Ischaemic stroke is a medical condition caused by occlusion of blood supply to the brain tissue thus forming a lesion. A lesion is zoned into a core associated with irreversible necrosis typically located at the center of the lesion, while reversible hypoxic changes in the outer regions of the lesion are termed as the penumbra. Early estimation of core and penumbra in ischaemic stroke is crucial for timely intervention with thrombolytic therapy to reverse the damage and restore normalcy. Multisequence magnetic resonance imaging (MRI) is commonly employed for clinical diagnosis. However, a sequence singly has not been found to be sufficiently able to differentiate between core and penumbra, while a combination of sequences is required to determine the extent of the damage. The challenge, however, is that with an increase in the number of sequences, it cognitively taxes the clinician to discover symptomatic biomarkers in these images. In this paper, we present a data-driven fully automated method for estimation of core and penumbra in ischaemic lesions using diffusion-weighted imaging (DWI) and perfusion-weighted imaging (PWI) sequence maps of MRI. The method employs recent developments in convolutional neural networks (CNN) for semantic segmentation in medical images. In the absence of availability of a large amount of labeled data, the CNN is trained using an adversarial approach employing cross-entropy as a segmentation loss along with losses aggregated from three discriminators of which two employ relativistic visual Turing test. This method is experimentally validated on the ISLES-2015 dataset through three-fold cross-validation to obtain with an average Dice score of 0.82 and 0.73 for segmentation of penumbra and core respectively.
Brain lesion and anatomy segmentation in magnetic resonance images are fundamental tasks in neuroimaging research and clinical practice. Given enough training data, convolutional neuronal networks (CNN) proved to outperform all existent techniques in both tasks independently. However, to date, little work has been done regarding simultaneous learning of brain lesion and anatomy segmentation from disjoint datasets. In this work we focus on training a single CNN model to predict brain tissue and lesion segmentations using heterogeneous datasets labeled independently, according to only one of these tasks (a common scenario when using publicly available datasets). We show that label contradiction issues can arise in this case, and propose a novel adaptive cross entropy (ACE) loss function that makes such training possible. We provide quantitative evaluation in two different scenarios, benchmarking the proposed method in comparison with a multi-network approach. Our experiments suggest that ACE loss enables training of single models when standard cross entropy and Dice loss functions tend to fail. Moreover, we show that it is possible to achieve competitive results when comparing with multiple networks trained for independent tasks.
Cluster analysis has been widely used in various disciplines such as pattern recognition, computer vision, and data mining. In this work we investigate the applicability of two spatial clustering algorithms, namely DBSCAN and STING, to a new problem domain: Color segmentation of skin lesion (tumor) images. Automated segmentation is a key step in the computerized analysis of skin lesion images since the accuracy of the subsequent steps (feature extraction, classification, etc.) crucially depends on the accuracy of this very first step. In this paper, we develop two unsupervised methods for segmentation of skin lesion images: one based on DBSCAN clustering algorithm and the other based on STING clustering algorithm. Experiments on a database of over hundred skin lesion images show that DBSCAN-based segmentation algorithm performs significantly better than the STINGbased one.
We present a fully convolutional neural network for segmenting ischemic stroke lesions in CT perfusion images for the ISLES 2018 challenge. Treatment of stroke is time sensitive and current standards for lesion identification require manual segmentation, a time consuming and challenging process. Automatic segmentation methods present the possibility of accurately identifying lesions and improving treatment planning. Our model is based on the PSPNet, a network architecture that makes use of pyramid pooling to provide global and local contextual information. To learn the varying shapes of the lesions, we train our network using focal loss, a loss function designed for the network to focus on learning the more difficult samples. We compare our model to networks trained using the U-Net and V-Net architectures. Our approach demonstrates effective performance in lesion segmentation and ranked among the top performers at the challenge conclusion.
This short report describes our submission to the ISIC 2018 Challenge in Skin Lesion Analysis Towards Melanoma Detection for Task1 and Task 3. This work has been accomplished by a team of researchers at the University of Dayton Signal and Image Processing Lab. Our proposed approach is computationally efficient are combines information from both deep learning and handcrafted features. For Task3, we form a new type of image features, called hybrid features, which has stronger discrimination ability than single method features. These features are utilized as inputs to a decision-making model that is based on a multiclass Support Vector Machine (SVM) classifier. The proposed technique is evaluated on online validation databases. Our score was 0.841 with SVM classifier on the validation dataset.