Photoacoustic Tomography

Combined optoacoustic (OptA) and ultrasound imaging is a promising modality across a wide range of pathologies. Its use in clinical research, however, is limited by a lack of analysis software accessible to users without programming expertise. Existing tools are either script-based engineering frameworks or proprietary vendor applications. We present OPTARI, an open-source graphical software application to facilitate large-scale clinical optoacoustic-ultrasound (OPUS) studies. OPTARI builds on the napari image viewer and the PATATO toolkit for OptA data processing. It supports native vendor and open HDF5 data formats, aligns with the IPASC standard, and is distributed as a standalone executable. Features include region-of-interest annotation, reconstruction, chromophore unmixing, deep-learning-based tissue segmentation, and temporal and spectral analysis modules. OPTARI offers a combination of features for clinical study analysis that none of the compared tools provide. The automated tissue segmentation produced results comparable to expert labeling for muscle tissue, and batch processing reduced analysis time from minutes to under one second per scan. The tool is used in ongoing clinical OPUS studies. OPTARI connects engineering frameworks with medical research and provides an open-source basis for reproducible and standardized analysis in clinical OptA imaging studies.

The joint reconstruction of the initial pressure and spatially varying sound speed in photoacoustic tomography from boundary measurements is considered. A regularized data-driven framework is proposed in which the unknown fields are represented in finite-dimensional wavelet spaces and fixed nonlinear features generated by an untrained convolutional neural network (CNN) are used to reconstruct the initial-pressure coefficients through Tikhonov-regularized least squares. A learned coefficient-space prior is subsequently used to infer the squared sound-speed coefficients. Numerical experiments demonstrate accurate reconstruction on held-out data and strong generalization to previously unseen phantom geometries. The frozen reconstruction map also remains stable under measurement noise not represented during training, with only minor changes in reconstruction accuracy for noise levels up to $10\%$. In comparison with the supervised trained-CNN approach considered in this work, the untrained representation yields substantially smaller reconstruction errors while requiring approximately one-sixth of the computational time. These results demonstrate that fixed random convolutional features combined with regularized coefficient-space learning provide an efficient and robust approach to joint reconstruction in photoacoustic tomography.

We propose a data-driven framework for estimating the Bayesian Cramér-Rao bound (CRB) in high-dimensional imaging systems with complex, analytically intractable priors. Direct CRB computation is challenging in this setting due to the need to model the prior score and to form and invert the Bayesian Fisher information matrix in very high dimensions. To address these issues, we first reformulate the inverse problem in the latent space of a pre-trained variational autoencoder, thereby dramatically reducing the dimensionality of the bound estimation problem while preserving the spatial structure of the images. The Bayesian CRB is formed in this latent space and mapped back to the native parameter space using a change-of-variables formula. Second, to learn the latent prior score, we introduce a new sliced score matching objective defined in a Bochner space endowed with an $H^1(Ω)$ Sobolev norm in space. This "Bochner-space sliced score matching" objective is consistent with standard sliced score matching, but penalizes errors in the spatial gradients of the score, suppressing high-frequency artifacts that otherwise contaminate the resulting CRB estimates. We validate the approach on a stylized quantitative photoacoustic computed tomography (qPACT) breast imaging problem with over one million unknown parameters, using a foundation-model autoencoder derived from Stable Diffusion. The proposed method yields stable, artifact-free Bayesian CRB estimates that reflect the highly non-Gaussian structure of the learned prior and reveal the substantial impact of the prior on the relative performance of competing qPACT design schemes.

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.

Photoacoustic computed tomography (PACT) combines optical absorption contrast with acoustic detection for high-resolution deep-tissue imaging. A persistent challenge is that unknown speed-of-sound (SoS) heterogeneity changes acoustic time-of-flight, causing defocusing artifacts when reconstruction assumes a uniform SoS. Existing SoS-adaptive methods either rely on calibrated acoustic priors or optimize dense physical medium models, which becomes expensive and difficult to scale in 3D. We propose PAGS, a differentiable framework for blind autofocusing PACT via speed-of-sound-adaptive Gaussian splatting. PAGS represents the initial pressure field with sparse Gaussian photoacoustic (PA) sources and replaces explicit medium recovery with a compact anisotropic path-averaged SoS (ASoS) field parameterized by spherical harmonic probes. This latent propagation field directly controls source-to-transducer arrival-time alignment, while an analytic Gaussian acoustic projection maps the source representation to transducer signals efficiently. The resulting closed-loop signal-domain optimization jointly updates the Gaussian PA source parameters and the ASoS field from measured data, without calibrated SoS priors. Experiments on simulated and physical phantom data demonstrate improved reconstruction sharpness under heterogeneous acoustic media, robustness to sparse-view sampling, and computational benefits from the analytic Gaussian projection.

