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Register a new userStar Shape Prior in Fully Convolutional Networks for Skin Lesion Segmentation
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Added by
Zahra Mirikharaji
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Semantic segmentation is an important preliminary step towards automatic medical image interpretation. Recently deep convolutional neural networks have become the first choice for the task of pixel-wise class prediction. While incorporating prior knowledge about the structure of target objects has proven effective in traditional energy-based segmentation approaches, there has not been a clear way for encoding prior knowledge into deep learning frameworks. In this work, we propose a new loss term that encodes the star shape prior into the loss function of an end-to-end trainable fully convolutional network (FCN) framework. We penalize non-star shape segments in FCN prediction maps to guarantee a global structure in segmentation results. Our experiments demonstrate the advantage of regularizing FCN parameters by the star shape prior and our results on the ISBI 2017 skin segmentation challenge data set achieve the first rank in the segmentation task among $21$ participating teams.
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We desgin a novel fully convolutional network architecture for shapes, denoted by Shape Fully Convolutional Networks (SFCN). 3D shapes are represented as graph structures in the SFCN architecture, based on novel graph convolution and pooling operations, which are similar to convolution and pooling operations used on images. Meanwhile, to build our SFCN architecture in the original image segmentation fully convolutional network (FCN) architecture, we also design and implement a generating operation} with bridging function. This ensures that the convolution and pooling operation we have designed can be successfully applied in the original FCN architecture. In this paper, we also present a new shape segmentation approach based on SFCN. Furthermore, we allow more general and challenging input, such as mixed datasets of different categories of shapes} which can prove the ability of our generalisation. In our approach, SFCNs are trained triangles-to-triangles by using three low-level geometric features as input. Finally, the feature voting-based multi-label graph cuts is adopted to optimise the segmentation results obtained by SFCN prediction. The experiment results show that our method can effectively learn and predict mixed shape datasets of either similar or different characteristics, and achieve excellent segmentation results.
For several skin conditions such as vitiligo, accurate segmentation of lesions from skin images is the primary measure of disease progression and severity. Existing methods for vitiligo lesion segmentation require manual intervention. Unfortunately, manual segmentation is time and labor-intensive, as well as irreproducible between physicians. We introduce a convolutional neural network (CNN) that quickly and robustly performs vitiligo skin lesion segmentation. Our CNN has a U-Net architecture with a modified contracting path. We use the CNN to generate an initial segmentation of the lesion, then refine it by running the watershed algorithm on high-confidence pixels. We train the network on 247 images with a variety of lesion sizes, complexity, and anatomical sites. The network with our modifications noticeably outperforms the state-of-the-art U-Net, with a Jaccard Index (JI) score of 73.6% (compared to 36.7%). Moreover, our method requires only a few seconds for segmentation, in contrast with the previously proposed semi-autonomous watershed approach, which requires 2-29 minutes per image.
Multiple Sclerosis (MS) is an autoimmune disease that leads to lesions in the central nervous system. Magnetic resonance (MR) images provide sufficient imaging contrast to visualize and detect lesions, particularly those in the white matter. Quantitative measures based on various features of lesions have been shown to be useful in clinical trials for evaluating therapies. Therefore robust and accurate segmentation of white matter lesions from MR images can provide important information about the disease status and progression. In this paper, we propose a fully convolutional neural network (CNN) based method to segment white matter lesions from multi-contrast MR images. The proposed CNN based method contains two convolutional pathways. The first pathway consists of multiple parallel convolutional filter banks catering to multiple MR modalities. In the second pathway, the outputs of the first one are concatenated and another set of convolutional filters are applied. The output of this last pathway produces a membership function for lesions that may be thresholded to obtain a binary segmentation. The proposed method is evaluated on a dataset of 100 MS patients, as well as the ISBI 2015 challenge data consisting of 14 patients. The comparison is performed against four publicly available MS lesion segmentation methods. Significant improvement in segmentation quality over the competing methods is demonstrated on various metrics, such as Dice and false positive ratio. While evaluating on the ISBI 2015 challenge data, our method produces a score of 90.48, where a score of 90 is considered to be comparable to a human rater.
In this paper, we present a conceptually simple, strong, and efficient framework for panoptic segmentation, called Panoptic FCN. Our approach aims to represent and predict foreground things and background stuff in a unified fully convolutional pipeline. In particular, Panoptic FCN encodes each object instance or stuff category into a specific kernel weight with the proposed kernel generator and produces the prediction by convolving the high-resolution feature directly. With this approach, instance-aware and semantically consistent properties for things and stuff can be respectively satisfied in a simple generate-kernel-then-segment workflow. Without extra boxes for localization or instance separation, the proposed approach outperforms previous box-based and -free models with high efficiency on COCO, Cityscapes, and Mapillary Vistas datasets with single scale input. Our code is made publicly available at https://github.com/Jia-Research-Lab/PanopticFCN.
The segmentation of skin lesions is a crucial task in clinical decision support systems for the computer aided diagnosis of skin lesions. Although deep learning-based approaches have improved segmentation performance, these models are often susceptible to class imbalance in the data, particularly, the fraction of the image occupied by the background healthy skin. Despite variations of the popular Dice loss function being proposed to tackle the class imbalance problem, the Dice loss formulation does not penalize misclassifications of the background pixels. We propose a novel metric-based loss function using the Matthews correlation coefficient, a metric that has been shown to be efficient in scenarios with skewed class distributions, and use it to optimize deep segmentation models. Evaluations on three skin lesion image datasets: the ISBI ISIC 2017 Skin Lesion Segmentation Challenge dataset, the DermoFit Image Library, and the PH2 dataset, show that models trained using the proposed loss function outperform those trained using Dice loss by 11.25%, 4.87%, and 0.76% respectively in the mean Jaccard index. The code is available at https://github.com/kakumarabhishek/MCC-Loss.
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