This paper introduces a deep neural network based method, i.e., DeepOrganNet, to generate and visualize fully high-fidelity 3D / 4D organ geometric models from single-view medical images with complicated background in real time. Traditional 3D / 4D medical image reconstruction requires near hundreds of projections, which cost insufferable computational time and deliver undesirable high imaging / radiation dose to human subjects. Moreover, it always needs further notorious processes to segment or extract the accurate 3D organ models subsequently. The computational time and imaging dose can be reduced by decreasing the number of projections, but the reconstructed image quality is degraded accordingly. To our knowledge, there is no method directly and explicitly reconstructing multiple 3D organ meshes from a single 2D medical grayscale image on the fly. Given single-view 2D medical images, e.g., 3D / 4D-CT projections or X-ray images, our end-to-end DeepOrganNet framework can efficiently and effectively reconstruct 3D / 4D lung models with a variety of geometric shapes by learning the smooth deformation fields from multiple templates based on a trivariate tensor-product deformation technique, leveraging an informative latent descriptor extracted from input 2D images. The proposed method can guarantee to generate high-quality and high-fidelity manifold meshes for 3D / 4D lung models; while, all current deep learning based approaches on the shape reconstruction from a single image cannot. The major contributions of this work are to accurately reconstruct the 3D organ shapes from 2D single-view projection, significantly improve the procedure time to allow on-the-fly visualization, and dramatically reduce the imaging dose for human subjects. Experimental results are evaluated and compared with the traditional reconstruction method and the state-of-the-art in deep learning, by using extensive 3D and 4D examples, including both synthetic phantom and real patient datasets. The efficiency of the proposed method shows that it only needs several milliseconds to generate organ meshes with 10K vertices, which has great potential to be used in real-time image guided radiation therapy (IGRT).
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Harmony: A Generic Unsupervised Approach for Disentangling Semantic Content from Parameterized Transformations
In many real-life image analysis applications, particularly in biomedical research domains, the objects of interest undergo multiple transformations that alter their visual properties while keeping the semantic content unchanged. Disentangling images into semantic content factors and transformations can provide significant benefits into many domain-specific image analysis tasks. To this end, we propose a generic unsupervised framework, Harmony, that simultaneously and explicitly disentangles semantic content from multiple parameterized transformations. Harmony leverages a simple cross-contrastive learning framework with multiple explicitly parameterized latent representations to disentangle content from transformations. To demonstrate the efficacy of Harmony, we apply it to disentangle image semantic content from several parameterized transformations (rotation, translation, scaling, and contrast). Harmony achieves significantly improved disentanglement over the baseline models on several image datasets of diverse domains. With such disentanglement, Harmony is demonstrated to incentivize bioimage analysis research by modeling structural heterogeneity of macromolecules from cryo-ET images and learning transformation-invariant representations of protein particles from single-particle cryo-EM images. Harmony also performs very well in disentangling content from 3D transformations and can perform coarse and fast alignment of 3D cryo-ET subtomograms. Therefore, Harmony is generalizable to many other imaging domains and can potentially be extended to domains beyond imaging as well.
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- NSF-PAR ID:
- 10327697
- Date Published:
- Journal Name:
- IEEE Conference on Computer Vision and Pattern Recognition
- ISSN:
- 2163-6648
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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null (Ed.)Abstract Background Cryo-electron tomography is an important and powerful technique to explore the structure, abundance, and location of ultrastructure in a near-native state. It contains detailed information of all macromolecular complexes in a sample cell. However, due to the compact and crowded status, the missing edge effect, and low signal to noise ratio (SNR), it is extremely challenging to recover such information with existing image processing methods. Cryo-electron tomogram simulation is an effective solution to test and optimize the performance of the above image processing methods. The simulated images could be regarded as the labeled data which covers a wide range of macromolecular complexes and ultrastructure. To approximate the crowded cellular environment, it is very important to pack these heterogeneous structures as tightly as possible. Besides, simulating non-deformable and deformable components under a unified framework also need to be achieved. Result In this paper, we proposed a unified framework for simulating crowded cryo-electron tomogram images including non-deformable macromolecular complexes and deformable ultrastructures. A macromolecule was approximated using multiple balls with fixed relative positions to reduce the vacuum volume. A ultrastructure, such as membrane and filament, was approximated using multiple balls with flexible relative positions so that this structure could deform under force field. In the experiment, 400 macromolecules of 20 representative types were packed into simulated cytoplasm by our framework, and numerical verification proved that our method has a smaller volume and higher compression ratio than the baseline single-ball model. We also packed filaments, membranes and macromolecules together, to obtain a simulated cryo-electron tomogram image with deformable structures. The simulated results are closer to the real Cryo-ET, making the analysis more difficult. The DOG particle picking method and the image segmentation method are tested on our simulation data, and the experimental results show that these methods still have much room for improvement. Conclusion The proposed multi-ball model can achieve more crowded packaging results and contains richer elements with different properties to obtain more realistic cryo-electron tomogram simulation. This enables users to simulate cryo-electron tomogram images with non-deformable macromolecular complexes and deformable ultrastructures under a unified framework. To illustrate the advantages of our framework in improving the compression ratio, we calculated the volume of simulated macromolecular under our multi-ball method and traditional single-ball method. We also performed the packing experiment of filaments and membranes to demonstrate the simulation ability of deformable structures. Our method can be used to do a benchmark by generating large labeled cryo-ET dataset and evaluating existing image processing methods. Since the content of the simulated cryo-ET is more complex and crowded compared with previous ones, it will pose a greater challenge to existing image processing methods.more » « less
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Abstract Motivation Cryo-Electron Tomography (cryo-ET) is a 3D imaging technology that enables the visualization of subcellular structures in situ at near-atomic resolution. Cellular cryo-ET images help in resolving the structures of macromolecules and determining their spatial relationship in a single cell, which has broad significance in cell and structural biology. Subtomogram classification and recognition constitute a primary step in the systematic recovery of these macromolecular structures. Supervised deep learning methods have been proven to be highly accurate and efficient for subtomogram classification, but suffer from limited applicability due to scarcity of annotated data. While generating simulated data for training supervised models is a potential solution, a sizeable difference in the image intensity distribution in generated data as compared with real experimental data will cause the trained models to perform poorly in predicting classes on real subtomograms.
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Availabilityand implementation https://github.com/xulabs/aitom.
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Accepted Manuscript1.0
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