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Carlos Uribe

Publications and source records attributed to Carlos Uribe.

17 recordsLinked to original sources

Beyond the Tumor: Recurrence-Prone Radiomics for Prognostication in Negative PSMA PET/CT scans of Prostate Cancer

In patients with biochemical recurrence of prostate cancer and negative PSMA PET/CT, radiomics features extracted from recurrence-prone organs can predict clinical progression and progression-free survival. In a cohort of 132 patients, combining PET/CT radiomics with clinical variables significantly improved prognostic performance (C-index 0.74 vs. 0.65). Model performance was influenced by reader diagnostic certainty and remained robust on external validation. These findings suggest that radiomics from visually negative scans capture subclinical disease and provide added value for risk stratification.

physics.med-ph

Predictive Dosimetry in PSMA-Targeted Radiopharmaceutical Therapies: A PBPK Modeling and Machine Learning Study

Predictive dosimetry is central to enabling personalized radiopharmaceutical therapy (RPT), particularly in prostate specific membrane antigen (PSMA) targeted theranostics. In this work, we develop a three layer computational framework that integrates physiologically based pharmacokinetic (PBPK) modeling with machine learning (ML) to predict both physical (AUC, absorbed dose) and biological (BED, EQD2) dosimetric endpoints in tumors and major organs. In the first layer, we generated 640 virtual patients using PBPK simulations of F-18, Ga-68, and Cu-64 labeled PSMA PET tracers paired with Lu-177 PSMA therapy, producing 15360 tumor and organ time activity curves (TACs) under realistic biological variability and PET-like noise. In the second layer, TACs were transformed into quantitative kinetic features and mapped to physical and biological dose metrics. In the third layer, ML models (Random Forest, Extra Trees, Ridge, Gradient Boosting, and XGBoost) were trained to predict RPT doses from PET derived features, with performance evaluated using mean absolute percentage error (MAPE) and R2. Cu-64 PSMA-617 based PET yielded the most robust predictions, achieving tumor dose MAPE as low as 8 percent and 10 to 20 percent for normal organs, while F-18 DCFPyL showed volume dependent performance and Ga-68 PSMA-11 exhibited higher variability. SHAP analysis revealed that peak uptake, clearance, and early kinetic features dominated predictive performance across organs and endpoints. This PBPK ML framework enables scalable, physiology informed predictive dosimetry and provides a foundation for trial design and patient specific treatment planning in PSMA targeted RPT. These results demonstrate that pre therapy PET can serve as a reliable surrogate for post therapy dosimetry, enabling scalable personalization of PSMA targeted RPT.

physics.med-ph

Click, Predict, Trust: Clinician-in-the-Loop AI Segmentation for Lung Cancer CT-Based Prognosis within the Knowledge-to-Action Framework

Lung cancer remains the leading cause of cancer mortality, with CT imaging central to screening, prognosis, and treatment. Manual segmentation is variable and time-intensive, while deep learning (DL) offers automation but faces barriers to clinical adoption. Guided by the Knowledge-to-Action framework, this study develops a clinician-in-the-loop DL pipeline to enhance reproducibility, prognostic accuracy, and clinical trust. Multi-center CT data from 999 patients across 12 public datasets were analyzed using five DL models (3D Attention U-Net, ResUNet, VNet, ReconNet, SAM-Med3D), benchmarked against expert contours on whole and click-point cropped images. Segmentation reproducibility was assessed using 497 PySERA-extracted radiomic features via Spearman correlation, ICC, Wilcoxon tests, and MANOVA, while prognostic modeling compared supervised (SL) and semi-supervised learning (SSL) across 38 dimensionality reduction strategies and 24 classifiers. Six physicians qualitatively evaluated masks across seven domains, including clinical meaningfulness, boundary quality, prognostic value, trust, and workflow integration. VNet achieved the best performance (Dice = 0.83, IoU = 0.71), radiomic stability (mean correlation = 0.76, ICC = 0.65), and predictive accuracy under SSL (accuracy = 0.88, F1 = 0.83). SSL consistently outperformed SL across models. Radiologists favored VNet for peritumoral representation and smoother boundaries, preferring AI-generated initial masks for refinement rather than replacement. These results demonstrate that integrating VNet with SSL yields accurate, reproducible, and clinically trusted CT-based lung cancer prognosis, highlighting a feasible path toward physician-centered AI translation.

