Automatic detection of subsolid pulmonary nodules in thoracic computed tomography images

Towards automatic pulmonary nodule management in lung cancer screening with deep learning

The introduction of lung cancer screening programs will produce an unprecedented amount of chest CT scans in the near future, which radiologists will have to read in order to decide on a patient follow-up strategy. According to the current guidelines, the workup of screen-detected nodules strongly relies on nodule size and nodule type. In this paper, we present a deep learning system based on multi-stream multi-scale convolutional networks, which automatically classifies all nodule types relevant for nodule workup. The system processes raw CT data containing a nodule without the need for any additional information such as nodule segmentation or nodule size and learns a representation of 3D data by analyzing an arbitrary number of 2D views of a given nodule. The deep learning system was trained with data from the Italian MILD screening trial and validated on an independent set of data from the Danish DLCST screening trial. We analyze the advantage of processing nodules at multiple scales with a multi-stream convolutional network architecture, and we show that the proposed deep learning system achieves performance at classifying nodule type that surpasses the one of classical machine learning approaches and is within the inter-observer variability among four experienced human observers.

Multilevel Contextual 3-D CNNs for False Positive Reduction in Pulmonary Nodule Detection

OBJECTIVE

False positive reduction is one of the most crucial components in an automated pulmonary nodule detection system, which plays an important role in lung cancer diagnosis and early treatment. The objective of this paper is to effectively address the challenges in this task and therefore to accurately discriminate the true nodules from a large number of candidates.

METHODS

We propose a novel method employing three-dimensional (3-D) convolutional neural networks (CNNs) for false positive reduction in automated pulmonary nodule detection from volumetric computed tomography (CT) scans. Compared with its 2-D counterparts, the 3-D CNNs can encode richer spatial information and extract more representative features via their hierarchical architecture trained with 3-D samples. More importantly, we further propose a simple yet effective strategy to encode multilevel contextual information to meet the challenges coming with the large variations and hard mimics of pulmonary nodules.

RESULTS

The proposed framework has been extensively validated in the LUNA16 challenge held in conjunction with ISBI 2016, where we achieved the highest competition performance metric (CPM) score in the false positive reduction track.

CONCLUSION

Experimental results demonstrated the importance and effectiveness of integrating multilevel contextual information into 3-D CNN framework for automated pulmonary nodule detection in volumetric CT data.

SIGNIFICANCE

While our method is tailored for pulmonary nodule detection, the proposed framework is general and can be easily extended to many other 3-D object detection tasks from volumetric medical images, where the targeting objects have large variations and are accompanied by a number of hard mimics.

Computer-aided detection of pulmonary nodules using dynamic self-adaptive template matching and a FLDA classifier

Improving the performance of computer-aided detection (CAD) system for pulmonary nodules is still an important issue for its future clinical applications. This study aims to develop a new CAD scheme for pulmonary nodule detection based on dynamic self-adaptive template matching and Fisher linear discriminant analysis (FLDA) classifier. We first segment and repair lung volume by using OTSU algorithm and three-dimensional (3D) region growing. Next, the suspicious regions of interest (ROIs) are extracted and filtered by applying 3D dot filtering and thresholding method. Then, pulmonary nodule candidates are roughly detected with 3D dynamic self-adaptive template matching. Finally, we optimally select 11 image features and apply FLDA classifier to reduce false positive detections. The performance of the new method is validated by comparing with other methods through experiments using two groups of public datasets from Lung Image Database Consortium (LIDC) and ANODE09. By a 10-fold cross-validation experiment, the new CAD scheme finally has achieved a sensitivity of 90.24% and a false-positive (FP) of 4.54 FP/scan on average for the former dataset, and a sensitivity of 84.1% with 5.59 FP/scan for the latter. By comparing with other previously reported CAD schemes tested on the same datasets, the study proves that this new scheme can yield higher and more robust results in detecting pulmonary nodules.

Automatic detection of large pulmonary solid nodules in thoracic CT images

PURPOSE

Current computer-aided detection (CAD) systems for pulmonary nodules in computed tomography (CT) scans have a good performance for relatively small nodules, but often fail to detect the much rarer larger nodules, which are more likely to be cancerous. We present a novel CAD system specifically designed to detect solid nodules larger than 10 mm.

