body2vec: 3D Point Cloud Reconstruction for Precise Anthropometry with Handheld Devices

Current point cloud extraction methods based on photogrammetry generate large amounts of spurious detections that hamper useful 3D mesh reconstructions or, even worse, the possibility of adequate measurements. Moreover, noise removal methods for point clouds are complex, slow and incapable to cope with semantic noise. In this work, we present body2vec, a model-based body segmentation tool that uses a specifically trained Neural Network architecture. Body2vec is capable to perform human body point cloud reconstruction from videos taken on hand-held devices (smartphones or tablets), achieving high quality anthropometric measurements. The main contribution of the proposed workflow is to perform a background removal step, thus avoiding the spurious points generation that is usual in photogrammetric reconstruction. A group of 60 persons were taped with a smartphone, and the corresponding point clouds were obtained automatically with standard photogrammetric methods. We used as a 3D silver standard the clean meshes obtained at the same time with LiDAR sensors post-processed and noise-filtered by expert anthropological biologists. Finally, we used as gold standard anthropometric measurements of the waist and hip of the same people, taken by expert anthropometrists. Applying our method to the raw videos significantly enhanced the quality of the results of the point cloud as compared with the LiDAR-based mesh, and of the anthropometric measurements as compared with the actual hip and waist perimeter measured by the anthropometrists. In both contexts, the resulting quality of body2vec is equivalent to the LiDAR reconstruction.Fil: Trujillo Jiménez, Magda Alexandra. Universidad Nacional del Sur. Departamento de Ingeniería Eléctrica y de Computadoras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Navarro, Pablo Eugenio. Universidad Nacional del Sur. Departamento de Ingeniería Eléctrica y de Computadoras; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina. Universidad Nacional de la Patagonia "San Juan Bosco"; ArgentinaFil: Pazos, Bruno Alfredo. Universidad Nacional del Sur. Departamento de Ingeniería Eléctrica y de Computadoras; Argentina. Universidad Nacional de la Patagonia "San Juan Bosco"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Morales, Arturo Leonardo. Universidad Nacional de la Patagonia "San Juan Bosco"; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentina. Universidad Nacional del Sur. Departamento de Ingeniería Eléctrica y de Computadoras; ArgentinaFil: Ramallo, Virginia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Paschetta, Carolina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: de Azevedo, Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Ruderman, Anahí. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Perez, Luis Orlando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; ArgentinaFil: Delrieux, Claudio Augusto. Universidad Nacional del Sur. Departamento de Ingeniería Eléctrica y de Computadoras; ArgentinaFil: Gonzalez-Jose, Rolando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico de Ciencias Sociales y Humanas; Argentin

From Fully-Supervised Single-Task to Semi-Supervised Multi-Task Deep Learning Architectures for Segmentation in Medical Imaging Applications

