Reconstruction of 3D erythrocyte or red blood cell (RBC) morphology from partial observations, such as microscope images, is essential for understanding the physiology of RBC aging and the pathology of various RBC disorders. In this study, we propose a multi-fidelity neural network (MFNN) approach to fuse high-fidelity cross-sections of an RBC, with a morphologically similar low-fidelity reference 3D RBC shape to recover its full 3D surface. The MFNN predictor combines a convolutional neural network trained on low-fidelity reference RBC data with a feedforward neural network that captures nonlinear morphological correlations, and augments training with surface area and volume constraints for regularization in the low-fidelity branch. This approach is theoretically grounded by a topological homeomorphism between a sphere and 3D RBC surfaces, with training data generated by dissipative particle dynamics simulations of stomatocyte-discocyte-echinocyte transformation. Benchmarking across diverse RBC shapes observed in normal and aged populations, our results show that the MFNN predictor can reconstruct complex RBC morphologies with over 95% coordinate accuracy when provided with at least two orthogonal cross-sections. It is observed that informative oblique cross-sections intersecting spicule tips of echinocytes improve both local and global feature reconstruction, highlighting the value of feature-aware sampling. Our study further evaluates the influence of sampling strategies, shape dissimilarity, and noise, showing enhanced robustness under physically constrained training. Altogether, these results demonstrate the capability of MFNN to reconstruct the 3D shape of normal and aged RBCs from partial cross-sections as observed in conventional microscope images, which could facilitate the quantitative analysis of RBC morphological parameters in normal and disease-related RBC samples.

Background and Objective: Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultra-structure of the brain. In this work, we introduce a freely available Matlab-based gACSON software for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes of brain tissue samples. Methods: The software is equipped with a graphical user interface (GUI). It automatically segments the intra-axonal space of myelinated axons and their corresponding myelin sheaths and allows manual segmentation, proofreading, and interactive correction of the segmented components. Results: We illustrate the use of the software by segmenting and analyzing myelinated axons in six 3D-EM volumes of rat somatosensory cortex after sham surgery or traumatic brain injury (TBI). Our results suggest that the equivalent diameter of myelinated axons in somatosensory cortex was decreased in TBI animals five months after the injury. Conclusions: Our results indicate that gACSON is a valuable tool for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes. Introduction Assessing the structure of the brain is critical to better understanding its normal and abnormal functioning. Advances in electron microscopy (EM) now allow three-dimensional (3D) imaging of hundreds of micrometers of tissue with nanometer-scale resolution, providing new opportunities to study the ultrastructure of the brain [1, 2]. Quantitative analysis of 3D-EM data, such as morphological assessment of ultrastructure, spatial distribution or connectivity of cells, requires the instance segmentation of individual ultrastructural components [3, 4, 5]. Performing this segmentation manually is tedious, if not impossible, due to the large size and enormous number of components in typical 3D-EM data.

Abstract-- We present a computational framework for simulating filaments interacting with rigid bodies through contact. Filaments are challenging to simulate due to their codimen-sionality, i.e., they are one-dimensional structures embedded in three-dimensional space. Existing methods often assume that filaments remain permanently attached to rigid bodies. Our framework unifies discrete elastic rod (DER) modeling, a pressure field patch contact model, and a convex contact formulation to accurately simulate frictional interactions between slender filaments and rigid bodies - capabilities not previously achievable. Owing to the convex formulation of contact, each time step can be solved to global optimality, guaranteeing complementarity between contact velocity and impulse. Finally, we demonstrate its applicability in both soft robotics, such as a stochastic filament-based gripper, and deformable object manipulation, such as shoelace tying, providing a versatile simulator for systems involving complex filament-filament and filament-rigid body interactions.

Despite explosive expansion of artificial intelligence based on artificial neural networks (ANNs), these are employed as "black boxes'', as it is unclear how, during learning, they form memories or develop unwanted features, including spurious memories and catastrophic forgetting. Much research is available on isolated aspects of learning ANNs, but due to their high dimensionality and non-linearity, their comprehensive analysis remains a challenge. In ANNs, knowledge is thought to reside in connection weights or in attractor basins, but these two paradigms are not linked explicitly. Here we comprehensively analyse mechanisms of memory formation in an 81-neuron Hopfield network undergoing Hebbian learning by revealing bifurcations leading to formation and destruction of attractors and their basin boundaries. We show that, by affecting evolution of connection weights, the applied stimuli induce a pitchfork and then a cascade of saddle-node bifurcations creating new attractors with their basins that can code true or spurious memories, and an abrupt disappearance of old memories (catastrophic forgetting). With successful learning, new categories are represented by the basins of newly born point attractors, and their boundaries by the stable manifolds of new saddles. With this, memorisation and forgetting represent two manifestations of the same mechanism. Our strategy to analyse high-dimensional learning ANNs is universal and applicable to recurrent ANNs of any form. The demonstrated mechanisms of memory formation and of catastrophic forgetting shed light on the operation of a wider class of recurrent ANNs and could aid the development of approaches to mitigate their flaws.