cs.CV

Artificial intelligence for simplified patient-centered dosimetry in radiopharmaceutical therapies

KEY WORDS: Artificial Intelligence (AI), Theranostics, Dosimetry, Radiopharmaceutical Therapy (RPT), Patient-friendly dosimetry KEY POINTS - The rapid evolution of radiopharmaceutical therapy (RPT) highlights the growing need for personalized and patient-centered dosimetry. - Artificial Intelligence (AI) offers solutions to the key limitations in current dosimetry calculations. - The main advances on AI for simplified dosimetry toward patient-friendly RPT are reviewed. - Future directions on the role of AI in RPT dosimetry are discussed.

physics.med-ph

Uncertainty Propagation from Projections to Region Counts in Tomographic Imaging: Application to Radiopharmaceutical Dosimetry

Radiopharmaceutical therapies (RPTs) present a major opportunity to improve cancer therapy. Although many current RPTs use the same injected activity for all patients, there is interest in using absorbed dose measurements to enable personalized prescriptions. Image-based absorbed dose calculations incur uncertainties from calibration factors, partial volume effects and segmentation methods. While previously published dose estimation protocols incorporate these uncertainties, they do not account for uncertainty originating from the reconstruction process itself with the propagation of Poisson noise from projection data. This effect should be accounted for to adequately estimate the total uncertainty in absorbed dose estimates. This paper proposes a computationally practical algorithm that propagates uncertainty from projection data through clinical reconstruction algorithms to obtain uncertainties on the total measured counts within volumes of interest (VOIs). The algorithm is first validated on ${}^{177}$Lu and ${}^{225}$Ac phantom data by comparing estimated uncertainties from individual SPECT acquisitions to empirical estimates obtained from multiple acquisitions. It is then applied to (i) Monte Carlo and (ii) multi-time point ${}^{177}$Lu-DOTATATE and ${}^{225}$Ac-PSMA-617 patient data for time integrated activity (TIA) uncertainty estimation. The outcomes of this work are two-fold: (i) the proposed uncertainty algorithm is validated, and (ii) a blueprint is established for how the algorithm can be inform dosimetry protocols via TIA uncertainty estimation. The proposed algorithm is made publicly available in the open-source image reconstruction library PyTomography.

physics.med-ph

Computationally Efficient Collimator-Detector Response Compensation in High Energy SPECT using 1D Convolutions and Rotations

Modeling of the collimator-detector response (CDR) in SPECT reconstruction enables improved resolution and accuracy, and is thus important for quantitative imaging applications such as dosimetry. The implementation of CDR modeling, however, can become a computational bottleneck when there are substantial components of septal penetration and scatter in the acquired data, since a direct convolution-based approach requires large 2D kernels. This work proposes a 1D convolution and rotation-based CDR model that reduces reconstruction times but maintains consistency with models that employ 2D convolutions. To enable open-source development and use of these models in image reconstruction, we release a SPECTPSFToolbox repository for the PyTomography project on GitHub.

physics.med-ph

How to Segment in 3D Using 2D Models: Automated 3D Segmentation of Prostate Cancer Metastatic Lesions on PET Volumes Using Multi-angle Maximum Intensity Projections and Diffusion Models

Prostate specific membrane antigen (PSMA) positron emission tomography/computed tomography (PET/CT) imaging provides a tremendously exciting frontier in visualization of prostate cancer (PCa) metastatic lesions. However, accurate segmentation of metastatic lesions is challenging due to low signal-to-noise ratios and variable sizes, shapes, and locations of the lesions. This study proposes a novel approach for automated segmentation of metastatic lesions in PSMA PET/CT 3D volumetric images using 2D denoising diffusion probabilistic models (DDPMs). Instead of 2D trans-axial slices or 3D volumes, the proposed approach segments the lesions on generated multi-angle maximum intensity projections (MA-MIPs) of the PSMA PET images, then obtains the final 3D segmentation masks from 3D ordered subset expectation maximization (OSEM) reconstruction of 2D MA-MIPs segmentations. Our proposed method achieved superior performance compared to state-of-the-art 3D segmentation approaches in terms of accuracy and robustness in detecting and segmenting small metastatic PCa lesions. The proposed method has significant potential as a tool for quantitative analysis of metastatic burden in PCa patients.

