ENHANCE (ENriching Health data by ANnotations of Crowd and Experts): A case study for skin lesion classification

We present ENHANCE, an open dataset with multiple annotations to complement the existing ISIC and PH2 skin lesion classification datasets. This dataset contains annotations of visual ABC (asymmetry, border, colour) features from non-expert annotation sources: undergraduate students, crowd workers from Amazon MTurk and classic image processing algorithms. In this paper we first analyse the correlations between the annotations and the diagnostic label of the lesion, as well as study the agreement between different annotation sources. Overall we find weak correlations of non-expert annotations with the diagnostic label, and low agreement between different annotation sources. We then study multi-task learning (MTL) with the annotations as additional labels, and show that non-expert annotations can improve (ensembles of) state-of-the-art convolutional neural networks via MTL. We hope that our dataset can be used in further research into multiple annotations and/or MTL. All data and models are available on Github: https://github.com/raumannsr/ENHANCE

LVNet: Light-Weight Model for Left Ventricle Segmentation for Short Axis Views in Echocardiographic Imaging

Lightweight segmentation models are becoming more popular for fast diagnosis on small and low cost medical imaging devices. This study focuses on the segmentation of the left ventricle (LV) in cardiac ultrasound (US) images. A new lightweight model [LV network (LVNet)] is proposed for segmentation, which gives the benefits of requiring fewer parameters but with improved segmentation performance in terms of Dice score (DS). The proposed model is compared with state-of-the-art methods, such as UNet, MiniNetV2, and fully convolutional dense dilated network (FCdDN). The model proposed comes with a post-processing pipeline that further enhances the segmentation results. In general, the training is done directly using the segmentation mask as the output and the US image as the input of the model. A new strategy for segmentation is also introduced in addition to the direct training method used. Compared with the UNet model, an improvement in DS performance as high as 5% for segmentation with papillary (WP) muscles was found, while showcasing an improvement of 18.5% when the papillary muscles are excluded. The model proposed requires only 5% of the memory required by a UNet model. LVNet achieves a better trade-off between the number of parameters and its segmentation performance as compared with other conventional models.</p

Parameter Optimization for Image Denoising Based on Block Matching and 3D Collaborative Filtering

Clinical MRI images are generally corrupted by random noise during acquisition with blurred subtle structure features. Many denoising methods have been proposed to remove noise from corrupted images at the expense of distorted structure features. Therefore, there is always compromise between removing noise and preserving structure information for denoising methods. For a specific denoising method, it is crucial to tune it so that the best tradeoff can be obtained. In this paper, we define several cost functions to assess the quality of noise removal and that of structure information preserved in the denoised image. Strength Pareto Evolutionary Algorithm 2 (SPEA2) is utilized to simultaneously optimize the cost functions by modifying parameters associated with the denoising methods. The effectiveness of the algorithm is demonstrated by applying the proposed optimization procedure to enhance the image denoising results using block matching and 3D collaborative filtering. Experimental results show that the proposed optimization algorithm can significantly improve the performance of image denoising methods in terms of noise removal and structure information preservation

Hybrid Committee Classifier for a Computerized Colonic Polyp Detection System

We present a hybrid committee classifier for computer-aided detection (CAD) of colonic polyps in CT colonography (CTC). The classifier involved an ensemble of support vector machines (SVM) and neural networks (NN) for classification, a progressive search algorithm for selecting a set of features used by the SVMs and a floating search algorithm for selecting features used by the NNs. A total of 102 quantitative features were calculated for each polyp candidate found by a prototype CAD system. 3 features were selected for each of 7 SVM classifiers which were then combined to form a committee of SVMs classifier. Similarly, features (numbers varied from 10-20) were selected for 11 NN classifiers which were again combined to form a NN committee classifier. Finally, a hybrid committee classifier was defined by combining the outputs of both the SVM and NN committees. The method was tested on CTC scans (supine and prone views) of 29 patients, in terms of the partial area under a free response receiving operation characteristic (FROC) curve (AUC). Our results showed that the hybrid committee classifier performed the best for the prone scans and was comparable to other classifiers for the supine scans

Deep learning based correction of RF field induced inhomogeneities for T2w prostate imaging at 7 T

