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      Three-Dimensional Semantic Segmentation of Pituitary Adenomas Based on the Deep Learning Framework-nnU-Net: A Clinical Perspective

      , , , , , , , ,
      Micromachines
      MDPI AG

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          Abstract

          This study developed and evaluated nnU-Net models for three-dimensional semantic segmentation of pituitary adenomas (PAs) from contrast-enhanced T1 (T1ce) images, with aims to train a deep learning-based model cost-effectively and apply it to clinical practice. Methods: This study was conducted in two phases. In phase one, two models were trained with nnUNet using distinct PA datasets. Model 1 was trained with 208 PAs in total, and model 2 was trained with 109 primary nonfunctional pituitary adenomas (NFPA). In phase two, the performances of the two models were investigated according to the Dice similarity coefficient (DSC) in the leave-out test dataset. Results: Both models performed well (DSC > 0.8) for PAs with volumes > 1000 mm3, but unsatisfactorily (DSC < 0.5) for PAs < 1000 mm3. Conclusions: Both nnU-Net models showed good segmentation performance for PAs > 1000 mm3 (75% of the dataset) and limited performance for PAs < 1000 mm3 (25% of the dataset). Model 2 trained with fewer samples was more cost-effective. We propose to combine the use of model-based segmentation for PA > 1000 mm3 and manual segmentation for PA < 1000 mm3 in clinical practice at the current stage.

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          nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation

          Biomedical imaging is a driver of scientific discovery and a core component of medical care and is being stimulated by the field of deep learning. While semantic segmentation algorithms enable image analysis and quantification in many applications, the design of respective specialized solutions is non-trivial and highly dependent on dataset properties and hardware conditions. We developed nnU-Net, a deep learning-based segmentation method that automatically configures itself, including preprocessing, network architecture, training and post-processing for any new task. The key design choices in this process are modeled as a set of fixed parameters, interdependent rules and empirical decisions. Without manual intervention, nnU-Net surpasses most existing approaches, including highly specialized solutions on 23 public datasets used in international biomedical segmentation competitions. We make nnU-Net publicly available as an out-of-the-box tool, rendering state-of-the-art segmentation accessible to a broad audience by requiring neither expert knowledge nor computing resources beyond standard network training.
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            Fully Convolutional Networks for Semantic Segmentation.

            Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, improve on the previous best result in semantic segmentation. Our key insight is to build "fully convolutional" networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet, the VGG net, and GoogLeNet) into fully convolutional networks and transfer their learned representations by fine-tuning to the segmentation task. We then define a skip architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional networks achieve improved segmentation of PASCAL VOC (30% relative improvement to 67.2% mean IU on 2012), NYUDv2, SIFT Flow, and PASCAL-Context, while inference takes one tenth of a second for a typical image.
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              Metrics for evaluating 3D medical image segmentation: analysis, selection, and tool

              Background Medical Image segmentation is an important image processing step. Comparing images to evaluate the quality of segmentation is an essential part of measuring progress in this research area. Some of the challenges in evaluating medical segmentation are: metric selection, the use in the literature of multiple definitions for certain metrics, inefficiency of the metric calculation implementations leading to difficulties with large volumes, and lack of support for fuzzy segmentation by existing metrics. Result First we present an overview of 20 evaluation metrics selected based on a comprehensive literature review. For fuzzy segmentation, which shows the level of membership of each voxel to multiple classes, fuzzy definitions of all metrics are provided. We present a discussion about metric properties to provide a guide for selecting evaluation metrics. Finally, we propose an efficient evaluation tool implementing the 20 selected metrics. The tool is optimized to perform efficiently in terms of speed and required memory, also if the image size is extremely large as in the case of whole body MRI or CT volume segmentation. An implementation of this tool is available as an open source project. Conclusion We propose an efficient evaluation tool for 3D medical image segmentation using 20 evaluation metrics and provide guidelines for selecting a subset of these metrics that is suitable for the data and the segmentation task.
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                Author and article information

                Journal
                Micromachines
                Micromachines
                MDPI AG
                2072-666X
                December 2021
                November 29 2021
                : 12
                : 12
                : 1473
                Article
                10.3390/mi12121473
                34945322
                eb7fb5f1-5893-449a-8372-29767982b927
                © 2021

                https://creativecommons.org/licenses/by/4.0/

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