physics.med-ph

Thyroidiomics: An Automated Pipeline for Segmentation and Classification of Thyroid Pathologies from Scintigraphy Images

The objective of this study was to develop an automated pipeline that enhances thyroid disease classification using thyroid scintigraphy images, aiming to decrease assessment time and increase diagnostic accuracy. Anterior thyroid scintigraphy images from 2,643 patients were collected and categorized into diffuse goiter (DG), multinodal goiter (MNG), and thyroiditis (TH) based on clinical reports, and then segmented by an expert. A ResUNet model was trained to perform auto-segmentation. Radiomic features were extracted from both physician (scenario 1) and ResUNet segmentations (scenario 2), followed by omitting highly correlated features using Spearman's correlation, and feature selection using Recursive Feature Elimination (RFE) with XGBoost as the core. All models were trained under leave-one-center-out cross-validation (LOCOCV) scheme, where nine instances of algorithms were iteratively trained and validated on data from eight centers and tested on the ninth for both scenarios separately. Segmentation performance was assessed using the Dice similarity coefficient (DSC), while classification performance was assessed using metrics, such as precision, recall, F1-score, accuracy, area under the Receiver Operating Characteristic (ROC AUC), and area under the precision-recall curve (PRC AUC). ResUNet achieved DSC values of 0.84$\pm$0.03, 0.71$\pm$0.06, and 0.86$\pm$0.02 for MNG, TH, and DG, respectively. Classification in scenario 1 achieved an accuracy of 0.76$\pm$0.04 and a ROC AUC of 0.92$\pm$0.02 while in scenario 2, classification yielded an accuracy of 0.74$\pm$0.05 and a ROC AUC of 0.90$\pm$0.02. The automated pipeline demonstrated comparable performance to physician segmentations on several classification metrics across different classes, effectively reducing assessment time while maintaining high diagnostic accuracy. Code available at: https://github.com/ahxmeds/thyroidiomics.git.

eess.IV

Novel Method to Estimate Kinetic Microparameters from Dynamic Whole-Body Imaging in Regular-Axial Field-of-View PET Scanners

For whole-body (WB) kinetic modeling based on a typical PET scanner, a multi-pass multi-bed scanning protocol is necessary given the limited axial field-of-view. Such a protocol introduces loss of early-dynamics in time-activity curves (TACs) and sparsity in TAC measurements, inducing uncertainty in parameter estimation when using least-squares estimation (LSE) (i.e., common standard) especially for kinetic microparameters. We present a method to reliably estimate microparameters, enabling accurate parametric imaging, on regular-axial field-of-view PET scanners. Our method, denoted parameter combination-driven estimation (PCDE), relies on generation of reference truth TAC database, and subsequently selecting, the best parameter combination as the one arriving at TAC with highest total similarity score (TSS), focusing on general image quality, overall visibility, and tumor detectability metrics. Our technique has two distinctive characteristics: 1) improved probability of having one-on-one mapping between early and late dynamics in TACs (the former missing from typical protocols), and 2) use of multiple aspects of TACs in selection of best fits. To evaluate our method against conventional LSE, we plotted tradeoff curves for noise and bias. In addition, the overall SNR and spatial noise were calculated and compared. Furthermore, CNR and TBR were also calculated. We also tested our proposed method on patient data (18F-DCFPyL PET scans) to further verify clinical applicability. Significantly improved general image quality performance was verified in microparametric images (e.g. noise-bias performance). The overall visibility and tumor detectability were also improved. Finally, for our patient studies, improved overall visibility and tumor detectability were demonstrated in micoparametric images, compared to use of conventional parameter estimation.