METHODS

The proposed detection pipeline is initiated by a three-dimensional lung segmentation algorithm optimized to include large nodules attached to the pleural wall via morphological processing. An additional preprocessing is used to mask out structures outside the pleural space to ensure that pleural and parenchymal nodules have a similar appearance. Next, nodule candidates are obtained via a multistage process of thresholding and morphological operations, to detect both larger and smaller candidates. After segmenting each candidate, a set of 24 features based on intensity, shape, blobness, and spatial context are computed. A radial basis support vector machine (SVM) classifier was used to classify nodule candidates, and performance was evaluated using ten-fold cross-validation on the full publicly available lung image database consortium database.

RESULTS

The proposed CAD system reaches a sensitivity of 98.3% (234/238) and 94.1% (224/238) large nodules at an average of 4.0 and 1.0 false positives/scan, respectively.

CONCLUSIONS

The authors conclude that the proposed dedicated CAD system for large pulmonary nodules can identify the vast majority of highly suspicious lesions in thoracic CT scans with a small number of false positives.

Pulmonary Nodule Detection in CT Images: False Positive Reduction Using Multi-View Convolutional Networks

We propose a novel Computer-Aided Detection (CAD) system for pulmonary nodules using multi-view convolutional networks (ConvNets), for which discriminative features are automatically learnt from the training data. The network is fed with nodule candidates obtained by combining three candidate detectors specifically designed for solid, subsolid, and large nodules. For each candidate, a set of 2-D patches from differently oriented planes is extracted. The proposed architecture comprises multiple streams of 2-D ConvNets, for which the outputs are combined using a dedicated fusion method to get the final classification. Data augmentation and dropout are applied to avoid overfitting. On 888 scans of the publicly available LIDC-IDRI dataset, our method reaches high detection sensitivities of 85.4% and 90.1% at 1 and 4 false positives per scan, respectively. An additional evaluation on independent datasets from the ANODE09 challenge and DLCST is performed. We showed that the proposed multi-view ConvNets is highly suited to be used for false positive reduction of a CAD system.

Advanced imaging tools in pulmonary nodule detection and surveillance

Lung cancer is a leading cause of death worldwide. The National Lung Screening Trial has demonstrated that lung cancer screening can reduce lung cancer specific and all cause mortality. With approval of national coverage for lung cancer screening, it is expected that an increase in exams related to pulmonary nodule detection and surveillance will ensue. Advanced imaging technologies for nodule detection and surveillance will be more important than ever. While computed tomography (CT) remains the modality of choice, other emerging modalities such as magnetic resonance imaging provides viable alternatives to CT.

Semantic representation of reported measurements in radiology

Background

In radiology, a vast amount of diverse data is generated, and unstructured reporting is standard. Hence, much useful information is trapped in free-text form, and often lost in translation and transmission. One relevant source of free-text data consists of reports covering the assessment of changes in tumor burden, which are needed for the evaluation of cancer treatment success. Any change of lesion size is a critical factor in follow-up examinations. It is difficult to retrieve specific information from unstructured reports and to compare them over time. Therefore, a prototype was implemented that demonstrates the structured representation of findings, allowing selective review in consecutive examinations and thus more efficient comparison over time.

Methods

We developed a semantic Model for Clinical Information (MCI) based on existing ontologies from the Open Biological and Biomedical Ontologies (OBO) library. MCI is used for the integrated representation of measured image findings and medical knowledge about the normal size of anatomical entities. An integrated view of the radiology findings is realized by a prototype implementation of a ReportViewer. Further, RECIST (Response Evaluation Criteria In Solid Tumors) guidelines are implemented by SPARQL queries on MCI. The evaluation is based on two data sets of German radiology reports: An oncologic data set consisting of 2584 reports on 377 lymphoma patients and a mixed data set consisting of 6007 reports on diverse medical and surgical patients. All measurement findings were automatically classified as abnormal/normal using formalized medical background knowledge, i.e., knowledge that has been encoded into an ontology. A radiologist evaluated 813 classifications as correct or incorrect. All unclassified findings were evaluated as incorrect.