We present a novel approach to variational volume reconstruction from sparse, noisy slice data using the Deep Ritz method. Motivated by biomedical imaging applications such as MRI-based slice-to-volume reconstruction (SVR), our approach addresses three key challenges: (i) the reliance on image segmentation to extract boundaries from noisy grayscale slice images, (ii) the need to reconstruct volumes from a limited number of slice planes, and (iii) the computational expense of traditional mesh-based methods. We formulate a variational objective that combines a regression loss designed to avoid image segmentation by operating on noisy slice data directly with a modified Cahn-Hilliard energy incorporating anisotropic diffusion to regularize the reconstructed geometry. We discretize the phase field with a neural network, approximate the objective at each optimization step with Monte Carlo integration, and use ADAM to find the minimum of the approximated variational objective. While the stochastic integration may not yield the true solution to the variational problem, we demonstrate that our method reliably produces high-quality reconstructed volumes in a matter of seconds, even when the slice data is sparse and noisy.

Structural drawings are widely used in many fields, e.g., mechanical engineering, civil engineering, etc. In civil engineering, structural drawings serve as the main communication tool between architects, engineers, and builders to avoid conflicts, act as legal documentation, and provide a reference for future maintenance or evaluation needs. They are often organized using key elements such as title/subtitle blocks, scales, plan views, elevation view, sections, and detailed sections, which are annotated with standardized symbols and line types for interpretation by engineers and contractors. Despite advances in software capabilities, the task of generating a structural drawing remains labor-intensive and time-consuming for structural engineers. Here we introduce a novel generative AI-based method for generating structural drawings employing a large language model (LLM) agent. The method incorporates a retrieval-augmented generation (RAG) technique using externally-sourced facts to enhance the accuracy and reliability of the language model. This method is capable of understanding varied natural language descriptions, processing these to extract necessary information, and generating code to produce the desired structural drawing in AutoCAD. The approach developed, demonstrated and evaluated herein enables the efficient and direct conversion of a structural drawing's natural language description into an AutoCAD drawing, significantly reducing the workload compared to current working process associated with manual drawing production, facilitating the typical iterative process of engineers for expressing design ideas in a simplified way.

Since weather forecasts are fundamentally uncertain, reliable decision making requires information on the likelihoods of future weather scenarios. We explore the sensitivity of machine learning weather prediction (MLWP) using the 24h Pangu Weather ML model of Huawei to errors in the initial conditions with a specific kind of Singular Vector (SV) perturbations. Our Arnoldi-SV (A-SV) method does not need linear nor adjoint model versions and is applicable to numerical weather prediction (NWP) as well as MLWP. It observes error growth within a given optimization time window by iteratively applying a forecast model to perturbed model states. This creates a Krylov subspace, implicitly based on a matrix operator, which approximates the local error growth. Each iteration adds new dimensions to the Krylov space and its leading right SVs are expected to turn into directions of growing errors. We show that A-SV indeed finds dynamically meaningful perturbation patterns for the 24h Pangu Weather model, which grow right from the beginning of the forecast rollout. These perturbations describe local unstable modes and could be a basis to initialize MLWP ensembles. Since we start A-SV from random noise perturbations, the algorithm transforms noise into perturbations conditioned on a given reference state - a process that is akin to the denoising process of the generic diffusion based ML model of GenCast, therefor we briefly discuss similarities and differences.

Anatomical trees are critical for clinical diagnosis and treatment planning, yet their complex and diverse geometry make accurate representation a significant challenge. Motivated by the latest advances in large language models, we introduce an autoregressive method for synthesizing anatomical trees. Our approach first embeds vessel structures into a learned discrete vocabulary using a VQ-VAE architecture, then models their generation autoregressively with a GPT-2 model. This method effectively captures intricate geometries and branching patterns, enabling realistic vascular tree synthesis. Comprehensive qualitative and quantitative evaluations reveal that our technique achieves high-fidelity tree reconstruction with compact discrete representations. Moreover, our B-spline representation of vessel cross-sections preserves critical morphological details that are often overlooked in previous' methods parameterizations. To the best of our knowledge, this work is the first to generate blood vessels in an autoregressive manner. Code is available at https://github.com/LIA-DiTella/VesselGPT-MICCAI.