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Register a new userThe Medical Segmentation Decathlon
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International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD) - a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to non AI experts.
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In recent years, deep learning based methods have shown success in essential medical image analysis tasks such as segmentation. Post-processing and refining the results of segmentation is a common practice to decrease the misclassifications originating from the segmentation network. In addition to widely used methods like Conditional Random Fields (CRFs) which focus on the structure of the segmented volume/area, a graph-based recent approach makes use of certain and uncertain points in a graph and refines the segmentation according to a small graph convolutional network (GCN). However, there are two drawbacks of the approach: most of the edges in the graph are assigned randomly and the GCN is trained independently from the segmentation network. To address these issues, we define a new neighbor-selection mechanism according to feature distances and combine the two networks in the training procedure. According to the experimental results on pancreas segmentation from Computed Tomography (CT) images, we demonstrate improvement in the quantitative measures. Also, examining the dynamic neighbors created by our method, edges between semantically similar image parts are observed. The proposed method also shows qualitative enhancements in the segmentation maps, as demonstrated in the visual results.
Accurate image segmentation is crucial for medical imaging applications. The prevailing deep learning approaches typically rely on very large training datasets with high-quality manual annotations, which are often not available in medical imaging. We introduce Annotation-effIcient Deep lEarning (AIDE) to handle imperfect datasets with an elaborately designed cross-model self-correcting mechanism. AIDE improves the segmentation Dice scores of conventional deep learning models on open datasets possessing scarce or noisy annotations by up to 30%. For three clinical datasets containing 11,852 breast images of 872 patients from three medical centers, AIDE consistently produces segmentation maps comparable to those generated by the fully supervised counterparts as well as the manual annotations of independent radiologists by utilizing only 10% training annotations. Such a 10-fold improvement of efficiency in utilizing experts labels has the potential to promote a wide range of biomedical applications.
Deep learning has successfully been leveraged for medical image segmentation. It employs convolutional neural networks (CNN) to learn distinctive image features from a defined pixel-wise objective function. However, this approach can lead to less output pixel interdependence producing incomplete and unrealistic segmentation results. In this paper, we present a fully automatic deep learning method for robust medical image segmentation by formulating the segmentation problem as a recurrent framework using two systems. The first one is a forward system of an encoder-decoder CNN that predicts the segmentation result from the input image. The predicted probabilistic output of the forward system is then encoded by a fully convolutional network (FCN)-based context feedback system. The encoded feature space of the FCN is then integrated back into the forward systems feed-forward learning process. Using the FCN-based context feedback loop allows the forward system to learn and extract more high-level image features and fix previous mistakes, thereby improving prediction accuracy over time. Experimental results, performed on four different clinical datasets, demonstrate our methods potential application for single and multi-structure medical image segmentation by outperforming the state of the art methods. With the feedback loop, deep learning methods can now produce results that are both anatomically plausible and robust to low contrast images. Therefore, formulating image segmentation as a recurrent framework of two interconnected networks via context feedback loop can be a potential method for robust and efficient medical image analysis.
Processing medical data to find abnormalities is a time-consuming and costly task, requiring tremendous efforts from medical experts. Therefore, Ai has become a popular tool for the automatic processing of medical data, acting as a supportive tool for doctors. AI tools highly depend on data for training the models. However, there are several constraints to access to large amounts of medical data to train machine learning algorithms in the medical domain, e.g., due to privacy concerns and the costly, time-consuming medical data annotation process. To address this, in this paper we present a novel synthetic data generation pipeline called SinGAN-Seg to produce synthetic medical data with the corresponding annotated ground truth masks. We show that these synthetic data generation pipelines can be used as an alternative to bypass privacy concerns and as an alternative way to produce artificial segmentation datasets with corresponding ground truth masks to avoid the tedious medical data annotation process. As a proof of concept, we used an open polyp segmentation dataset. By training UNet++ using both the real polyp segmentation dataset and the corresponding synthetic dataset generated from the SinGAN-Seg pipeline, we show that the synthetic data can achieve a very close performance to the real data when the real segmentation datasets are large enough. In addition, we show that synthetic data generated from the SinGAN-Seg pipeline improving the performance of segmentation algorithms when the training dataset is very small. Since our SinGAN-Seg pipeline is applicable for any medical dataset, this pipeline can be used with any other segmentation datasets.
Recently, a growing interest has been seen in deep learning-based semantic segmentation. UNet, which is one of deep learning networks with an encoder-decoder architecture, is widely used in medical image segmentation. Combining multi-scale features is one of important factors for accurate segmentation. UNet++ was developed as a modified Unet by designing an architecture with nested and dense skip connections. However, it does not explore sufficient information from full scales and there is still a large room for improvement. In this paper, we propose a novel UNet 3+, which takes advantage of full-scale skip connections and deep supervisions. The full-scale skip connections incorporate low-level details with high-level semantics from feature maps in different scales; while the deep supervision learns hierarchical representations from the full-scale aggregated feature maps. The proposed method is especially benefiting for organs that appear at varying scales. In addition to accuracy improvements, the proposed UNet 3+ can reduce the network parameters to improve the computation efficiency. We further propose a hybrid loss function and devise a classification-guided module to enhance the organ boundary and reduce the over-segmentation in a non-organ image, yielding more accurate segmentation results. The effectiveness of the proposed method is demonstrated on two datasets. The code is available at: github.com/ZJUGiveLab/UNet-Version
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