Agnes Mayr

Matthias Schwab, Mathias Pamminger, Christian Kremser et al.

Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) imaging is considered the in vivo reference standard for assessing infarct size (IS) and microvascular obstruction (MVO) in ST-elevation myocardial infarction (STEMI) patients. However, the exact quantification of those markers of myocardial infarct severity remains challenging and very time-consuming. As LGE distribution patterns can be quite complex and hard to delineate from the blood pool or epicardial fat, automatic segmentation of LGE CMR images is challenging. In this work, we propose a cascaded framework of two-dimensional and three-dimensional convolutional neural networks (CNNs) which enables to calculate the extent of myocardial infarction in a fully automated way. By artificially generating segmentation errors which are characteristic for 2D CNNs during training of the cascaded framework we are enforcing the detection and correction of 2D segmentation errors and hence improve the segmentation accuracy of the entire method. The proposed method was trained and evaluated on two publicly available datasets. We perform comparative experiments where we show that our framework outperforms state-of-the-art reference methods in segmentation of myocardial infarction. Furthermore, in extensive ablation studies we show the advantages that come with the proposed error correcting cascaded method. The code of this project is publicly available at https://github.com/matthi99/EcorC.git

Marawan Elbatel, Mohamed Ghonim, Jiaji Mao et al.

Automated segmentation of liver lesions on non-contrast computed tomography (NCCT) is clinically important but fundamentally challenging, particularly in low-resource settings across Africa and Asia where contrast agents are frequently unavailable. Progress has been limited by the absence of annotated NCCT benchmarks. Here we describe the TriALS challenge for automated liver lesion segmentation under contrast-limited conditions, supported by a multi-centre dataset of 150 cases with four-phase CT acquisitions (600 volumes) from Egyptian and Chinese institutions. Algorithms were evaluated on 70 cases from three institutions, including an independent external cohort. The top-performing method achieved a mean venous-phase Dice of 0.754, consistent with human-level performance, yet dropped to 0.57 on NCCT. On external validation, the leading method outperformed off-the-shelf models by up to 28% in Dice on NCCT. Algorithm performance was most strongly predicted by training data scale and pre-training strategy. A cross-year comparison exposed a persistent perceptual barrier on NCCT that scaling pre-training alone cannot overcome. Data, annotations, and code are available at https://github.com/xmed-lab/TriALS.

Matthias Schwab, Agnes Mayr, Markus Haltmeier

The recent emergence of deep learning has led to a great deal of work on designing supervised deep semantic segmentation algorithms. As in many tasks sufficient pixel-level labels are very difficult to obtain, we propose a method which combines a Gaussian mixture model (GMM) with unsupervised deep learning techniques. In the standard GMM the pixel values with each sub-region are modelled by a Gaussian distribution. In order to identify the different regions, the parameter vector that minimizes the negative log-likelihood (NLL) function regarding the GMM has to be approximated. For this task, usually iterative optimization methods such as the expectation-maximization (EM) algorithm are used. In this paper, we propose to estimate these parameters directly from the image using a convolutional neural network (CNN). We thus change the iterative procedure in the EM algorithm replacing the expectation-step by a gradient-step with regard to the networks parameters. This means that the network is trained to minimize the NLL function of the GMM which comes with at least two advantages. As once trained, the network is able to predict label probabilities very quickly compared with time consuming iterative optimization methods. Secondly, due to the deep image prior our method is able to partially overcome one of the main disadvantages of GMM, which is not taking into account correlation between neighboring pixels, as it assumes independence between them. We demonstrate the advantages of our method in various experiments on the example of myocardial infarct segmentation on multi-sequence MRI images.