Due to the unpredictable location, fuzzy texture, and diverse shape, accurate segmentation of the kidney tumor in CT images is an important yet challenging task. To this end, we, in this paper, present a cascaded trainable segmentation model termed as Crossbar-Net. Our method combines two novel schemes: 1) we originally proposed the crossbar patches, which consists of two orthogonal non-squared patches (i.e., the vertical patch and horizontal patch). The crossbar patches are able to capture both the global and local appearance information of the kidney tumors from both the vertical and horizontal directions simultaneously. 2) With the obtained crossbar patches, we iteratively train two sub-models (i.e., horizontal sub-model and vertical sub-model) in a cascaded training manner. During the training, the trained sub-models are encouraged to become more focused on the difficult parts of the tumor automatically (i.e., mis-segmented regions). Specifically, the vertical (horizontal) sub-model is required to help segment the mis-segmented regions for the horizontal (vertical) sub-model. Thus, the two sub-models could complement each other to achieve the self-improvement until convergence. In the experiment, we evaluate our method on a real CT kidney tumor dataset which is collected from 94 different patients including 3500 CT slices. Compared with state-of-the-art segmentation methods, the results demonstrate the superior performance of our method on the Dice similarity coefficient, true positive fraction, centroid distance, and Hausdorff distance. Moreover, to exploit the generalization to other segmentation tasks, we also extend our Crossbar-Net to two related segmentation tasks: 1) cardiac segmentation in MR images and 2) breast mass segmentation in X-ray images, showing the promising results for these two tasks. Our implementation is released at https: github.com Qianyu1226 Crossbar-Net.
Although the attempts of developing the specific deep feature-based methods for segmenting kidney tumor are very limited, the related deep feature-based segmentation methods for segmenting other medical organs can be borrowed to our task. @cite_0 use multiple deep networks to segment biological neuron membranes with squared patches which were sampled by sliding-window, while the sliding-window leads to a large patch redundancy and label imbalance. @cite_10 devise a multi-branch CNN model to segment lung nodules. @cite_8 propose a cascaded deep domain adaptation model to segment the prostate. @cite_6 present a cascade architecture of CNNs to segment glioblastomas in MR images.
@cite_0 @cite_10 @cite_6 @cite_8
1884191083 2949362008 2962687389 2891179298
Abstract In this paper, we present a fully automatic brain tumor segmentation method based on Deep Neural Networks (DNNs). The proposed networks are tailored to glioblastomas (both low and high grade) pictured in MR images. By their very nature, these tumors can appear anywhere in the brain and have almost any kind of shape, size, and contrast. These reasons motivate our exploration of a machine learning solution that exploits a flexible, high capacity DNN while being extremely efficient. Here, we give a description of different model choices that we’ve found to be necessary for obtaining competitive performance. We explore in particular different architectures based on Convolutional Neural Networks (CNN), i.e. DNNs specifically adapted to image data. We present a novel CNN architecture which differs from those traditionally used in computer vision. Our CNN exploits both local features as well as more global contextual features simultaneously. Also, different from most traditional uses of CNNs, our networks use a final layer that is a convolutional implementation of a fully connected layer which allows a 40 fold speed up. We also describe a 2-phase training procedure that allows us to tackle difficulties related to the imbalance of tumor labels. Finally, we explore a cascade architecture in which the output of a basic CNN is treated as an additional source of information for a subsequent CNN. Results reported on the 2013 BRATS test data-set reveal that our architecture improves over the currently published state-of-the-art while being over 30 times faster. Convolutional Neural Networks (CNN) are state-of-the-art models for many image classification tasks. However, to recognize cancer subtypes automatically, training a CNN on gigapixel resolution Whole Slide Tissue Images (WSI) is currently computationally impossible. The differentiation of cancer subtypes is based on cellular-level visual features observed on image patch scale. Therefore, we argue that in this situation, training a patch-level classifier on image patches will perform better than or similar to an image-level classifier. The challenge becomes how to intelligently combine patch-level classification results and model the fact that not all patches will be discriminative. We propose to train a decision fusion model to aggregate patch-level predictions given by patch-level CNNs, which to the best of our knowledge has not been shown before. Furthermore, we formulate a novel Expectation-Maximization (EM) based method that automatically locates discriminative patches robustly by utilizing the spatial relationships of patches. We apply our method to the classification of glioma and non-small-cell lung carcinoma cases into subtypes. The classification accuracy of our method is similar to the inter-observer agreement between pathologists. Although it is impossible to train CNNs on WSIs, we experimentally demonstrate using a comparable non-cancer dataset of smaller images that a patch-based CNN can outperform an image-based CNN. A cascade of fully convolutional neural networks is proposed to segment multi-modal Magnetic Resonance (MR) images with brain tumor into background and three hierarchical regions: whole tumor, tumor core and enhancing tumor core. The cascade is designed to decompose the multi-class segmentation problem into a sequence of three binary segmentation problems according to the subregion hierarchy. The whole tumor is segmented in the first step and the bounding box of the result is used for the tumor core segmentation in the second step. The enhancing tumor core is then segmented based on the bounding box of the tumor core segmentation result. Our networks consist of multiple layers of anisotropic and dilated convolution filters, and they are combined with multi-view fusion to reduce false positives. Residual connections and multi-scale predictions are employed in these networks to boost the segmentation performance. Experiments with BraTS 2017 validation set show that the proposed method achieved average Dice scores of 0.7859, 0.9050, 0.8378 for enhancing tumor core, whole tumor and tumor core, respectively. The corresponding values for BraTS 2017 testing set were 0.7831, 0.8739, and 0.7748, respectively. We present an adversarial domain adaptation based deep learning approach for automatic tumor segmentation from T2-weighted MRI. Our approach is composed of two steps: (i) a tumor-aware unsupervised cross-domain adaptation (CT to MRI), followed by (ii) semi-supervised tumor segmentation using Unet trained with synthesized and limited number of original MRIs. We introduced a novel target specific loss, called tumor-aware loss, for unsupervised cross-domain adaptation that helps to preserve tumors on synthesized MRIs produced from CT images. In comparison, state-of-the art adversarial networks trained without our tumor-aware loss produced MRIs with ill-preserved or missing tumors. All networks were trained using labeled CT images from 377 patients with non-small cell lung cancer obtained from the Cancer Imaging Archive and unlabeled T2w MRIs from a completely unrelated cohort of 6 patients with pre-treatment and 36 on-treatment scans. Next, we combined 6 labeled pre-treatment MRI scans with the synthesized MRIs to boost tumor segmentation accuracy through semi-supervised learning. Semi-supervised training of cycle-GAN produced a segmentation accuracy of 0.66 computed using Dice Score Coefficient (DSC). Our method trained with only synthesized MRIs produced an accuracy of 0.74 while the same method trained in semi-supervised setting produced the best accuracy of 0.80 on test. Our results show that tumor-aware adversarial domain adaptation helps to achieve reasonably accurate cancer segmentation from limited MRI data by leveraging large CT datasets.