Avi Ben-Cohen

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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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  • 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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  • 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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  • 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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  • Improving CNN Training using Disentanglement for Liver Lesion Classification in CT

    Training data is the key component in designing algorithms for medical image analysis and in many cases it is the main bottleneck in achieving good results. Recent progress in image generation has enabled the training of neural network based solutions using synthetic data. A key factor in the generation of new samples is controlling the important appearance features and potentially being able to generate a new sample of a specific class with different variants. In this work we suggest the synthesis of new data by mixing the class specified and unspecified representation of different factors in the training data. Our experiments on liver lesion classification in CT show an average improvement of 7.4

    11/01/2018 ∙ by Avi Ben-Cohen, et al. ∙ 0 share

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