Professional Education

  • Master of Science, Technion, Israel Instite of Technology (2008)
  • Doctor of Philosophy, Technion, Israel Instite of Technology (2013)
  • Bachelor of Science, Ben Gurion University Of The Negev (2006)


All Publications

  • Deep Learning for Brain MRI Segmentation: State of the Art and Future Directions. Journal of digital imaging Akkus, Z., Galimzianova, A., Hoogi, A., Rubin, D. L., Erickson, B. J. 2017


    Quantitative analysis of brain MRI is routine for many neurological diseases and conditions and relies on accurate segmentation of structures of interest. Deep learning-based segmentation approaches for brain MRI are gaining interest due to their self-learning and generalization ability over large amounts of data. As the deep learning architectures are becoming more mature, they gradually outperform previous state-of-the-art classical machine learning algorithms. This review aims to provide an overview of current deep learning-based segmentation approaches for quantitative brain MRI. First we review the current deep learning architectures used for segmentation of anatomical brain structures and brain lesions. Next, the performance, speed, and properties of deep learning approaches are summarized and discussed. Finally, we provide a critical assessment of the current state and identify likely future developments and trends.

    View details for DOI 10.1007/s10278-017-9983-4

    View details for PubMedID 28577131

  • Adaptive local window for level set segmentation of CT and MRI liver lesions. Medical image analysis Hoogi, A., Beaulieu, C. F., Cunha, G. M., Heba, E., Sirlin, C. B., Napel, S., Rubin, D. L. 2017; 37: 46-55


    We propose a novel method, the adaptive local window, for improving level set segmentation technique. The window is estimated separately for each contour point, over iterations of the segmentation process, and for each individual object. Our method considers the object scale, the spatial texture, and the changes of the energy functional over iterations. Global and local statistics are considered by calculating several gray level co-occurrence matrices. We demonstrate the capabilities of the method in the domain of medical imaging for segmenting 233 images with liver lesions. To illustrate the strength of our method, those lesions were screened by either Computed Tomography or Magnetic Resonance Imaging. Moreover, we analyzed images using three different energy models. We compared our method to a global level set segmentation, to a local framework that uses predefined fixed-size square windows and to a local region-scalable fitting model. The results indicate that our proposed method outperforms the other methods in terms of agreement with the manual marking and dependence on contour initialization or the energy model used. In case of complex lesions, such as low contrast lesions, heterogeneous lesions, or lesions with a noisy background, our method shows significantly better segmentation with an improvement of 0.25 ± 0.13 in Dice similarity coefficient, compared with state of the art fixed-size local windows (Wilcoxon, p < 0.001).

    View details for DOI 10.1016/

    View details for PubMedID 28157660

    View details for PubMedCentralID PMC5393306

  • Adaptive Estimation of Active Contour Parameters Using Convolutional Neural Networks and Texture Analysis IEEE TRANSACTIONS ON MEDICAL IMAGING Hoogi, A., Subramaniam, A., Veerapaneni, R., Rubin, D. L. 2017; 36 (3): 781-791
  • Improved Patch-Based Automated Liver Lesion Classification by Separate Analysis of the Interior and Boundary Regions IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS Diamant, I., Hoogi, A., Beaulieu, C. F., Safdari, M., Klang, E., Amitai, M., Greenspan, H., Rubin, D. L. 2016; 20 (6): 1585-1594


    The bag-of-visual-words (BoVW) method with construction of a single dictionary of visual words has been used previously for a variety of classification tasks in medical imaging, including the diagnosis of liver lesions. In this paper, we describe a novel method for automated diagnosis of liver lesions in portal-phase computed tomography (CT) images that improves over single-dictionary BoVW methods by using an image patch representation of the interior and boundary regions of the lesions. Our approach captures characteristics of the lesion margin and of the lesion interior by creating two separate dictionaries for the margin and the interior regions of lesions ("dual dictionaries" of visual words). Based on these dictionaries, visual word histograms are generated for each region of interest within the lesion and its margin. For validation of our approach, we used two datasets from two different institutions, containing CT images of 194 liver lesions (61 cysts, 80 metastasis, and 53 hemangiomas). The final diagnosis of each lesion was established by radiologists. The classification accuracy for the images from the two institutions was 99% and 88%, respectively, and 93% for a combined dataset. Our new BoVW approach that uses dual dictionaries shows promising results. We believe the benefits of our approach may generalize to other application domains within radiology.

    View details for DOI 10.1109/JBHI.2015.2478255

    View details for Web of Science ID 000389846700014

    View details for PubMedID 26372661

    View details for PubMedCentralID PMC5164871

  • Automated classification of brain tumor type in whole-slide digital pathology images using local representative tiles MEDICAL IMAGE ANALYSIS Barker, J., Hoogi, A., Depeursinge, A., Rubin, D. L. 2016; 30: 60-71


    Computerized analysis of digital pathology images offers the potential of improving clinical care (e.g. automated diagnosis) and catalyzing research (e.g. discovering disease subtypes). There are two key challenges thwarting computerized analysis of digital pathology images: first, whole slide pathology images are massive, making computerized analysis inefficient, and second, diverse tissue regions in whole slide images that are not directly relevant to the disease may mislead computerized diagnosis algorithms. We propose a method to overcome both of these challenges that utilizes a coarse-to-fine analysis of the localized characteristics in pathology images. An initial surveying stage analyzes the diversity of coarse regions in the whole slide image. This includes extraction of spatially localized features of shape, color and texture from tiled regions covering the slide. Dimensionality reduction of the features assesses the image diversity in the tiled regions and clustering creates representative groups. A second stage provides a detailed analysis of a single representative tile from each group. An Elastic Net classifier produces a diagnostic decision value for each representative tile. A weighted voting scheme aggregates the decision values from these tiles to obtain a diagnosis at the whole slide level. We evaluated our method by automatically classifying 302 brain cancer cases into two possible diagnoses (glioblastoma multiforme (N = 182) versus lower grade glioma (N = 120)) with an accuracy of 93.1 % (p < 0.001). We also evaluated our method in the dataset provided for the 2014 MICCAI Pathology Classification Challenge, in which our method, trained and tested using 5-fold cross validation, produced a classification accuracy of 100% (p < 0.001). Our method showed high stability and robustness to parameter variation, with accuracy varying between 95.5% and 100% when evaluated for a wide range of parameters. Our approach may be useful to automatically differentiate between the two cancer subtypes.

    View details for DOI 10.1016/

    View details for Web of Science ID 000373546800005

    View details for PubMedID 26854941