Hayit Greenspan

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  • Endotracheal Tube Detection and Segmentation in Chest Radiographs using Synthetic Data

    Chest radiographs are frequently used to verify the correct intubation of patients in the emergency room. Fast and accurate identification and localization of the endotracheal (ET) tube is critical for the patient. In this study we propose a novel automated deep learning scheme for accurate detection and segmentation of the ET tubes. Development of automatic systems using deep learning networks for classification and segmentation require large annotated data which is not always available. Here we present an approach for synthesizing ET tubes in real X-ray images. We suggest a method for training the network, first with synthetic data and then with real X-ray images in a fine-tuning phase, which allows the network to train on thousands of cases without annotating any data. The proposed method was tested on 477 real chest radiographs from a public dataset and reached AUC of 0.99 in classifying the presence vs. absence of the ET tube, along with outputting high quality ET tube segmentation maps.

    08/20/2019 ∙ by Maayan Frid-Adar, et al. ∙ 18 share

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  • The Liver Tumor Segmentation Benchmark (LiTS)

    In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LITS) organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2016 and International Conference On Medical Image Computing Computer Assisted Intervention (MICCAI) 2017. Twenty four valid state-of-the-art liver and liver tumor segmentation algorithms were applied to a set of 131 computed tomography (CT) volumes with different types of tumor contrast levels (hyper-/hypo-intense), abnormalities in tissues (metastasectomie) size and varying amount of lesions. The submitted algorithms have been tested on 70 undisclosed volumes. The dataset is created in collaboration with seven hospitals and research institutions and manually reviewed by independent three radiologists. We found that not a single algorithm performed best for liver and tumors. The best liver segmentation algorithm achieved a Dice score of 0.96(MICCAI) whereas for tumor segmentation the best algorithm evaluated at 0.67(ISBI) and 0.70(MICCAI). The LITS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.

    01/13/2019 ∙ by Patrick Bilic, et al. ∙ 8 share

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  • Virtual PET Images from CT Data Using Deep Convolutional Networks: Initial Results

    In this work we present a novel system for PET estimation using CT scans. We explore the use of fully convolutional networks (FCN) and conditional generative adversarial networks (GAN) to export PET data from CT data. Our dataset includes 25 pairs of PET and CT scans where 17 were used for training and 8 for testing. The system was tested for detection of malignant tumors in the liver region. Initial results look promising showing high detection performance with a TPR of 92.3 expansion of the current system to the entire body using a much larger dataset. Such a system can be used for tumor detection and drug treatment evaluation in a CT-only environment instead of the expansive and radioactive PET-CT scan.

    07/30/2017 ∙ by Avi Ben-Cohen, et al. ∙ 0 share

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  • Modeling the Intra-class Variability for Liver Lesion Detection using a Multi-class Patch-based CNN

    Automatic detection of liver lesions in CT images poses a great challenge for researchers. In this work we present a deep learning approach that models explicitly the variability within the non-lesion class, based on prior knowledge of the data, to support an automated lesion detection system. A multi-class convolutional neural network (CNN) is proposed to categorize input image patches into sub-categories of boundary and interior patches, the decisions of which are fused to reach a binary lesion vs non-lesion decision. For validation of our system, we use CT images of 132 livers and 498 lesions. Our approach shows highly improved detection results that outperform the state-of-the-art fully convolutional network. Automated computerized tools, as shown in this work, have the potential in the future to support the radiologists towards improved detection.

    07/19/2017 ∙ by Maayan Frid-Adar, et al. ∙ 0 share

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  • Synthetic Data Augmentation using GAN for Improved Liver Lesion Classification

    In this paper, we present a data augmentation method that generates synthetic medical images using Generative Adversarial Networks (GANs). We propose a training scheme that first uses classical data augmentation to enlarge the training set and then further enlarges the data size and its diversity by applying GAN techniques for synthetic data augmentation. Our method is demonstrated on a limited dataset of computed tomography (CT) images of 182 liver lesions (53 cysts, 64 metastases and 65 hemangiomas). The classification performance using only classic data augmentation yielded 78.6 88.4 significantly increased to 85.7

    01/08/2018 ∙ by Maayan Frid-Adar, et al. ∙ 0 share

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  • Anatomical Data Augmentation For CNN based Pixel-wise Classification

    In this work we propose a method for anatomical data augmentation that is based on using slices of computed tomography (CT) examinations that are adjacent to labeled slices as another resource of labeled data for training the network. The extended labeled data is used to train a U-net network for a pixel-wise classification into different hepatic lesions and normal liver tissues. Our dataset contains CT examinations from 140 patients with 333 CT images annotated by an expert radiologist. We tested our approach and compared it to the conventional training process. Results indicate superiority of our method. Using the anatomical data augmentation we achieved an improvement of 3 in the success rate, 5

    01/07/2018 ∙ by Avi Ben-Cohen, et al. ∙ 0 share

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  • GAN-based Synthetic Medical Image Augmentation for increased CNN Performance in Liver Lesion Classification

