Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userAutomatic CT Segmentation from Bounding Box Annotations using Convolutional Neural Networks
293
0
0.0
(
0
)
Added by
Yuanpeng Liu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Accurate segmentation for medical images is important for clinical diagnosis. Existing automatic segmentation methods are mainly based on fully supervised learning and have an extremely high demand for precise annotations, which are very costly and time-consuming to obtain. To address this problem, we proposed an automatic CT segmentation method based on weakly supervised learning, by which one could train an accurate segmentation model only with weak annotations in the form of bounding boxes. The proposed method is composed of two steps: 1) generating pseudo masks with bounding box annotations by k-means clustering, and 2) iteratively training a 3D U-Net convolutional neural network as a segmentation model. Some data pre-processing methods are used to improve performance. The method was validated on four datasets containing three types of organs with a total of 627 CT volumes. For liver, spleen and kidney segmentation, it achieved an accuracy of 95.19%, 92.11%, and 91.45%, respectively. Experimental results demonstrate that our method is accurate, efficient, and suitable for clinical use.
rate research
Read More
Automatic segmentation of the liver and hepatic lesions is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT and MRI abdomen images using cascaded fully convolutional neural networks (CFCNs) enabling the segmentation of a large-scale medical trial or quantitative image analysis. We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input for a second FCN. The second FCN solely segments lesions within the predicted liver ROIs of step 1. CFCN models were trained on an abdominal CT dataset comprising 100 hepatic tumor volumes. Validations on further datasets show that CFCN-based semantic liver and lesion segmentation achieves Dice scores over 94% for liver with computation times below 100s per volume. We further experimentally demonstrate the robustness of the proposed method on an 38 MRI liver tumor volumes and the public 3DIRCAD dataset.
Colorectal cancer is the third most common cancer-related death after lung cancer and breast cancer worldwide. The risk of developing colorectal cancer could be reduced by early diagnosis of polyps during a colonoscopy. Computer-aided diagnosis systems have the potential to be applied for polyp screening and reduce the number of missing polyps. In this paper, we compare the performance of different deep learning architectures as feature extractors, i.e. ResNet, DenseNet, InceptionV3, InceptionResNetV2 and SE-ResNeXt in the encoder part of a U-Net architecture. We validated the performance of presented ensemble models on the CVC-Clinic (GIANA 2018) dataset. The DenseNet169 feature extractor combined with U-Net architecture outperformed the other counterparts and achieved an accuracy of 99.15%, Dice similarity coefficient of 90.87%, and Jaccard index of 83.82%.
Automatic segmentation of the liver and its lesion is an important step towards deriving quantitative biomarkers for accurate clinical diagnosis and computer-aided decision support systems. This paper presents a method to automatically segment liver and lesions in CT abdomen images using cascaded fully convolutional neural networks (CFCNs) and dense 3D conditional random fields (CRFs). We train and cascade two FCNs for a combined segmentation of the liver and its lesions. In the first step, we train a FCN to segment the liver as ROI input for a second FCN. The second FCN solely segments lesions from the predicted liver ROIs of step 1. We refine the segmentations of the CFCN using a dense 3D CRF that accounts for both spatial coherence and appearance. CFCN models were trained in a 2-fold cross-validation on the abdominal CT dataset 3DIRCAD comprising 15 hepatic tumor volumes. Our results show that CFCN-based semantic liver and lesion segmentation achieves Dice scores over 94% for liver with computation times below 100s per volume. We experimentally demonstrate the robustness of the proposed method as a decision support system with a high accuracy and speed for usage in daily clinical routine.
Segmentation of mandibles in CT scans during virtual surgical planning is crucial for 3D surgical planning in order to obtain a detailed surface representation of the patients bone. Automatic segmentation of mandibles in CT scans is a challenging task due to large variation in their shape and size between individuals. In order to address this challenge we propose a convolutional neural network approach for mandible segmentation in CT scans by considering the continuum of anatomical structures through different planes. The proposed convolutional neural network adopts the architecture of the U-Net and then combines the resulting 2D segmentations from three different planes into a 3D segmentation. We implement such a segmentation approach on 11 neck CT scans and then evaluate the performance. We achieve an average dice coefficient of $ 0.89 $ on two testing mandible segmentation. Experimental results show that our proposed approach for mandible segmentation in CT scans exhibits high accuracy.
This paper presents a method for automatic segmentation, localization, and identification of vertebrae in arbitrary 3D CT images. Many previous works do not perform the three tasks simultaneously even though requiring a priori knowledge of which part of the anatomy is visible in the 3D CT images. Our method tackles all these tasks in a single multi-stage framework without any assumptions. In the first stage, we train a 3D Fully Convolutional Networks to find the bounding boxes of the cervical, thoracic, and lumbar vertebrae. In the second stage, we train an iterative 3D Fully Convolutional Networks to segment individual vertebrae in the bounding box. The input to the second networks have an auxiliary channel in addition to the 3D CT images. Given the segmented vertebra regions in the auxiliary channel, the networks output the next vertebra. The proposed method is evaluated in terms of segmentation, localization, and identification accuracy with two public datasets of 15 3D CT images from the MICCAI CSI 2014 workshop challenge and 302 3D CT images with various pathologies introduced in [1]. Our method achieved a mean Dice score of 96%, a mean localization error of 8.3 mm, and a mean identification rate of 84%. In summary, our method achieved better performance than all existing works in all the three metrics.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