At ultrahigh field strengths images of the body are hampered by B1-field inhomogeneities. These present themselves as inhomogeneous signal intensity and contrast, which is regarded as a “bias field” to the ideal image. Current bias field correction methods, such as the N4 algorithm, assume a low frequency bias field, which is not sufficiently valid for T2w images at 7 T. In this work we propose a deep learning based bias field correction method to address this issue for T2w prostate images at 7 T. By combining simulated B1-field distributions of a multi-transmit setup at 7 T with T2w prostate images at 1.5 T, we generated artificial 7 T images for which the homogeneous counterpart was available. Using these paired data, we trained a neural network to correct the bias field. We predicted either a homogeneous image (t-Image neural network) or the bias field (t-Biasf neural network). In addition, we experimented with the single-channel images of the receive array and the corresponding sum of magnitudes of this array as the input image. Testing was carried out on four datasets: the test split of the synthetic training dataset, volunteer and patient images at 7 T, and patient images at 3 T. For the test split, the performance was evaluated using the structural similarity index measure, Wasserstein distance, and root mean squared error. For all other test data, the features Homogeneity and Energy derived from the gray level co-occurrence matrix (GLCM) were used to quantify the improvement. For each test dataset, the proposed method was compared with the current gold standard: the N4 algorithm. Additionally, a questionnaire was filled out by two clinical experts to assess the homogeneity and contrast preservation of the 7 T datasets. All four proposed neural networks were able to substantially reduce the B1-field induced inhomogeneities in T2w 7 T prostate images. By visual inspection, the images clearly look more homogeneous, which is confirmed by the increase in Homogeneity and Energy in the GLCM, and the questionnaire scores from two clinical experts. Occasionally, changes in contrast within the prostate were observed, although much less for the t-Biasf network than for the t-Image network. Further, results on the 3 T dataset demonstrate that the proposed learning based approach is on par with the N4 algorithm. The results demonstrate that the trained networks were capable of reducing the B1-field induced inhomogeneities for prostate imaging at 7 T. The quantitative evaluation showed that all proposed learning based correction techniques outperformed the N4 algorithm. Of the investigated methods, the single-channel t-Biasf neural network proves most reliable for bias field correction.</p

Deep learning based correction of RF field induced inhomogeneities for T2w prostate imaging at 7 T

At ultrahigh field strengths images of the body are hampered by B1-field inhomogeneities. These present themselves as inhomogeneous signal intensity and contrast, which is regarded as a “bias field” to the ideal image. Current bias field correction methods, such as the N4 algorithm, assume a low frequency bias field, which is not sufficiently valid for T2w images at 7 T. In this work we propose a deep learning based bias field correction method to address this issue for T2w prostate images at 7 T. By combining simulated B1-field distributions of a multi-transmit setup at 7 T with T2w prostate images at 1.5 T, we generated artificial 7 T images for which the homogeneous counterpart was available. Using these paired data, we trained a neural network to correct the bias field. We predicted either a homogeneous image (t-Image neural network) or the bias field (t-Biasf neural network). In addition, we experimented with the single-channel images of the receive array and the corresponding sum of magnitudes of this array as the input image. Testing was carried out on four datasets: the test split of the synthetic training dataset, volunteer and patient images at 7 T, and patient images at 3 T. For the test split, the performance was evaluated using the structural similarity index measure, Wasserstein distance, and root mean squared error. For all other test data, the features Homogeneity and Energy derived from the gray level co-occurrence matrix (GLCM) were used to quantify the improvement. For each test dataset, the proposed method was compared with the current gold standard: the N4 algorithm. Additionally, a questionnaire was filled out by two clinical experts to assess the homogeneity and contrast preservation of the 7 T datasets. All four proposed neural networks were able to substantially reduce the B1-field induced inhomogeneities in T2w 7 T prostate images. By visual inspection, the images clearly look more homogeneous, which is confirmed by the increase in Homogeneity and Energy in the GLCM, and the questionnaire scores from two clinical experts. Occasionally, changes in contrast within the prostate were observed, although much less for the t-Biasf network than for the t-Image network. Further, results on the 3 T dataset demonstrate that the proposed learning based approach is on par with the N4 algorithm. The results demonstrate that the trained networks were capable of reducing the B1-field induced inhomogeneities for prostate imaging at 7 T. The quantitative evaluation showed that all proposed learning based correction techniques outperformed the N4 algorithm. Of the investigated methods, the single-channel t-Biasf neural network proves most reliable for bias field correction.</p

Direct Classification of Type 2 Diabetes From Retinal Fundus Images in a Population-based Sample From The Maastricht Study

