Add to Chrome
Add to Firefox
Add to EdgeClass-Aware Cartilage Segmentation for Autonomous US-CT Registration in Robotic Intercostal Ultrasound Imaging
Jun 06, 2024
Ultrasound imaging has been widely used in clinical examinations owing to the advantages of being portable, real-time, and radiation-free. Considering the potential of extensive deployment of autonomous examination systems in hospitals, robotic US imaging has attracted increased attention. However, due to the inter-patient variations, it is still challenging to have an optimal path for each patient, particularly for thoracic applications with limited acoustic windows, e.g., intercostal liver imaging. To address this problem, a class-aware cartilage bone segmentation network with geometry-constraint post-processing is presented to capture patient-specific rib skeletons. Then, a dense skeleton graph-based non-rigid registration is presented to map the intercostal scanning path from a generic template to individual patients. By explicitly considering the high-acoustic impedance bone structures, the transferred scanning path can be precisely located in the intercostal space, enhancing the visibility of internal organs by reducing the acoustic shadow. To evaluate the proposed approach, the final path mapping performance is validated on five distinct CTs and two volunteer US data, resulting in ten pairs of CT-US combinations. Results demonstrate that the proposed graph-based registration method can robustly and precisely map the path from CT template to individual patients (Euclidean error: $2.21\pm1.11~mm$).
MMCBE: Multi-modality Dataset for Crop Biomass Estimation and Beyond
Apr 17, 2024Crop biomass, a critical indicator of plant growth, health, and productivity, is invaluable for crop breeding programs and agronomic research. However, the accurate and scalable quantification of crop biomass remains inaccessible due to limitations in existing measurement methods. One of the obstacles impeding the advancement of current crop biomass prediction methodologies is the scarcity of publicly available datasets. Addressing this gap, we introduce a new dataset in this domain, i.e. Multi-modality dataset for crop biomass estimation (MMCBE). Comprising 216 sets of multi-view drone images, coupled with LiDAR point clouds, and hand-labelled ground truth, MMCBE represents the first multi-modality one in the field. This dataset aims to establish benchmark methods for crop biomass quantification and foster the development of vision-based approaches. We have rigorously evaluated state-of-the-art crop biomass estimation methods using MMCBE and ventured into additional potential applications, such as 3D crop reconstruction from drone imagery and novel-view rendering. With this publication, we are making our comprehensive dataset available to the broader community.
Latent-based Diffusion Model for Long-tailed Recognition
Apr 06, 2024Long-tailed imbalance distribution is a common issue in practical computer vision applications. Previous works proposed methods to address this problem, which can be categorized into several classes: re-sampling, re-weighting, transfer learning, and feature augmentation. In recent years, diffusion models have shown an impressive generation ability in many sub-problems of deep computer vision. However, its powerful generation has not been explored in long-tailed problems. We propose a new approach, the Latent-based Diffusion Model for Long-tailed Recognition (LDMLR), as a feature augmentation method to tackle the issue. First, we encode the imbalanced dataset into features using the baseline model. Then, we train a Denoising Diffusion Implicit Model (DDIM) using these encoded features to generate pseudo-features. Finally, we train the classifier using the encoded and pseudo-features from the previous two steps. The model's accuracy shows an improvement on the CIFAR-LT and ImageNet-LT datasets by using the proposed method.
Backpropagation-free Network for 3D Test-time Adaptation
Mar 27, 2024
Real-world systems often encounter new data over time, which leads to experiencing target domain shifts. Existing Test-Time Adaptation (TTA) methods tend to apply computationally heavy and memory-intensive backpropagation-based approaches to handle this. Here, we propose a novel method that uses a backpropagation-free approach for TTA for the specific case of 3D data. Our model uses a two-stream architecture to maintain knowledge about the source domain as well as complementary target-domain-specific information. The backpropagation-free property of our model helps address the well-known forgetting problem and mitigates the error accumulation issue. The proposed method also eliminates the need for the usually noisy process of pseudo-labeling and reliance on costly self-supervised training. Moreover, our method leverages subspace learning, effectively reducing the distribution variance between the two domains. Furthermore, the source-domain-specific and the target-domain-specific streams are aligned using a novel entropy-based adaptive fusion strategy. Extensive experiments on popular benchmarks demonstrate the effectiveness of our method. The code will be available at https://github.com/abie-e/BFTT3D.
Spatial Transcriptomics Analysis of Zero-shot Gene Expression Prediction
Jan 26, 2024Spatial transcriptomics (ST) captures gene expression within distinct regions (i.e., windows) of a tissue slide. Traditional supervised learning frameworks applied to model ST are constrained to predicting expression from slide image windows for gene types seen during training, failing to generalize to unseen gene types. To overcome this limitation, we propose a semantic guided network (SGN), a pioneering zero-shot framework for predicting gene expression from slide image windows. Considering a gene type can be described by functionality and phenotype, we dynamically embed a gene type to a vector per its functionality and phenotype, and employ this vector to project slide image windows to gene expression in feature space, unleashing zero-shot expression prediction for unseen gene types. The gene type functionality and phenotype are queried with a carefully designed prompt from a pre-trained large language model (LLM). On standard benchmark datasets, we demonstrate competitive zero-shot performance compared to past state-of-the-art supervised learning approaches.