Results

The proposed approach allows the automatic classification of findings with an accuracy of 96.4 % for oncologic reports and 92.9 % for mixed reports. The ReportViewer permits efficient comparison of measured findings from consecutive examinations. The implementation of RECIST guidelines with SPARQL enhances the quality of the selection and comparison of target lesions as well as the corresponding treatment response evaluation.

Conclusions

The developed MCI enables an accurate integrated representation of reported measurements and medical knowledge. Thus, measurements can be automatically classified and integrated in different decision processes. The structured representation is suitable for improved integration of clinical findings during decision-making. The proposed ReportViewer provides a longitudinal overview of the measurements.

Lung nodule and cancer detection in computed tomography screening

Fundamental to the diagnosis of lung cancer in computed tomography (CT) scans is the detection and interpretation of lung nodules. As the capabilities of CT scanners have advanced, higher levels of spatial resolution reveal tinier lung abnormalities. Not all detected lung nodules should be reported; however, radiologists strive to detect all nodules that might have relevance to cancer diagnosis. Although medium to large lung nodules are detected consistently, interreader agreement and reader sensitivity for lung nodule detection diminish substantially as the nodule size falls below 8 to 10 mm. The difficulty in establishing an absolute reference standard presents a challenge to the reliability of studies performed to evaluate lung nodule detection. In the interest of improving detection performance, investigators are using eye tracking to analyze the effectiveness with which radiologists search CT scans relative to their ability to recognize nodules within their search path in order to determine whether strategies might exist to improve performance across readers. Beyond the viewing of transverse CT reconstructions, image processing techniques such as thin-slab maximum-intensity projections are used to substantially improve reader performance. Finally, the development of computer-aided detection has continued to evolve with the expectation that one day it will serve routinely as a tireless partner to the radiologist to enhance detection performance without significant prolongation of the interpretive process. This review provides an introduction to the current understanding of these varied issues as we enter the era of widespread lung cancer screening.

Computer-aided detection of pulmonary nodules: a comparative study using the public LIDC/IDRI database

Objectives

To benchmark the performance of state-of-the-art computer-aided detection (CAD) of pulmonary nodules using the largest publicly available annotated CT database (LIDC/IDRI), and to show that CAD finds lesions not identified by the LIDC’s four-fold double reading process.

Methods

The LIDC/IDRI database contains 888 thoracic CT scans with a section thickness of 2.5 mm or lower. We report performance of two commercial and one academic CAD system. The influence of presence of contrast, section thickness, and reconstruction kernel on CAD performance was assessed. Four radiologists independently analyzed the false positive CAD marks of the best CAD system.

Results

The updated commercial CAD system showed the best performance with a sensitivity of 82 % at an average of 3.1 false positive detections per scan. Forty-five false positive CAD marks were scored as nodules by all four radiologists in our study.

Conclusions

On the largest publicly available reference database for lung nodule detection in chest CT, the updated commercial CAD system locates the vast majority of pulmonary nodules at a low false positive rate. Potential for CAD is substantiated by the fact that it identifies pulmonary nodules that were not marked during the extensive four-fold LIDC annotation process.

Key Points

• CAD systems should be validated on public, heterogeneous databases.

• The LIDC/IDRI database is an excellent database for benchmarking nodule CAD.

• CAD can identify the majority of pulmonary nodules at a low false positive rate.

• CAD can identify nodules missed by an extensive two-stage annotation process.

Automatic classification of pulmonary peri-fissural nodules in computed tomography using an ensemble of 2D views and a convolutional neural network out-of-the-box

In this paper, we tackle the problem of automatic classification of pulmonary peri-fissural nodules (PFNs). The classification problem is formulated as a machine learning approach, where detected nodule candidates are classified as PFNs or non-PFNs. Supervised learning is used, where a classifier is trained to label the detected nodule. The classification of the nodule in 3D is formulated as an ensemble of classifiers trained to recognize PFNs based on 2D views of the nodule. In order to describe nodule morphology in 2D views, we use the output of a pre-trained convolutional neural network known as OverFeat. We compare our approach with a recently presented descriptor of pulmonary nodule morphology, namely Bag of Frequencies, and illustrate the advantages offered by the two strategies, achieving performance of AUC = 0.868, which is close to the one of human experts.