Type 2 Diabetes (T2D) is a chronic metabolic disorder that can lead to blindness and cardiovascular disease. Information about early stage T2D might be present in retinal fundus images, but to what extent these images can be used for a screening setting is still unknown. In this study, deep neural networks were employed to differentiate between fundus images from individuals with and without T2D. We investigated three methods to achieve high classification performance, measured by the area under the receiver operating curve (ROC-AUC). A multi-target learning approach to simultaneously output retinal biomarkers as well as T2D works best (AUC = 0.746 [$\pm$0.001]). Furthermore, the classification performance can be improved when images with high prediction uncertainty are referred to a specialist. We also show that the combination of images of the left and right eye per individual can further improve the classification performance (AUC = 0.758 [$\pm$0.003]), using a simple averaging approach. The results are promising, suggesting the feasibility of screening for T2D from retinal fundus images.Comment: to be published in the proceeding of SPIE - Medical Imaging 2020, 6 pages, 1 figur

Assessment of algorithms for mitosis detection in breast cancer histopathology images

The proliferative activity of breast tumors, which is routinely estimated by counting of mitotic figures in hematoxylin and eosin stained histology sections, is considered to be one of the most important prognostic markers. However, mitosis counting is laborious, subjective and may suffer from low inter-observer agreement. With the wider acceptance of whole slide images in pathology labs, automatic image analysis has been proposed as a potential solution for these issues. In this paper, the results from the Assessment of Mitosis Detection Algorithms 2013 (AMIDA13) challenge are described. The challenge was based on a data set consisting of 12 training and 11 testing subjects, with more than one thousand annotated mitotic figures by multiple observers. Short descriptions and results from the evaluation of eleven methods are presented. The top performing method has an error rate that is comparable to the inter-observer agreement among pathologists

Cross-scanner and cross-protocol multi-shell diffusion MRI data harmonization: algorithms and result

Cross-scanner and cross-protocol variability of diffusion magnetic resonance imaging (dMRI) data are known to be major obstacles in multi-site clinical studies since they limit the ability to aggregate dMRI data and derived measures. Computational algorithms that harmonize the data and minimize such variability are critical to reliably combine datasets acquired from different scanners and/or protocols, thus improving the statistical power and sensitivity of multi-site studies. Different computational approaches have been proposed to harmonize diffusion MRI data or remove scanner-specific differences. To date, these methods have mostly been developed for or evaluated on single b-value diffusion MRI data. In this work, we present the evaluation results of 19 algorithms that are developed to harmonize the cross-scanner and cross-protocol variability of multi-shell diffusion MRI using a benchmark database. The proposed algorithms rely on various signal representation approaches and computational tools, such as rotational invariant spherical harmonics, deep neural networks and hybrid biophysical and statistical approaches. The benchmark database consists of data acquired from the same subjects on two scanners with different maximum gradient strength (80 and 300 ​mT/m) and with two protocols. We evaluated the performance of these algorithms for mapping multi-shell diffusion MRI data across scanners and across protocols using several state-of-the-art imaging measures. The results show that data harmonization algorithms can reduce the cross-scanner and cross-protocol variabilities to a similar level as scan-rescan variability using the same scanner and protocol. In particular, the LinearRISH algorithm based on adaptive linear mapping of rotational invariant spherical harmonics features yields the lowest variability for our data in predicting the fractional anisotropy (FA), mean diffusivity (MD), mean kurtosis (MK) and the rotationally invariant spherical harmonic (RISH) features. But other algorithms, such as DIAMOND, SHResNet, DIQT, CMResNet show further improvement in harmonizing the return-to-origin probability (RTOP). The performance of different approaches provides useful guidelines on data harmonization in future multi-site studies

Crowd disagreement of medical images is informative

Classifiers for medical image analysis are often trained with a single consensus label, based on combining labels given by experts or crowds. However, disagreement between annotators may be informative, and thus removing it may not be the best strategy. As a proof of concept, we predict whether a skin lesion from the ISIC 2017 dataset is a melanoma or not, based on crowd annotations of visual characteristics of that lesion. We compare using the mean annotations, illustrating consensus, to standard deviations and other distribution moments, illustrating disagreement. We show that the mean annotations perform best, but that the disagreement measures are still informative. We also make the crowd annotations used in this paper available at https://figshare.com/s/5cbbce14647b66286544