnostic accuracy compared to ASiR-V in the assessment of hypovascular liver lesions, in particular for lesions ≤ 0.5 cm.Clinical relevance statementDeep learning image reconstruction algorithm demonstrates higher diagnostic accuracy compared to iterative reconstruction in the identification of hypovascular liver lesions, especially for lesions ≤ 0.5 cm.Key points• Iterative reconstruction algorithm impacts image texture, with negative effects on diagnostic capabilities. • Medium-strength deep learning image reconstruction algorithm outperforms iterative reconstruction in the diagnostic accuracy of ≤ 0.5 cm hypovascular liver lesions (93.9% vs 78.8%), also granting higher objective and subjective image quality. • Deep learning image reconstruction algorithm can be safely implemented in routine abdominal CT protocols in place of iterative reconstruction.
| S-EPMC10957592 | biostudies-literature
Project description:PurposeTo evaluate the effect of a deep learning-based reconstruction (DLR) method on the conspicuity of hypovascular hepatic metastases on abdominal CT images.Materials and methodsThis retrospective study with institutional review board approval included 58 patients with hypovascular hepatic metastases. A radiologist recorded the standard deviation of attenuation in the paraspinal muscle as the image noise and the contrast-to-noise ratio (CNR). CNR was calculated as region of interest ([ROI]L - ROIT)/N, where ROIL is the mean liver parenchyma attenuation, ROIT, the mean tumor attenuation, and N, the noise. Two other radiologists graded the conspicuity of the liver lesion on a five-point scale where 1 is unidentifiable and 5 is detected without diagnostic compromise. Only the smallest liver lesion in each patient, classified as smaller or larger than 10 mm, was evaluated. The difference between hybrid iterative reconstruction (IR) and DLR images was determined by using a two-sided Wilcoxon signed-rank test.ResultsThe image noise was significantly lower, and the CNR was significantly higher on DLR images than hybrid IR images (median image noise: 19.2 vs 12.8 HU, P < .001; median CNR: tumors < 10 mm: 1.9 vs 2.5; tumors > 10 mm: 1.7 vs 2.2, both P < .001). The scores for liver lesions were significantly higher for DLR images than hybrid IR images (P < .01 for both in tumors smaller or larger than 10 mm).ConclusionDLR improved the quality of abdominal CT images for the evaluation of hypovascular hepatic metastases.© RSNA, 2019Supplemental material is available for this article.
| S-EPMC8017421 | biostudies-literature
Project description:Prognosis of primary pontine hemorrhage (PPH) is important for treatment planning and patient management. However, only few clinical factors were reported to have prognostic value to PPH. Here, we propose a deep learning (DL) model that mines high-dimensional prognostic information from computed tomography (CT) images and combines clinical factors for predicting individualized prognosis of PPH. We proposed a multi-task DL model to learn high-dimensional CT features of hematoma and perihematomal areas for predicting the risk of 30-day mortality, 90-day mortality and 90-day functional outcome of PPH simultaneously. We further explored the combination of the DL model and clinical factors by building a combined model. All the models were trained in a training cohort (n = 219) and tested in an independent testing cohort (n = 35). The DL model achieved area under the curve (AUC) of 0.886, 0.886, and 0.759 in predicting 30-day mortality, 90-day mortality and 90-day functional outcome of PPH in the independent testing cohort, which improved over the previously reported new PPH score and the clinical model. When combining the DL model and clinical factors, the combined model achieved improved performance (AUC = 0.920, 0.941, and 0.894), indicating that DL model mines CT information that complements clinical factors. Through DL visualization technique, we found that the internal structure of hematoma and its expansion to perihematomal regions are important for predicting the prognosis of PPH. This DL model provides an easy-to-use way for predicting individualized prognosis of PPH by mining high-dimensional information from CT images, and showed improvement over clinical factors and present methods.
