Purpose Automated segmentation of anatomical structures in medical image analysis is a prerequisite for autonomous diagnosis as well as various computer and robot aided interventions. Recent methods based on deep convolutional neural networks (CNN) have outperformed former heuristic methods. However, those methods were primarily evaluated on rigid, real-world environments. In this study, existing segmentation methods were evaluated for their use on a new dataset of transoral endoscopic exploration. Methods Four machine learning based methods SegNet, UNet, ENet and ErfNet were trained with supervision on a novel 7-class dataset of the human larynx. The dataset contains 536 manually segmented images from two patients during laser incisions. The Intersection-over-Union (IoU) evaluation metric was used to measure the accuracy of each method. Data augmentation and network ensembling were employed to increase segmentation accuracy. Stochastic inference was used to show uncertainties of the individual models. Patient-to-patient transfer was investigated using patient-specific fine-tuning. Results In this study, a weighted average ensemble network of UNet and ErfNet was best suited for the segmentation of laryngeal soft tissue with a mean IoU of 84.7 . The highest efficiency was achieved by ENet with a mean inference time of 9.22 ms per image. It is shown that 10 additional images from a new patient are sufficient for patient-specific fine-tuning. Conclusion CNN-based methods for semantic segmentation are applicable to endoscopic images of laryngeal soft tissue. The segmentation can be used for active constraints or to monitor morphological changes and autonomously detect pathologies. Further improvements could be achieved by using a larger dataset or training the models in a self-supervised manner on additional unlabeled data.
More sophisticated methods are based on mathematical models and rely on finding the parameters with which the output of the model minimizes an error or energy function. Some of these approaches require ground truth examples prior to or during the segmentation task. In atlas-based segmentation, for example, a manually segmented atlas'', which acts as a-priori anatomical information, is matched onto the input image @cite_24 . This turns the segmentation problem to a registration problem. The error-minimizing transformation between the images is also applied to the a-priori segmentation, which results in the segmentation of the input image. A good result requires a large atlas database, which must be considered during segmentation time, thus making atlas-based segmentation not applicable in environments with real-time demands.
@cite_24
1998070036
Abstract: Normal and abnormal brains can be segmented by registering the target image with an atlas. Here, an atlas is defined as the combination of an intensity image (template) and its segmented image (the atlas labels). After registering the atlas template and the target image, the atlas labels are propagated to the target image. We define this process as atlas-based segmentation. In recent years, researchers have investigated registration algorithms to match atlases to query subjects and also strategies for atlas construction. In this paper we present a review of the automated approaches for atlas-based segmentation of magnetic resonance brain images. We aim to point out the strengths and weaknesses of atlas-based methods and suggest new research directions. We use two different criteria to present the methods. First, we refer to the algorithms according to their atlas-based strategy: label propagation, multi-atlas methods, and probabilistic techniques. Subsequently, we classify the methods according to their medical target: the brain and its internal structures, tissue segmentation in healthy subjects, tissue segmentation in fetus, neonates and elderly subjects, and segmentation of damaged brains. A quantitative comparison of the results reported in the literature is also presented.