Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userFully Automated 3D Segmentation of MR-Imaged Calf Muscle Compartments: Neighborhood Relationship Enhanced Fully Convolutional Network
107
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Automated segmentation of individual calf muscle compartments from 3D magnetic resonance (MR) images is essential for developing quantitative biomarkers for muscular disease progression and its prediction. Achieving clinically acceptable results is a challenging task due to large variations in muscle shape and MR appearance. Although deep convolutional neural networks (DCNNs) achieved improved accuracy in various image segmentation tasks, certain problems such as utilizing long-range information and incorporating high-level constraints remain unsolved. We present a novel fully convolutional network (FCN), called FilterNet, that utilizes contextual information in a large neighborhood and embeds edge-aware constraints for individual calf muscle compartment segmentations. An encoder-decoder architecture with flexible backbone blocks is used to systematically enlarge convolution receptive field and preserve information at all resolutions. Edge positions derived from the FCN output muscle probability maps are explicitly regularized using kernel-based edge detection in an end-to-end optimization framework. Our FilterNet was evaluated on 40 T1-weighted MR images of 10 healthy and 30 diseased subjects by 4-fold cross-validation. Mean DICE coefficients of 88.00%--91.29% and mean absolute surface positioning errors of 1.04--1.66 mm were achieved for the five 3D muscle compartments.
rate research
Read More
Cardiac imaging known as echocardiography is a non-invasive tool utilized to produce data including images and videos, which cardiologists use to diagnose cardiac abnormalities in general and myocardial infarction (MI) in particular. Echocardiography machines can deliver abundant amounts of data that need to be quickly analyzed by cardiologists to help them make a diagnosis and treat cardiac conditions. However, the acquired data quality varies depending on the acquisition conditions and the patients responsiveness to the setup instructions. These constraints are challenging to doctors especially when patients are facing MI and their lives are at stake. In this paper, we propose an innovative real-time end-to-end fully automated model based on convolutional neural networks (CNN) to detect MI depending on regional wall motion abnormalities (RWMA) of the left ventricle (LV) from videos produced by echocardiography. Our model is implemented as a pipeline consisting of a 2D CNN that performs data preprocessing by segmenting the LV chamber from the apical four-chamber (A4C) view, followed by a 3D CNN that performs a binary classification to detect if the segmented echocardiography shows signs of MI. We trained both CNNs on a dataset composed of 165 echocardiography videos each acquired from a distinct patient. The 2D CNN achieved an accuracy of 97.18% on data segmentation while the 3D CNN achieved 90.9% of accuracy, 100% of precision and 95% of recall on MI detection. Our results demonstrate that creating a fully automated system for MI detection is feasible and propitious.
Renal compartment segmentation on CT images targets on extracting the 3D structure of renal compartments from abdominal CTA images and is of great significance to the diagnosis and treatment for kidney diseases. However, due to the unclear compartment boundary, thin compartment structure and large anatomy variation of 3D kidney CT images, deep-learning based renal compartment segmentation is a challenging task. We propose a novel weakly supervised learning framework, Cycle Prototype Network, for 3D renal compartment segmentation. It has three innovations: 1) A Cycle Prototype Learning (CPL) is proposed to learn consistency for generalization. It learns from pseudo labels through the forward process and learns consistency regularization through the reverse process. The two processes make the model robust to noise and label-efficient. 2) We propose a Bayes Weakly Supervised Module (BWSM) based on cross-period prior knowledge. It learns prior knowledge from cross-period unlabeled data and perform error correction automatically, thus generates accurate pseudo labels. 3) We present a Fine Decoding Feature Extractor (FDFE) for fine-grained feature extraction. It combines global morphology information and local detail information to obtain feature maps with sharp detail, so the model will achieve fine segmentation on thin structures. Our model achieves Dice of 79.1% and 78.7% with only four labeled images, achieving a significant improvement by about 20% than typical prototype model PANet.
Segmentation of multiple organs-at-risk (OARs) is essential for radiation therapy treatment planning and other clinical applications. We developed an Automated deep Learning-based Abdominal Multi-Organ segmentation (ALAMO) framework based on 2D U-net and a densely connected network structure with tailored design in data augmentation and training procedures such as deep connection, auxiliary supervision, and multi-view. The model takes in multi-slice MR images and generates the output of segmentation results. Three-Tesla T1 VIBE (Volumetric Interpolated Breath-hold Examination) images of 102 subjects were collected and used in our study. Ten OARs were studied, including the liver, spleen, pancreas, left/right kidneys, stomach, duodenum, small intestine, spinal cord, and vertebral bodies. Two radiologists manually labeled and obtained the consensus contours as the ground-truth. In the complete cohort of 102, 20 samples were held out for independent testing, and the rest were used for training and validation. The performance was measured using volume overlapping and surface distance. The ALAMO framework generated segmentation labels in good agreement with the manual results. Specifically, among the 10 OARs, 9 achieved high Dice Similarity Coefficients (DSCs) in the range of 0.87-0.96, except for the duodenum with a DSC of 0.80. The inference completes within one minute for a 3D volume of 320x288x180. Overall, the ALAMO model matches the state-of-the-art performance. The proposed ALAMO framework allows for fully automated abdominal MR segmentation with high accuracy and low memory and computation time demands.
We desgin a novel fully convolutional network architecture for shapes, denoted by Shape Fully Convolutional Networks (SFCN). 3D shapes are represented as graph structures in the SFCN architecture, based on novel graph convolution and pooling operations, which are similar to convolution and pooling operations used on images. Meanwhile, to build our SFCN architecture in the original image segmentation fully convolutional network (FCN) architecture, we also design and implement a generating operation} with bridging function. This ensures that the convolution and pooling operation we have designed can be successfully applied in the original FCN architecture. In this paper, we also present a new shape segmentation approach based on SFCN. Furthermore, we allow more general and challenging input, such as mixed datasets of different categories of shapes} which can prove the ability of our generalisation. In our approach, SFCNs are trained triangles-to-triangles by using three low-level geometric features as input. Finally, the feature voting-based multi-label graph cuts is adopted to optimise the segmentation results obtained by SFCN prediction. The experiment results show that our method can effectively learn and predict mixed shape datasets of either similar or different characteristics, and achieve excellent segmentation results.
Fully convolutional neural networks give accurate, per-pixel prediction for input images and have applications like semantic segmentation. However, a typical FCN usually requires lots of floating point computation and large run-time memory, which effectively limits its usability. We propose a method to train Bit Fully Convolution Network (BFCN), a fully convolutional neural network that has low bit-width weights and activations. Because most of its computation-intensive convolutions are accomplished between low bit-width numbers, a BFCN can be accelerated by an efficient bit-convolution implementation. On CPU, the dot product operation between two bit vectors can be reduced to bitwise operations and popcounts, which can offer much higher throughput than 32-bit multiplications and additions. To validate the effectiveness of BFCN, we conduct experiments on the PASCAL VOC 2012 semantic segmentation task and Cityscapes. Our BFCN with 1-bit weights and 2-bit activations, which runs 7.8x faster on CPU or requires less than 1% resources on FPGA, can achieve comparable performance as the 32-bit counterpart.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