Medical imaging is routinely performed in clinics worldwide for the diagnosis and treatment of numerous medical conditions in children and adults. With the advent of these medical imaging modalities, radiologists can visualize both the structure of the body as well as the tissues within the body. However, analyzing these high-dimensional (2D/3D/4D) images demands a significant amount of time and effort from radiologists. Hence, there is an ever-growing need for medical image computing tools to extract relevant information from the image data to help radiologists perform efficiently. Image analysis based on machine learning has pivotal potential to improve the entire medical imaging pipeline, providing support for clinical decision-making and computer-aided diagnosis. To be effective in addressing challenging image analysis tasks such as classification, detection, registration, and segmentation, specifically for medical imaging applications, deep learning approaches have shown significant improvement in performance. While deep learning has shown its potential in a variety of medical image analysis problems including segmentation, motion estimation, etc., generalizability is still an unsolved problem and many of these successes are achieved at the cost of a large pool of datasets. For most practical applications, getting access to a copious dataset can be very difficult, often impossible. Annotation is tedious and time-consuming. This cost is further amplified when annotation must be done by a clinical expert in medical imaging applications. Additionally, the applications of deep learning in the real-world clinical setting are still limited due to the lack of reliability caused by the limited prediction capabilities of some deep learning models. Moreover, while using a CNN in an automated image analysis pipeline, it’s critical to understand which segmentation results are problematic and require further manual examination. To this extent, the estimation of uncertainty calibration in a semi-supervised setting for medical image segmentation is still rarely reported. This thesis focuses on developing and evaluating optimized machine learning models for a variety of medical imaging applications, ranging from fully-supervised, single-task learning to semi-supervised, multi-task learning that makes efficient use of annotated training data. The contributions of this dissertation are as follows: (1) developing a fully-supervised, single-task transfer learning for the surgical instrument segmentation from laparoscopic images; and (2) utilizing supervised, single-task, transfer learning for segmenting and digitally removing the surgical instruments from endoscopic/laparoscopic videos to allow the visualization of the anatomy being obscured by the tool. The tool removal algorithms use a tool segmentation mask and either instrument-free reference frames or previous instrument-containing frames to fill in (inpaint) the instrument segmentation mask; (3) developing fully-supervised, single-task learning via efficient weight pruning and learned group convolution for accurate left ventricle (LV), right ventricle (RV) blood pool and myocardium localization and segmentation from 4D cine cardiac MR images; (4) demonstrating the use of our fully-supervised memory-efficient model to generate dynamic patient-specific right ventricle (RV) models from cine cardiac MRI dataset via an unsupervised learning-based deformable registration field; and (5) integrating a Monte Carlo dropout into our fully-supervised memory-efficient model with inherent uncertainty estimation, with the overall goal to estimate the uncertainty associated with the obtained segmentation and error, as a means to flag regions that feature less than optimal segmentation results; (6) developing semi-supervised, single-task learning via self-training (through meta pseudo-labeling) in concert with a Teacher network that instructs the Student network by generating pseudo-labels given unlabeled input data; (7) proposing largely-unsupervised, multi-task learning to demonstrate the power of a simple combination of a disentanglement block, variational autoencoder (VAE), generative adversarial network (GAN), and a conditioning layer-based reconstructor for performing two of the foremost critical tasks in medical imaging — segmentation of cardiac structures and reconstruction of the cine cardiac MR images; (8) demonstrating the use of 3D semi-supervised, multi-task learning for jointly learning multiple tasks in a single backbone module – uncertainty estimation, geometric shape generation, and cardiac anatomical structure segmentation of the left atrial cavity from 3D Gadolinium-enhanced magnetic resonance (GE-MR) images. This dissertation summarizes the impact of the contributions of our work in terms of demonstrating the adaptation and use of deep learning architectures featuring different levels of supervision to build a variety of image segmentation tools and techniques that can be used across a wide spectrum of medical image computing applications centered on facilitating and promoting the wide-spread computer-integrated diagnosis and therapy data science

Enhancing Mesh Deformation Realism: Dynamic Mesostructure Detailing and Procedural Microstructure Synthesis