Bag-of-frequencies: a descriptor of pulmonary nodules in computed tomography images

We present a novel descriptor for the characterization of pulmonary nodules in computed tomography (CT) images. The descriptor encodes information on nodule morphology and has scale-invariant and rotation-invariant properties. Information on nodule morphology is captured by sampling intensity profiles along circular patterns on spherical surfaces centered on the nodule, in a multi-scale fashion. Each intensity profile is interpreted as a periodic signal, where the Fourier transform is applied, obtaining a spectrum. A library of spectra is created and labeled via unsupervised clustering, obtaining a Bag-of-Frequencies, which is used to assign each spectra a label. The descriptor is obtained as the histogram of labels along all the spheres. Additional contributions are a technique to estimate the nodule size, based on the sampling strategy, as well as a technique to choose the most informative plane to cut a 2-D view of the nodule in the 3-D image. We evaluate the descriptor on several nodule morphology classification problems, namely discrimination of nodules versus vascular structures and characterization of spiculation. We validate the descriptor on data from European screening trials NELSON and DLCST and we compare it with state-of-the-art approaches for 3-D shape description in medical imaging and computer vision, namely SPHARM and 3-D SIFT, outperforming them in all the considered experiments.

Clinical Usefulness of HRCT in Assessing the Severity of Pneumocystis jirovecii Pneumonia: A Cross-sectional Study

The aim of this study was to investigate the clinical relevance of thoracic high-resolution computed tomography (HRCT) in evaluating the severity and outcome of Pneumocystis jirovecii pneumonia (PJP) in non-AIDS immunocompromised patients.We measured mean lung attenuation (MLA) and extent of increased attenuation (EIA) of PJP lesions on thoracic HRCT in 40 non-AIDS immunocompromised patients with PJP diagnosed by demonstration of the pathogens in cytological smears of bronchoalveolar lavage fluid. The MLA and EIA of PJP lesions on thoracic HRCT were used to investigate the severity of PJP. Clinically, the severity of PJP was determined by arterial oxygen tension/fraction of inspired oxygen concentration (PaO2/FiO2) ratio, acute physiology and chronic health evaluation (APACHE) II scores, the need of mechanical ventilation, and death.MLA highly correlated with EIA of PJP lesions (ρ = 0.906, P < 0.001). MLA and EIA of PJP lesions significantly correlated with PaO2/FiO2 (ρ = -0.481 and -0.370, respectively and P = 0.007 and 0.044, respectively). When intensive care unit (ICU) admission and HRCT performed were within 2 days, MLA and EIA of PJP lesions were significantly correlated with APACHE II score (ρ = 0.791 and 0.670, respectively and P = 0.001 and 0.009, respectively). There were significant differences in the values of MLA and EIA of PJP lesions between patients with and without assisted mechanical ventilator (MLA, median and [interquartile range, IQR, 25%, 75%] -516.44 [-572.10, -375.34] vs -649.27 [-715.62, -594.01], P < 0.001 and EIA, median and [IQR 25%, 75%] 0.75 [0.66, 0.82] vs 0.53 [0.45, 0.68], P = 0.003, respectively). The data of MLA and EIA of PJP lesions had limited value in identifying survivors and non-survivors.The MLA and EIA values of PJP lesions measured on thoracic HRCT might be valuable in assessing the severity of PJP in non-AIDS immunocompromised patients, but might have limited value in predicting the mortality of the patients.

Missed cancers in lung cancer screening--more than meets the eye

In lung cancer, early detection and diagnosis is of paramount importance. In 2011 the National Lung Screening Trial (NLST) demonstrated the effectiveness of computed tomography (CT) screening for lung cancer in reducing mortality, and results from other ongoing trials are expected to be published in the near future. A topic that has not been widely researched to date, however, is the cause for screening failure and missed lung cancers. In this issue of European Radiology, Scholten et al. describe a number of causes for false-negative screens. Some of the implications for CT screening and nodule management raised by this report are discussed. Key Points • Many causes exist for missed lung cancers in CT screening trials • Endobronchial structures, the hila and mediastinum are blind spots on screening CTs • The management of atypical nodular opacities on thoracic CT may be challenging.