biomedical imaging engineers

Abstract: Photoacoustic tomography (PAT) is a hybrid imaging modality that combines high optical contrast with high ultrasonic resolution for biomedical imaging applications. In this work, we investigate the inverse problem of recovering the initial pressure distribution from boundary measurements in the presence of nonlinear acoustic propagation and viscous attenuation effects. To model these phenomena more accurately, we consider a nonlinear damped viscoelastic wave equation incorporating spatially varying sound speed, temporal attenuation, and nonlinear propagation mechanisms. We first establish the well-posedness of the corresponding forward problem using a Galerkin approximation combined with energy estimates and a fixed-point argument. For the inverse problem, we derive existence, uniqueness, and local uniqueness results under suitable assumptions through a harmonic extension reduction, spectral Laplace transform techniques, and observability estimates. To numerically reconstruct the initial pressure field, we develop a hybrid reconstruction framework that combines a convolutional neural network (CNN) with a gradient-free optimization strategy based on the sequential quadratic Hamiltonian (SQH) method derived from Pontryagin's maximum principle. The CNN is used to generate an informative initial guess, while the SQH framework enforces the governing PDE dynamics during the reconstruction process. Numerical experiments demonstrate that the proposed hybrid strategy significantly improves reconstruction quality, contrast, and robustness compared to standalone time-reversal and CNN-based approaches.

Abstract: In scanning microscopy, drift causes the specimen to be sampled at positions displaced from the nominal probe positions. This displacement alters the spatial assignment of the recorded signals and biases quantitative measurements across two-dimensional imaging, channel-resolved spectroscopic mapping, and scan-position-resolved diffraction analysis. Here, we extend orthogonal-scan drift correction from 2D images to spectrum images and diffraction datasets. We demonstrate how to recover probe positions using either differently oriented multidimensional scans or structural reference images. The recovered positions are used either to resample the multidimensional data onto a regular grid or to assign each recorded signal to its corrected coordinate. Our method combines affine and non-rigid correction, requires no prior structural model, and is implemented as open-source, GPU-accelerated software that reduces processing times by two to three orders of magnitude, enabling routine and automated drift correction for quantitative multidimensional microscopy.

Abstract: The inverse problem of reconstructing optical properties, specifically absorption and scattering coefficients, in layered biological media from time-domain reflectance measurements remains a significant challenge for traditional analytical models. Inverse solvers based on the diffusion equation often struggle with structural heterogeneity, frequently yielding poor accuracy for superficial absorption and deep-layers scattering. In this work, we propose a machine learning framework as an alternative approach to reconstruct the optical properties of a bilayered medium, benchmarking its efficiency and accuracy against model-based algorithms. To overcome the intrinsic approximations of diffusion theory and inverse reconstruction, we generated a robust synthetic dataset of forward DTOF using exact Monte Carlo simulations at multiple source-detector distances. A machine learning pipeline was then trained on this dataset and validated against state-of-the-art model-based reconstruction methods. Besides the significant reconstruction speed-up, the machine learning approach achieves higher accuracy than model-based inverse solvers, further providing an estimate of the parameter space dimensionality without requiring any a priori information about the number of layers in the investigated geometry. Further enhancements in the reconstruction accuracy can be expected in future extensions of this work, by training the pipeline over multiple DTOF curves from the same medium, in a joint multi-distance reconstruction approach.

Abstract: Nanoscale imaging of mammalian brains is critical for connectomics. X-ray laminography enables high-throughput imaging of extended, plate-like biological specimens. However, the tilted acquisition geometry leads to incomplete Fourier-space coverage, giving rise to a missing-cone of information. Conventional reconstruction methods cannot recover unmeasured information within the cone, resulting in artifacts that distort fine brain structures. While resolving these requires modeling 3D structure, direct 3D deep learning approaches are limited by data scarcity and computational cost. Here we introduce LUCID (Laminography with Unified Consistent Diffusion), a framework that combines multi-view diffusion priors with projection-domain data consistency. LUCID integrates complementary 3D structural information while enforcing strict alignment with the laminography forward model. On simulated datasets, LUCID substantially improves spatial fidelity and restores missing Fourier components, outperforming baseline methods. Applied to experimental laminography data, LUCID generalizes robustly despite being trained exclusively on fully sampled tomographic volumes, and effectively recovers unmeasured Fourier information.