| S-EPMC9668666 | biostudies-literature
Project description:BackgroundThis study aims to evaluate the impact of a novel deep learning-based image reconstruction (DLIR) algorithm on the image quality in computed tomographic angiography (CTA) for pre-interventional planning of transcatheter aortic valve implantation (TAVI).MethodsWe analyzed 50 consecutive patients (median age 80 years, 25 men) who underwent TAVI planning CT on a 256-dectector-row CT. Images were reconstructed with adaptive statistical iterative reconstruction V (ASIR-V) and DLIR. Intravascular image noise, edge sharpness, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were quantified for ascending aorta, descending aorta, abdominal aorta and iliac arteries. Two readers (one radiologist and one interventional cardiologist) scored task-specific subjective image quality on a five-point scale.ResultsDLIR significantly reduced median image noise by 29-57% at all anatomical locations (all P<0.001). Accordingly, median SNR improved by 44-133% (all P<0.001) and median CNR improved by 44-125% (all P<0.001). DLIR significantly improved subjective image quality for all four pre-specified TAVI-specific tasks (measuring the annulus, assessing valve morphology and calcifications, the coronary ostia, and the suitability of the aorto-iliac access route) for both the radiologist and the interventional cardiologist (P≤0.001). Measurements of the aortic annulus circumference, area and diameter did not differ between ASIR-V and DLIR reconstructions (all P>0.05).ConclusionsDLIR significantly improves objective and subjective image quality in TAVI planning CT compared to a state-of-the-art iterative reconstruction without affecting measurements of the aortic annulus. This may provide an opportunity for further reductions in contrast medium volume in this population.
| S-EPMC9929406 | biostudies-literature
Project description:BackgroundEfforts to reduce the radiation dose have continued steadily, with new reconstruction techniques. Recently, image denoising algorithms using artificial neural networks, termed deep learning reconstruction (DLR), have been applied to CT image reconstruction to overcome the drawbacks of iterative reconstruction (IR). The purpose of our study was to compare the objective and subjective image quality of DLR and IR on pediatric abdomen and chest CT images.MethodsThis retrospective study included pediatric body CT images from February 2020 to October 2020, performed on 51 patients (34 boys and 17 girls; age 1-18 years). Non-contrast chest CT (n = 16), contrast-enhanced chest CT (n = 12), and contrast-enhanced abdomen CT (n = 23) images were included. Standard 50% adaptive statistical iterative reconstruction V (ASIR-V) images were compared to images with 100% ASIR-V and DLR at medium and high strengths. Attenuation, noise, contrast to noise ratio (CNR), and signal to noise (SNR) measurements were performed. Overall image quality, artifacts, and noise were subjectively assessed by two radiologists using a four-point scale (superior, average, suboptimal, and unacceptable). A phantom scan was performed including the dose range of the clinical images used in our study, and the noise power spectrum (NPS) was calculated. Quantitative and qualitative parameters were compared using repeated-measures analysis of variance (ANOVA) with Bonferroni correction and Wilcoxon signed-rank tests.ResultsDLR had better CNR and SNR than 50% ASIR-V in both pediatric chest and abdomen CT images. When compared with 50% ASIR-V, high strength DLR was associated with noise reduction in non-contrast chest CT (33.0%), contrast-enhanced chest CT (39.6%), and contrast-enhanced abdomen CT (38.7%) with increases in CNR at 149.1%, 105.8%, and 53.1% respectively. The subjective assessment of overall image quality and the noise was also better on DLR images (p < 0.001). However, there was no significant difference in artifacts between reconstruction methods. From NPS analysis, DLR methods showed a pattern of reducing the magnitude of noise while maintaining the texture.ConclusionCompared with 50% ASIR-V, DLR improved pediatric body CT images with significant noise reduction. However, artifacts were not improved by DLR, regardless of strength.
| S-EPMC8503996 | biostudies-literature
Project description:PurposeHigh-dimensional image features that underlie COVID-19 pneumonia remain opaque. We aim to compare feature engineering and deep learning methods to gain insights into the image features that drive CT-based for COVID-19 pneumonia prediction, and uncover CT image features significant for COVID-19 pneumonia from deep learning and radiomics framework.MethodsA total of 266 patients with COVID-19 and other viral pneumonia with clinical symptoms and CT signs similar to that of COVID-19 during the outbreak were retrospectively collected from three hospitals in China and the USA. All the pneumonia lesions on CT images were manually delineated by four radiologists. One hundred eighty-four patients (n = 93 COVID-19 positive; n = 91 COVID-19 negative; 24,216 pneumonia lesions from 12,001 CT image slices) from two hospitals from China served as discovery cohort for model development. Thirty-two patients (17 COVID-19 positive, 15 COVID-19 negative; 7883 pneumonia lesions from 3799 CT image slices) from a US hospital served as external validation cohort. A bi-directional adversarial network-based framework and PyRadiomics package were used to extract deep learning and radiomics features, respectively. Linear and Lasso classifiers were used to develop models predictive of COVID-19 versus non-COVID-19 viral pneumonia.Results120-dimensional deep learning image features and 120-dimensional radiomics features were extracted. Linear and Lasso classifiers identified 32 high-dimensional deep learning image features and 4 radiomics features associated with COVID-19 pneumonia diagnosis (P < 0.0001). Both models achieved sensitivity > 73% and specificity > 75% on external validation cohort with slight superior performance for radiomics Lasso classifier. Human expert diagnostic performance improved (increase by 16.5% and 11.6% in sensitivity and specificity, respectively) when using a combined deep learning-radiomics model.ConclusionsWe uncover specific deep learning and radiomics features to add insight into interpretability of machine learning algorithms and compare deep learning and radiomics models for COVID-19 pneumonia that might serve to augment human diagnostic performance.