Propomos uma solução para gerar dados de mapas de relevo dinâmicos para simular deformações em superfícies macias, com foco na pele humana. A solução incorpora a simulação de rugas ao nível mesoestrutural e utiliza texturas procedurais para adicionar detalhes de microestrutura estáticos. Oferece flexibilidade além da pele humana, permitindo a geração de padrões que imitam deformações em outros materiais macios, como couro, durante a animação. As soluções existentes para simular rugas e pistas de deformação frequentemente dependem de hardware especializado, que é dispendioso e de difícil acesso. Além disso, depender exclusivamente de dados capturados limita a direção artística e dificulta a adaptação a mudanças. Em contraste, a solução proposta permite a síntese dinâmica de texturas que se adaptam às deformações subjacentes da malha de forma fisicamente plausível. Vários métodos foram explorados para sintetizar rugas diretamente na geometria, mas sofrem de limitações como auto-interseções e maiores requisitos de armazenamento. A intervenção manual de artistas na criação de mapas de rugas e mapas de tensão permite controle, mas pode ser limitada em deformações complexas ou onde maior realismo seja necessário. O nosso trabalho destaca o potencial dos métodos procedimentais para aprimorar a geração de padrões de deformação dinâmica, incluindo rugas, com maior controle criativo e sem depender de dados capturados. A incorporação de padrões procedimentais estáticos melhora o realismo, e a abordagem pode ser estendida além da pele para outros materiais macios.We propose a solution for generating dynamic heightmap data to simulate deformations for soft surfaces, with a focus on human skin. The solution incorporates mesostructure-level wrinkles and utilizes procedural textures to add static microstructure details. It offers flexibility beyond human skin, enabling the generation of patterns mimicking deformations in other soft materials, such as leater, during animation. Existing solutions for simulating wrinkles and deformation cues often rely on specialized hardware, which is costly and not easily accessible. Moreover, relying solely on captured data limits artistic direction and hinders adaptability to changes. In contrast, our proposed solution provides dynamic texture synthesis that adapts to underlying mesh deformations. Various methods have been explored to synthesize wrinkles directly to the geometry, but they suffer from limitations such as self-intersections and increased storage requirements. Manual intervention by artists using wrinkle maps and tension maps provides control but may be limited to the physics-based simulations. Our research presents the potential of procedural methods to enhance the generation of dynamic deformation patterns, including wrinkles, with greater creative control and without reliance on captured data. Incorporating static procedural patterns improves realism, and the approach can be extended to other soft-materials beyond skin

Proceedings, MSVSCC 2014

Proceedings of the 8th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 17, 2014 at VMASC in Suffolk, Virginia

Deep Model for Improved Operator Function State Assessment

A deep learning framework is presented for engagement assessment using EEG signals. Deep learning is a recently developed machine learning technique and has been applied to many applications. In this paper, we proposed a deep learning strategy for operator function state (OFS) assessment. Fifteen pilots participated in a flight simulation from Seattle to Chicago. During the four-hour simulation, EEG signals were recorded for each pilot. We labeled 20- minute data as engaged and disengaged to fine-tune the deep network and utilized the remaining vast amount of unlabeled data to initialize the network. The trained deep network was then used to assess if a pilot was engaged during the four-hour simulation

Controllable Neural Synthesis for Natural Images and Vector Art

Neural image synthesis approaches have become increasingly popular over the last years due to their ability to generate photorealistic images useful for several applications, such as digital entertainment, mixed reality, synthetic dataset creation, computer art, to name a few. Despite the progress over the last years, current approaches lack two important aspects: (a) they often fail to capture long-range interactions in the image, and as a result, they fail to generate scenes with complex dependencies between their different objects or parts. (b) they often ignore the underlying 3D geometry of the shape/scene in the image, and as a result, they frequently lose coherency and details.My thesis proposes novel solutions to the above problems. First, I propose a neural transformer architecture that captures long-range interactions and context for image synthesis at high resolutions, leading to synthesizing interesting phenomena in scenes, such as reflections of landscapes onto water or flora consistent with the rest of the landscape, that was not possible to generate reliably with previous ConvNet- and other transformer-based approaches. The key idea of the architecture is to sparsify the transformer\u27s attention matrix at high resolutions, guided by dense attention extracted at lower image resolution. I present qualitative and quantitative results, along with user studies, demonstrating the effectiveness of the method, and its superiority compared to the state-of-the-art. Second, I propose a method that generates artistic images with the guidance of input 3D shapes. In contrast to previous methods, the use of a geometric representation of 3D shape enables the synthesis of more precise stylized drawings with fewer artifacts. My method outputs the synthesized images in a vector representation, enabling richer downstream analysis or editing in interactive applications. I also show that the method produces substantially better results than existing image-based methods, in terms of predicting artists’ drawings and in user evaluation of results