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Register a new userAutomatic hippocampal surface generation via 3D U-net and active shape modeling with hybrid particle swarm optimization
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Added by
Pinyuan Zhong
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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In this paper, we proposed and validated a fully automatic pipeline for hippocampal surface generation via 3D U-net coupled with active shape modeling (ASM). Principally, the proposed pipeline consisted of three steps. In the beginning, for each magnetic resonance image, a 3D U-net was employed to obtain the automatic hippocampus segmentation at each hemisphere. Secondly, ASM was performed on a group of pre-obtained template surfaces to generate mean shape and shape variation parameters through principal component analysis. Ultimately, hybrid particle swarm optimization was utilized to search for the optimal shape variation parameters that best match the segmentation. The hippocampal surface was then generated from the mean shape and the shape variation parameters. The proposed pipeline was observed to provide hippocampal surfaces at both hemispheres with high accuracy, correct anatomical topology, and sufficient smoothness.
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Convolutional neural network (CNN) is one of the most frequently used deep learning techniques. Various forms of models have been proposed and improved for learning at CNN. When learning with CNN, it is necessary to determine the optimal hyperparameters. However, the number of hyperparameters is so large that it is difficult to do it manually, so much research has been done on automation. A method that uses metaheuristic algorithms is attracting attention in research on hyperparameter optimization. Metaheuristic algorithms are naturally inspired and include evolution strategies, genetic algorithms, antcolony optimization and particle swarm optimization. In particular, particle swarm optimization converges faster than genetic algorithms, and various models have been proposed. In this paper, we propose CNN hyperparameter optimization with linearly decreasing weight particle swarm optimization (LDWPSO). In the experiment, the MNIST data set and CIFAR-10 data set, which are often used as benchmark data sets, are used. By optimizing CNN hyperparameters with LDWPSO, learning the MNIST and CIFAR-10 datasets, we compare the accuracy with a standard CNN based on LeNet-5. As a result, when using the MNIST dataset, the baseline CNN is 94.02% at the 5th epoch, compared to 98.95% for LDWPSO CNN, which improves accuracy. When using the CIFAR-10 dataset, the Baseline CNN is 28.07% at the 10th epoch, compared to 69.37% for the LDWPSO CNN, which greatly improves accuracy.
Polyps are the predecessors to colorectal cancer which is considered as one of the leading causes of cancer-related deaths worldwide. Colonoscopy is the standard procedure for the identification, localization, and removal of colorectal polyps. Due to variability in shape, size, and surrounding tissue similarity, colorectal polyps are often missed by the clinicians during colonoscopy. With the use of an automatic, accurate, and fast polyp segmentation method during the colonoscopy, many colorectal polyps can be easily detected and removed. The ``Medico automatic polyp segmentation challenge provides an opportunity to study polyp segmentation and build an efficient and accurate segmentation algorithm. We use the U-Net with pre-trained ResNet50 as the encoder for the polyp segmentation. The model is trained on Kvasir-SEG dataset provided for the challenge and tested on the organizers dataset and achieves a dice coefficient of 0.8154, Jaccard of 0.7396, recall of 0.8533, precision of 0.8532, accuracy of 0.9506, and F2 score of 0.8272, demonstrating the generalization ability of our model.
Sequential assembly with geometric primitives has drawn attention in robotics and 3D vision since it yields a practical blueprint to construct a target shape. However, due to its combinatorial property, a greedy method falls short of generating a sequence of volumetric primitives. To alleviate this consequence induced by a huge number of feasible combinations, we propose a combinatorial 3D shape generation framework. The proposed framework reflects an important aspect of human generation processes in real life -- we often create a 3D shape by sequentially assembling unit primitives with geometric constraints. To find the desired combination regarding combination evaluations, we adopt Bayesian optimization, which is able to exploit and explore efficiently the feasible regions constrained by the current primitive placements. An evaluation function conveys global structure guidance for an assembly process and stability in terms of gravity and external forces simultaneously. Experimental results demonstrate that our method successfully generates combinatorial 3D shapes and simulates more realistic generation processes. We also introduce a new dataset for combinatorial 3D shape generation. All the codes are available at url{https://github.com/POSTECH-CVLab/Combinatorial-3D-Shape-Generation}.
Automatic blood vessel extraction from 3D medical images is crucial for vascular disease diagnoses. Existing methods based on convolutional neural networks (CNNs) may suffer from discontinuities of extracted vessels when segmenting such thin tubular structures from 3D images. We argue that preserving the continuity of extracted vessels requires to take into account the global geometry. However, 3D convolutions are computationally inefficient, which prohibits the 3D CNNs from sufficiently large receptive fields to capture the global cues in the entire image. In this work, we propose a hybrid representation learning approach to address this challenge. The main idea is to use CNNs to learn local appearances of vessels in image crops while using another point-cloud network to learn the global geometry of vessels in the entire image. In inference, the proposed approach extracts local segments of vessels using CNNs, classifies each segment based on global geometry using the point-cloud network, and finally connects all the segments that belong to the same vessel using the shortest-path algorithm. This combination results in an efficient, fully-automatic and template-free approach to centerline extraction from 3D images. We validate the proposed approach on CTA datasets and demonstrate its superior performance compared to both traditional and CNN-based baselines.
Automatic segmentation of cardiac magnetic resonance imaging (MRI) facilitates efficient and accurate volume measurement in clinical applications. However, due to anisotropic resolution and ambiguous border (e.g., right ventricular endocardium), existing methods suffer from the degradation of accuracy and robustness in 3D cardiac MRI video segmentation. In this paper, we propose a novel Deformable U-Net (DeU-Net) to fully exploit spatio-temporal information from 3D cardiac MRI video, including a Temporal Deformable Aggregation Module (TDAM) and a Deformable Global Position Attention (DGPA) network. First, the TDAM takes a cardiac MRI video clip as input with temporal information extracted by an offset prediction network. Then we fuse extracted temporal information via a temporal aggregation deformable convolution to produce fused feature maps. Furthermore, to aggregate meaningful features, we devise the DGPA network by employing deformable attention U-Net, which can encode a wider range of multi-dimensional contextual information into global and local features. Experimental results show that our DeU-Net achieves the state-of-the-art performance on commonly used evaluation metrics, especially for cardiac marginal information (ASSD and HD).
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