Cross-modal and Cross-domain Knowledge Transfer for Label-free 3D Segmentation
Sep 19, 2023
Current state-of-the-art point cloud-based perception methods usually rely on large-scale labeled data, which requires expensive manual annotations. A natural option is to explore the unsupervised methodology for 3D perception tasks. However, such methods often face substantial performance-drop difficulties. Fortunately, we found that there exist amounts of image-based datasets and an alternative can be proposed, i.e., transferring the knowledge in the 2D images to 3D point clouds. Specifically, we propose a novel approach for the challenging cross-modal and cross-domain adaptation task by fully exploring the relationship between images and point clouds and designing effective feature alignment strategies. Without any 3D labels, our method achieves state-of-the-art performance for 3D point cloud semantic segmentation on SemanticKITTI by using the knowledge of KITTI360 and GTA5, compared to existing unsupervised and weakly-supervised baselines.
* 12 pages,4 figures,accepted
Thoracic Cartilage Ultrasound-CT Registration using Dense Skeleton Graph
Jul 07, 2023
Autonomous ultrasound (US) imaging has gained increased interest recently, and it has been seen as a potential solution to overcome the limitations of free-hand US examinations, such as inter-operator variations. However, it is still challenging to accurately map planned paths from a generic atlas to individual patients, particularly for thoracic applications with high acoustic-impedance bone structures under the skin. To address this challenge, a graph-based non-rigid registration is proposed to enable transferring planned paths from the atlas to the current setup by explicitly considering subcutaneous bone surface features instead of the skin surface. To this end, the sternum and cartilage branches are segmented using a template matching to assist coarse alignment of US and CT point clouds. Afterward, a directed graph is generated based on the CT template. Then, the self-organizing map using geographical distance is successively performed twice to extract the optimal graph representations for CT and US point clouds, individually. To evaluate the proposed approach, five cartilage point clouds from distinct patients are employed. The results demonstrate that the proposed graph-based registration can effectively map trajectories from CT to the current setup for displaying US views through limited intercostal space. The non-rigid registration results in terms of Hausdorff distance (Mean$\pm$SD) is 9.48$\pm$0.27 mm and the path transferring error in terms of Euclidean distance is 2.21$\pm$1.11 mm.
Skeleton Graph-based Ultrasound-CT Non-rigid Registration
May 14, 2023
Autonomous ultrasound (US) scanning has attracted increased attention, and it has been seen as a potential solution to overcome the limitations of conventional US examinations, such as inter-operator variations. However, it is still challenging to autonomously and accurately transfer a planned scan trajectory on a generic atlas to the current setup for different patients, particularly for thorax applications with limited acoustic windows. To address this challenge, we proposed a skeleton graph-based non-rigid registration to adapt patient-specific properties using subcutaneous bone surface features rather than the skin surface. To this end, the self-organization mapping is successively used twice to unify the input point cloud and extract the key points, respectively. Afterward, the minimal spanning tree is employed to generate a tree graph to connect all extracted key points. To appropriately characterize the rib cartilage outline to match the source and target point cloud, the path extracted from the tree graph is optimized by maximally maintaining continuity throughout each rib. To validate the proposed approach, we manually extract the US cartilage point cloud from one volunteer and seven CT cartilage point clouds from different patients. The results demonstrate that the proposed graph-based registration is more effective and robust in adapting to the inter-patient variations than the ICP (distance error mean/SD: 5.0/1.9 mm vs 8.6/6.7 mm on seven CTs).
A Heterogeneous Graph Based Framework for Multimodal Neuroimaging Fusion Learning
Oct 16, 2021
Here, we present a Heterogeneous Graph neural network for Multimodal neuroimaging fusion learning (HGM). Traditional GNN-based models usually assume the brain network is a homogeneous graph with single type of nodes and edges. However, vast literatures have shown the heterogeneity of the human brain especially between the two hemispheres. Homogeneous brain network is insufficient to model the complicated brain state. Therefore, in this work we firstly model the brain network as heterogeneous graph with multi-type nodes (i.e., left and right hemispheric nodes) and multi-type edges (i.e., intra- and inter-hemispheric edges). Besides, we also propose a self-supervised pre-training strategy based on heterogeneou brain network to address the overfitting problem due to the complex model and small sample size. Our results on two datasets show the superiority of proposed model over other multimodal methods for disease prediction task. Besides, ablation experiments show that our model with pre-training strategy can alleviate the problem of limited training sample size.
Weight Encode Reconstruction Network for Computed Tomography in a Semi-Case-Wise and Learning-Based Way
Oct 02, 2020
Classic algebraic reconstruction technology (ART) for computed tomography requires pre-determined weights of the voxels for projecting pixel values. However, such weight cannot be accurately obtained due to the limitation of the physical understanding and computation resources. In this study, we propose a semi-case-wise learning-based method named Weight Encode Reconstruction Network (WERNet) to tackle the issues mentioned above. The model is trained in a self-supervised manner without the label of a voxel set. It contains two branches, including the voxel weight encoder and the voxel attention part. Using gradient normalization, we are able to co-train the encoder and voxel set numerically stably. With WERNet, the reconstructed result was obtained with a cosine similarity greater than 0.999 with the ground truth. Moreover, the model shows the extraordinary capability of denoising comparing to the classic ART method. In the generalization test of the model, the encoder is transferable from a voxel set with complex structure to the unseen cases without the deduction of the accuracy.