Mahdi Saleh

Lennart Bastian, Alexander Baumann, Emily Hoppe et al.

Statistical shape models (SSMs) are an established way to represent the anatomy of a population with various clinically relevant applications. However, they typically require domain expertise, and labor-intensive landmark annotations to construct. We address these shortcomings by proposing an unsupervised method that leverages deep geometric features and functional correspondences to simultaneously learn local and global shape structures across population anatomies. Our pipeline significantly improves unsupervised correspondence estimation for SSMs compared to baseline methods, even on highly irregular surface topologies. We demonstrate this for two different anatomical structures: the thyroid and a multi-chamber heart dataset. Furthermore, our method is robust enough to learn from noisy neural network predictions, potentially enabling scaling SSMs to larger patient populations without manual segmentation annotation.

Miruna-Alexandra Gafencu, Yordanka Velikova, Mahdi Saleh et al.

Purpose: Ultrasound (US) imaging, while advantageous for its radiation-free nature, is challenging to interpret due to only partially visible organs and a lack of complete 3D information. While performing US-based diagnosis or investigation, medical professionals therefore create a mental map of the 3D anatomy. In this work, we aim to replicate this process and enhance the visual representation of anatomical structures. Methods: We introduce a point-cloud-based probabilistic DL method to complete occluded anatomical structures through 3D shape completion and choose US-based spine examinations as our application. To enable training, we generate synthetic 3D representations of partially occluded spinal views by mimicking US physics and accounting for inherent artifacts. Results: The proposed model performs consistently on synthetic and patient data, with mean and median differences of 2.02 and 0.03 in CD, respectively. Our ablation study demonstrates the importance of US physics-based data generation, reflected in the large mean and median difference of 11.8 CD and 9.55 CD, respectively. Additionally, we demonstrate that anatomic landmarks, such as the spinous process (with reconstruction CD of 4.73) and the facet joints (mean distance to GT of 4.96mm) are preserved in the 3D completion. Conclusion: Our work establishes the feasibility of 3D shape completion for lumbar vertebrae, ensuring the preservation of level-wise characteristics and successful generalization from synthetic to real data. The incorporation of US physics contributes to more accurate patient data completions. Notably, our method preserves essential anatomic landmarks and reconstructs crucial injections sites at their correct locations. The generated data and source code will be made publicly available (https://github.com/miruna20/Shape-Completion-in-the-Dark).

Mahdi Saleh, Michael Sommersperger, Nassir Navab et al.

In robotics, it's crucial to understand object deformation during tactile interactions. A precise understanding of deformation can elevate robotic simulations and have broad implications across different industries. We introduce a method using Physics-Encoded Graph Neural Networks (GNNs) for such predictions. Similar to robotic grasping and manipulation scenarios, we focus on modeling the dynamics between a rigid mesh contacting a deformable mesh under external forces. Our approach represents both the soft body and the rigid body within graph structures, where nodes hold the physical states of the meshes. We also incorporate cross-attention mechanisms to capture the interplay between the objects. By jointly learning geometry and physics, our model reconstructs consistent and detailed deformations. We've made our code and dataset public to advance research in robotic simulation and grasping.

Burak Bekci, Nassir Navab, Federico Tombari et al.

Shape completion, a crucial task in 3D computer vision, involves predicting and filling the missing regions of scanned or partially observed objects. Current methods expect known pose or canonical coordinates and do not perform well under varying rotations, limiting their real-world applicability. We introduce ESCAPE (Equivariant Shape Completion via Anchor Point Encoding), a novel framework designed to achieve rotation-equivariant shape completion. Our approach employs a distinctive encoding strategy by selecting anchor points from a shape and representing all points as a distance to all anchor points. This enables the model to capture a consistent, rotation-equivariant understanding of the object's geometry. ESCAPE leverages a transformer architecture to encode and decode the distance transformations, ensuring that generated shape completions remain accurate and equivariant under rotational transformations. Subsequently, we perform optimization to calculate the predicted shapes from the encodings. Experimental evaluations demonstrate that ESCAPE achieves robust, high-quality reconstructions across arbitrary rotations and translations, showcasing its effectiveness in real-world applications without additional pose estimation modules.