435 research outputs found
Classification of interstitial lung disease patterns with topological texture features
Topological texture features were compared in their ability to classify
morphological patterns known as 'honeycombing' that are considered indicative
for the presence of fibrotic interstitial lung diseases in high-resolution
computed tomography (HRCT) images. For 14 patients with known occurrence of
honey-combing, a stack of 70 axial, lung kernel reconstructed images were
acquired from HRCT chest exams. A set of 241 regions of interest of both
healthy and pathological (89) lung tissue were identified by an experienced
radiologist. Texture features were extracted using six properties calculated
from gray-level co-occurrence matrices (GLCM), Minkowski Dimensions (MDs), and
three Minkowski Functionals (MFs, e.g. MF.euler). A k-nearest-neighbor (k-NN)
classifier and a Multilayer Radial Basis Functions Network (RBFN) were
optimized in a 10-fold cross-validation for each texture vector, and the
classification accuracy was calculated on independent test sets as a
quantitative measure of automated tissue characterization. A Wilcoxon
signed-rank test was used to compare two accuracy distributions and the
significance thresholds were adjusted for multiple comparisons by the
Bonferroni correction. The best classification results were obtained by the MF
features, which performed significantly better than all the standard GLCM and
MD features (p < 0.005) for both classifiers. The highest accuracy was found
for MF.euler (97.5%, 96.6%; for the k-NN and RBFN classifier, respectively).
The best standard texture features were the GLCM features 'homogeneity' (91.8%,
87.2%) and 'absolute value' (90.2%, 88.5%). The results indicate that advanced
topological texture features can provide superior classification performance in
computer-assisted diagnosis of interstitial lung diseases when compared to
standard texture analysis methods.Comment: 8 pages, 5 figures, Proceedings SPIE Medical Imaging 201
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Prediction of progression in idiopathic pulmonary fibrosis using CT scans atbaseline: A quantum particle swarm optimization - Random forest approach
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease characterized by an unpredictable progressive declinein lung function. Natural history of IPF is unknown and the prediction of disease progression at the time ofdiagnosis is notoriously difficult. High resolution computed tomography (HRCT) has been used for the diagnosisof IPF, but not generally for monitoring purpose. The objective of this work is to develop a novel predictivemodel for the radiological progression pattern at voxel-wise level using only baseline HRCT scans. Mainly, thereare two challenges: (a) obtaining a data set of features for region of interest (ROI) on baseline HRCT scans andtheir follow-up status; and (b) simultaneously selecting important features from high-dimensional space, andoptimizing the prediction performance. We resolved the first challenge by implementing a study design andhaving an expert radiologist contour ROIs at baseline scans, depending on its progression status in follow-upvisits. For the second challenge, we integrated the feature selection with prediction by developing an algorithmusing a wrapper method that combines quantum particle swarm optimization to select a small number of featureswith random forest to classify early patterns of progression. We applied our proposed algorithm to analyzeanonymized HRCT images from 50 IPF subjects from a multi-center clinical trial. We showed that it yields aparsimonious model with 81.8% sensitivity, 82.2% specificity and an overall accuracy rate of 82.1% at the ROIlevel. These results are superior to other popular feature selections and classification methods, in that ourmethod produces higher accuracy in prediction of progression and more balanced sensitivity and specificity witha smaller number of selected features. Our work is the first approach to show that it is possible to use onlybaseline HRCT scans to predict progressive ROIs at 6 months to 1year follow-ups using artificial intelligence
Classification of lung disease in HRCT scans using integral geometry measures and functional data analysis
A framework for classification of chronic lung disease from high-resolution CT scans is presented. We use a set of features which measure the local morphology and topology of the 3D voxels within the lung parenchyma and apply functional data classification to the extracted features. We introduce the measures, Minkowski functionals, which derive from integral geometry and show results of classification on lungs containing various stages of chronic lung disease: emphysema, fibrosis and honey-combing. Once trained, the presented method is shown to be efficient and specific at characterising the distribution of disease in HRCT slices
Automatic Emphysema Detection using Weakly Labeled HRCT Lung Images
A method for automatically quantifying emphysema regions using
High-Resolution Computed Tomography (HRCT) scans of patients with chronic
obstructive pulmonary disease (COPD) that does not require manually annotated
scans for training is presented. HRCT scans of controls and of COPD patients
with diverse disease severity are acquired at two different centers. Textural
features from co-occurrence matrices and Gaussian filter banks are used to
characterize the lung parenchyma in the scans. Two robust versions of multiple
instance learning (MIL) classifiers, miSVM and MILES, are investigated. The
classifiers are trained with the weak labels extracted from the forced
expiratory volume in one minute (FEV) and diffusing capacity of the lungs
for carbon monoxide (DLCO). At test time, the classifiers output a patient
label indicating overall COPD diagnosis and local labels indicating the
presence of emphysema. The classifier performance is compared with manual
annotations by two radiologists, a classical density based method, and
pulmonary function tests (PFTs). The miSVM classifier performed better than
MILES on both patient and emphysema classification. The classifier has a
stronger correlation with PFT than the density based method, the percentage of
emphysema in the intersection of annotations from both radiologists, and the
percentage of emphysema annotated by one of the radiologists. The correlation
between the classifier and the PFT is only outperformed by the second
radiologist. The method is therefore promising for facilitating assessment of
emphysema and reducing inter-observer variability.Comment: Accepted at PLoS ON
Feature Representation Analysis of Deep Convolutional Neural Network using Two-stage Feature Transfer -An Application for Diffuse Lung Disease Classification-
Transfer learning is a machine learning technique designed to improve
generalization performance by using pre-trained parameters obtained from other
learning tasks. For image recognition tasks, many previous studies have
reported that, when transfer learning is applied to deep neural networks,
performance improves, despite having limited training data. This paper proposes
a two-stage feature transfer learning method focusing on the recognition of
textural medical images. During the proposed method, a model is successively
trained with massive amounts of natural images, some textural images, and the
target images. We applied this method to the classification task of textural
X-ray computed tomography images of diffuse lung diseases. In our experiment,
the two-stage feature transfer achieves the best performance compared to a
from-scratch learning and a conventional single-stage feature transfer. We also
investigated the robustness of the target dataset, based on size. Two-stage
feature transfer shows better robustness than the other two learning methods.