| S-EPMC7581467 | biostudies-literature
Project description:BackgroundAccurate assessment of coronavirus disease 2019 (COVID-19) lung involvement through chest radiograph plays an important role in effective management of the infection. This study aims to develop a two-step feature merging method to integrate image features from deep learning and radiomics to differentiate COVID-19, non-COVID-19 pneumonia and normal chest radiographs (CXR).MethodsIn this study, a deformable convolutional neural network (deformable CNN) was developed and used as a feature extractor to obtain 1,024-dimensional deep learning latent representation (DLR) features. Then 1,069-dimensional radiomics features were extracted from the region of interest (ROI) guided by deformable CNN's attention. The two feature sets were concatenated to generate a merged feature set for classification. For comparative experiments, the same process has been applied to the DLR-only feature set for verifying the effectiveness of feature concatenation.ResultsUsing the merged feature set resulted in an overall average accuracy of 91.0% for three-class classification, representing a statistically significant improvement of 0.6% compared to the DLR-only classification. The recall and precision of classification into the COVID-19 class were 0.926 and 0.976, respectively. The feature merging method was shown to significantly improve the classification performance as compared to using only deep learning features, regardless of choice of classifier (P value <0.0001). Three classes' F1-score were 0.892, 0.890, and 0.950 correspondingly (i.e., normal, non-COVID-19 pneumonia, COVID-19).ConclusionsA two-step COVID-19 classification framework integrating information from both DLR and radiomics features (guided by deep learning attention mechanism) has been developed. The proposed feature merging method has been shown to improve the performance of chest radiograph classification as compared to the case of using only deep learning features.
| S-EPMC9929417 | biostudies-literature
Project description:BackgroundDeep learning using convolutional neural networks (CNN) has achieved significant results in various fields that use images. Deep learning can automatically extract features from data, and CNN extracts image features by convolution processing. We assumed that increasing the image size using interpolation methods would result in an effective feature extraction. To investigate how interpolation methods change as the number of data increases, we examined and compared the effectiveness of data augmentation by inversion or rotation with image augmentation by interpolation when the image data for training were small. Further, we clarified whether image augmentation by interpolation was useful for CNN training. To examine the usefulness of interpolation methods in medical images, we used a Gender01 data set, which is a sex classification data set, on chest radiographs. For comparison of image enlargement using an interpolation method with data augmentation by inversion and rotation, we examined the results of two- and four-fold enlargement using a Bilinear method.ResultsThe average classification accuracy improved by expanding the image size using the interpolation method. The biggest improvement was noted when the number of training data was 100, and the average classification accuracy of the training model with the original data was 0.563. However, upon increasing the image size by four times using the interpolation method, the average classification accuracy significantly improved to 0.715. Compared with the data augmentation by inversion and rotation, the model trained using the Bilinear method showed an improvement in the average classification accuracy by 0.095 with 100 training data and 0.015 with 50,000 training data. Comparisons of the average classification accuracy of the chest X-ray images showed a stable and high-average classification accuracy using the interpolation method.ConclusionTraining the CNN by increasing the image size using the interpolation method is a useful method. In the future, we aim to conduct additional verifications using various medical images to further clarify the reason why image size is important.
| S-EPMC7924688 | biostudies-literature
Project description:Achieving seed germination quality standards poses a real challenge to seed companies as they are compelled to abide by strict certification rules, while having only partial seed separation solutions at their disposal. This discrepancy results with wasteful disqualification of seed lots holding considerable amounts of good seeds and further translates to financial losses and supply chain insecurity. Here, we present the first-ever generic germination prediction technology that is based on deep learning and RGB image data and facilitates seed classification by seed germinability and usability, two facets of germination fate. We show technology competence to render dozens of disqualified seed lots of seven vegetable crops, representing different genetics and production pipelines, industrially appropriate, and to adequately classify lots by utilizing available crop-level image data, instead of lot-specific data. These achievements constitute a major milestone in the deployment of this technology for industrial seed sorting by germination fate for multiple crops.
| S-EPMC8586350 | biostudies-literature