    Deep learning methods, and in particular convolutional neural networks (CNNs), have led to an enormous breakthrough in a wide range of computer vision tasks, primarily by using large-scale annotated datasets. However, obtaining such datasets in the medical domain remains a challenge. In this paper, we present methods for generating synthetic medical images using recently presented deep learning Generative Adversarial Networks (GANs). Furthermore, we show that generated medical images can be used for synthetic data augmentation, and improve the performance of CNN for medical image classification. Our novel method is demonstrated on a limited dataset of computed tomography (CT) images of 182 liver lesions (53 cysts, 64 metastases and 65 hemangiomas). We first exploit GAN architectures for synthesizing high quality liver lesion ROIs. Then we present a novel scheme for liver lesion classification using CNN. Finally, we train the CNN using classic data augmentation and our synthetic data augmentation and compare performance. In addition, we explore the quality of our synthesized examples using visualization and expert assessment. The classification performance using only classic data augmentation yielded 78.6 sensitivity and 88.4 the results increased to 85.7 that this approach to synthetic data augmentation can generalize to other medical classification applications and thus support radiologists' efforts to improve diagnosis.

    03/03/2018 ∙ by Maayan Frid-Adar, et al. ∙ 0 share

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  • Cross-Modality Synthesis from CT to PET using FCN and GAN Networks for Improved Automated Lesion Detection

    In this work we present a novel system for generation of virtual PET images using CT scans. We combine a fully convolutional network (FCN) with a conditional generative adversarial network (GAN) to generate simulated PET data from given input CT data. The synthesized PET can be used for false-positive reduction in lesion detection solutions. Clinically, such solutions may enable lesion detection and drug treatment evaluation in a CT-only environment, thus reducing the need for the more expensive and radioactive PET/CT scan. Our dataset includes 60 PET/CT scans from Sheba Medical center. We used 23 scans for training and 37 for testing. Different schemes to achieve the synthesized output were qualitatively compared. Quantitative evaluation was conducted using an existing lesion detection software, combining the synthesized PET as a false positive reduction layer for the detection of malignant lesions in the liver. Current results look promising showing a 28 positive per case from 2.9 to 2.1. The suggested solution is comprehensive and can be expanded to additional body organs, and different modalities.

    02/21/2018 ∙ by Avi Ben-Cohen, et al. ∙ 0 share

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  • A Mixture of Views Network with Applications to the Classification of Breast Microcalcifications

    In this paper we examine data fusion methods for multi-view data classification. We present a decision concept which explicitly takes into account the input multi-view structure, where for each case there is a different subset of relevant views. This data fusion concept, which we dub Mixture of Views, is implemented by a special purpose neural network architecture. It is demonstrated on the task of classifying breast microcalcifications as benign or malignant based on CC and MLO mammography views. The single view decisions are combined by a data-driven decision, according to the relevance of each view in a given case, into a global decision. The method is evaluated on a large multi-view dataset extracted from the standardized digital database for screening mammography (DDSM). The experimental results show that our method outperforms previously suggested fusion methods.

    03/19/2018 ∙ by Yaniv Shachor, et al. ∙ 0 share

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  • Improving the Segmentation of Anatomical Structures in Chest Radiographs using U-Net with an ImageNet Pre-trained Encoder

    Accurate segmentation of anatomical structures in chest radiographs is essential for many computer-aided diagnosis tasks. In this paper we investigate the latest fully-convolutional architectures for the task of multi-class segmentation of the lungs field, heart and clavicles in a chest radiograph. In addition, we explore the influence of using different loss functions in the training process of a neural network for semantic segmentation. We evaluate all models on a common benchmark of 247 X-ray images from the JSRT database and ground-truth segmentation masks from the SCR dataset. Our best performing architecture, is a modified U-Net that benefits from pre-trained encoder weights. This model outperformed the current state-of-the-art methods tested on the same benchmark, with Jaccard overlap scores of 96.1 for heart and 85.5

    10/04/2018 ∙ by Maayan Frid-Adar, et al. ∙ 0 share

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  • Lung Structures Enhancement in Chest Radiographs via CT based FCNN Training

    The abundance of overlapping anatomical structures appearing in chest radiographs can reduce the performance of lung pathology detection by automated algorithms (CAD) as well as the human reader. In this paper, we present a deep learning based image processing technique for enhancing the contrast of soft lung structures in chest radiographs using Fully Convolutional Neural Networks (FCNN). Two 2D FCNN architectures were trained to accomplish the task: The first performs 2D lung segmentation which is used for normalization of the lung area. The second FCNN is trained to extract lung structures. To create the training images, we employed Simulated X-Ray or Digitally Reconstructed Radiographs (DRR) derived from 516 scans belonging to the LIDC-IDRI dataset. By first segmenting the lungs in the CT domain, we are able to create a dataset of 2D lung masks to be used for training the segmentation FCNN. For training the extraction FCNN, we create DRR images of only voxels belonging to the 3D lung segmentation which we call "Lung X-ray" and use them as target images. Once the lung structures are extracted, the original image can be enhanced by fusing the original input x-ray and the synthesized "Lung X-ray". We show that our enhancement technique is applicable to real x-ray data, and display our results on the recently released NIH Chest X-Ray-14 dataset. We see promising results when training a DenseNet-121 based architecture to work directly on the lung enhanced X-ray images.

    10/14/2018 ∙ by Ophir Gozes, et al. ∙ 0 share

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