Photoacoustic tomography (PAT) combines the optical absorption contrast of biological tissue with the spatial resolution of ultrasound, yet recovering the initial pressure distribution from sparse-view sensor measurements remains an ill-posed inverse problem. Iterative compressive-sensing solvers and unrolled deep networks both retain a dependence on the system matrix at inference, which leaves real-time clinical reconstruction computationally expensive. This paper proposes the Sensor Attention Network (SAN), a Transformer-based architecture that treats the full time series of each sensor as a token and maps raw measurements directly to the reconstructed image without invoking the system matrix at inference. For training and benchmarking, an analytical k-space H-matrix is constructed and validated against the k-Wave pseudo-spectral solver under matched geometry, achieving a mean per-sensor Pearson correlation of 0.919 +/- 0.049, with k-space apodization and Gaussian temporal damping acting synergistically to reduce the energy-normalized mismatch by 49%. Trained with a vessel-weighted loss on 488 augmented samples and evaluated on 46 held-out samples against ISTA, split-Bregman total variation (SBTV), and learned ISTA (LISTA), SAN attains the highest mean SSIM (0.522) and PSNR (22.09 dB) and the lowest NMSE (0.233). Paired t-tests and Wilcoxon signed-rank tests confirm the superiority of SAN over LISTA on PSNR, NMSE, and Pearson correlation at p < 1e-8, and over ISTA and SBTV on all fidelity metrics. By bypassing the H-matrix at inference, SAN reduces reconstruction time by at least an order of magnitude, supporting real-time PAT reconstruction.

We study the deep image prior (DIP) framework applied to photoacoustic tomography (PAT) as an unsupervised reconstruction approach to mitigate limited-view artifacts and noise commonly encountered in experimental settings. Efficient implementation is achieved by employing recently published fast forward and adjoint algorithms for circular measurement geometries. Initialization via a fast inverse and total variation (TV) regularization are applied to further suppress noise and mitigate overfitting. For comparison, we compute a classical TV reconstruction. Our experiments comprise simulated PAT measurements under limited-view geometries and varying levels of added noise as well as experimental measurements together with using a digital twin for quality assessment. Our findings suggest that DIP framework provides an effective unsupervised strategy for robust PAT reconstruction even in the challenging case of a limited view geometry providing improvement in several quantitative measures over total variation reconstructions.

Photoacoustic tomography (PAT) is an emerging imaging modality that combines the complementary strengths of optical contrast and ultrasonic resolution. A central task is image reconstruction, where measured acoustic signals are used to recover the initial pressure distribution. For ideal point-like or line-like detectors, several efficient and fast reconstruction algorithms exist, including Fourier methods, filtered backprojection, and time reversal. However, when applied to data acquired with finite-size detectors, these methods yield systematically blurred images. Although sharper images can be obtained by compensating for finite-detector effects, supervised learning approaches typically require ground-truth images that may not be available in practice. We propose a self-supervised reconstruction method based on Noisier2Inverse that addresses finite-size detector effects without requiring ground-truth data. Our approach operates directly on noisy measurements and learns to recover high-quality PAT images in a ground-truth-free manner. Its key components are: (i) PAT-specific modeling that recasts the problem as angular deblurring; (ii) a Noisier2Inverse formulation in the polar domain that leverages the known angular point-spread function; and (iii) a novel, statistically grounded early-stopping rule. In experiments, the proposed method consistently outperforms alternative approaches that do not use supervised data and achieves performance close to supervised benchmarks, while remaining practical for real acquisitions with finite-size detectors.

Three-dimensional (3D) handheld photoacoustic tomography typically relies on bulky and expensive external positioning sensors to correct motion artifacts, which severely limits its clinical flexibility and accessibility. To address this challenge, we present PA-SFM, a tracker-free framework that leverages exclusively single-modality photoacoustic data for both sensor pose recovery and high-fidelity 3D reconstruction via differentiable acoustic radiation modeling. Unlike traditional structure-from-motion (SFM) methods based on visual features, PA-SFM integrates the acoustic wave equation into a differentiable programming pipeline. By leveraging a high-performance, GPU-accelerated acoustic radiation kernel, the framework simultaneously optimizes the 3D photoacoustic source distribution and the sensor array pose via gradient descent. To ensure robust convergence in freehand scenarios, we introduce a coarse-to-fine optimization strategy that incorporates geometric consistency checks and rigid-body constraints to eliminate motion outliers. We validated the proposed method through both numerical simulations and in-vivo rat experiments. The results demonstrate that PA-SFM achieves sub-millimeter positioning accuracy and restores high-resolution 3D vascular structures comparable to ground-truth benchmarks, offering a low-cost, software-defined solution for clinical freehand photoacoustic imaging. The source code is publicly available at https://github.com/JaegerCQ/PA-SFM.

Accurate estimation of the relative concentrations of chromophores in a spectroscopic photoacoustic (sPA) image can reveal immense structural, functional, and molecular information about physiological processes. However, due to nonlinearities and ill-posedness inherent to sPA imaging, concentration estimation is intractable. The Spectroscopic Photoacoustic Optical Inversion Autoencoder (SPOI-AE) aims to address the sPA optical inversion and spectral unmixing problems without assuming linearity. Herein, SPOI-AE was trained and tested on in vivo mouse lymph node sPA images with unknown ground truth chromophore concentrations. SPOI-AE better reconstructs input sPA pixels than conventional algorithms while providing biologically coherent estimates for optical parameters, chromophore concentrations, and the percent oxygen saturation of tissue. SPOI-AE's unmixing accuracy was validated using a simulated mouse lymph node phantom ground truth.