Moreover, we analyzed the feature representations obtained from DLDs imagery
inputs for each feature transfer models using a visualization method. We showed
that the two-stage feature transfer obtains both edge and textural features of
DLDs, which does not occur in conventional single-stage feature transfer
models.Comment: Preprint of the journal article to be published in IPSJ TOM-51.
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retained by the Information Processing Society of Japan (IPSJ). This material
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Novel lung imaging biomarkers and skin gene expression subsetting in dasatinib treatment of systemic sclerosis-associated interstitial lung disease.
BackgroundThere are no effective treatments or validated clinical response markers in systemic sclerosis (SSc). We assessed imaging biomarkers and performed gene expression profiling in a single-arm open-label clinical trial of tyrosine kinase inhibitor dasatinib in patients with SSc-associated interstitial lung disease (SSc-ILD).MethodsPrimary objectives were safety and pharmacokinetics. Secondary outcomes included clinical assessments, quantitative high-resolution computed tomography (HRCT) of the chest, serum biomarker assays and skin biopsy-based gene expression subset assignments. Clinical response was defined as decrease of >5 or >20% from baseline in the modified Rodnan Skin Score (MRSS). Pulmonary function was assessed at baseline and day 169.ResultsDasatinib was well-tolerated in 31 patients receiving drug for a median of nine months. No significant changes in clinical assessments or serum biomarkers were seen at six months. By quantitative HRCT, 65% of patients showed no progression of lung fibrosis, and 39% showed no progression of total ILD. Among 12 subjects with available baseline and post-treatment skin biopsies, three were improvers and nine were non-improvers. Improvers mapped to the fibroproliferative or normal-like subsets, while seven out of nine non-improvers were in the inflammatory subset (p = 0.0455). Improvers showed stability in forced vital capacity (FVC) and diffusing capacity for carbon monoxide (DLCO), while both measures showed a decline in non-improvers (p = 0.1289 and p = 0.0195, respectively). Inflammatory gene expression subset was associated with higher baseline HRCT score (p = 0.0556). Non-improvers showed significant increase in lung fibrosis (p = 0.0313).ConclusionsIn patients with SSc-ILD dasatinib treatment was associated with acceptable safety profile but no significant clinical efficacy. Patients in the inflammatory gene expression subset showed increase in skin fibrosis, decreasing pulmonary function and worsening lung fibrosis during the study. These findings suggest that target tissue-specific gene expression analyses can help match patients and therapeutic interventions in heterogeneous diseases such as SSc, and quantitative HRCT is useful for assessing clinical outcomes.Trial registrationClinicaltrials.gov NCT00764309
Semantic Segmentation of Pathological Lung Tissue with Dilated Fully Convolutional Networks
Early and accurate diagnosis of interstitial lung diseases (ILDs) is crucial
for making treatment decisions, but can be challenging even for experienced
radiologists. The diagnostic procedure is based on the detection and
recognition of the different ILD pathologies in thoracic CT scans, yet their
manifestation often appears similar. In this study, we propose the use of a
deep purely convolutional neural network for the semantic segmentation of ILD
patterns, as the basic component of a computer aided diagnosis (CAD) system for
ILDs. The proposed CNN, which consists of convolutional layers with dilated
filters, takes as input a lung CT image of arbitrary size and outputs the
corresponding label map. We trained and tested the network on a dataset of 172
sparsely annotated CT scans, within a cross-validation scheme. The training was
performed in an end-to-end and semi-supervised fashion, utilizing both labeled
and non-labeled image regions. The experimental results show significant
performance improvement with respect to the state of the art
Study Lung Tool: A Way to Understand HRTC Lung Parenchyma
Abstract-The purpose of the described system is to aid radiologists on their daily routine in the task of analyzing HRCT lung images and to contribute to a more accurate and fast diagnosis. We developed a framework -Study Lung Toolwith the objective of gather information from radiologists, in a systematic way. Using Study Lung Tool framework, the radiologist analyzes HRCT scans, outlines regions of typical pattern and characterizes the patterns. A database of typical patterns associated with common pulmonary diseases was created. The information gathered can be a valuable teaching tool to every one that intends to understand HRCT lung parenchyma. The proposed system discriminates between normal and abnormal patterns of lung parenchyma based on statistical texture analysis extracted from HRCT lung scans. An overall accuracy of 89,2%, a sensitivity of 92,7% and a specificity of 83,6% were achieved
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