physics.med-ph

Investigating heterogeneous PSMA ligand uptake inside parotid glands

The purpose was to investigate the spatial heterogeneity of prostate-specific membrane antigen (PSMA) positron emission tomography (PET) uptake within parotid glands. We aim to quantify patterns in well-defined regions to facilitate further investigations. Furthermore, we investigate whether uptake is correlated with computed tomography (CT) texture features. Parotid glands from [18F]DCFPyL PSMA PET/CT images of 30 prostate cancer patients were analyzed. Thresholding was used to define high-uptake regions, and uptake statistics were computed within various divisions. Spearman's rank correlation coefficient was calculated between PSMA PET uptake and the Grey Level Run Length Matrix (GLRLM) using a long and short run length emphasis (GLRLML and GLRLMS) in subregions of parotid glands. PSMA PET uptake was significantly higher (p < 0.001) in lateral/posterior regions of the glands than anterior/medial regions. Maximum uptake was found in the lateral half of parotid glands in 50 out of 60 glands. The difference in SUV between parotid halves is greatest when parotids are divided by a plane separating the anterior/medial and posterior/lateral halves symmetrically. PSMA PET uptake was significantly correlated with CT GLRLML (p < 0.001), and anti-correlated with CT GLRLMS (p < 0.001). Uptake of PSMA PET is heterogeneous within parotid glands, with uptake biased towards lateral and posterior regions. Uptake patterns within parotid glands were found to be strongly correlated with CT texture features, suggesting the possible future use of CT texture features as a proxy for inferring PSMA PET uptake in salivary glands.

physics.med-ph

Observer study-based evaluation of TGAN architecture used to generate oncological PET images

The application of computer-vision algorithms in medical imaging has increased rapidly in recent years. However, algorithm training is challenging due to limited sample sizes, lack of labeled samples, as well as privacy concerns regarding data sharing. To address these issues, we previously developed (Bergen et al. 2022) a synthetic PET dataset for Head and Neck (H and N) cancer using the temporal generative adversarial network (TGAN) architecture and evaluated its performance segmenting lesions and identifying radiomics features in synthesized images. In this work, a two-alternative forced-choice (2AFC) observer study was performed to quantitatively evaluate the ability of human observers to distinguish between real and synthesized oncological PET images. In the study eight trained readers, including two board-certified nuclear medicine physicians, read 170 real/synthetic image pairs presented as 2D-transaxial using a dedicated web app. For each image pair, the observer was asked to identify the real image and input their confidence level with a 5-point Likert scale. P-values were computed using the binomial test and Wilcoxon signed-rank test. A heat map was used to compare the response accuracy distribution for the signed-rank test. Response accuracy for all observers ranged from 36.2% [27.9-44.4] to 63.1% [54.8-71.3]. Six out of eight observers did not identify the real image with statistical significance, indicating that the synthetic dataset was reasonably representative of oncological PET images. Overall, this study adds validity to the realism of our simulated H&N cancer dataset, which may be implemented in the future to train AI algorithms while favoring patient confidentiality and privacy protection.

physics.med-ph

PyTomography: A Python Library for Medical Image Reconstruction

There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent literature, such as those that employ artificial intelligence. The purpose of this research was to create and evaluate a GPU-accelerated, open-source, and user-friendly image reconstruction library, designed to serve as a central platform for the development, validation, and deployment of various tomographic reconstruction algorithms. PyTomography was developed using Python and inherits the GPU-accelerated functionality of PyTorch and parallelproj for fast computations. Its flexible and modular design decouples system matrices, likelihoods, and reconstruction algorithms, simplifying the process of integrating new imaging modalities using various python tools. Example use cases demonstrate the software capabilities in parallel hole SPECT and listmode PET imaging. Overall, we have developed and publicly share PyTomography, a highly optimized and user-friendly software for medical image reconstruction, with a class hierarchy that fosters the development of novel imaging applications.

physics.med-ph

Neural blind deconvolution for deblurring and supersampling PSMA PET

Objective: To simultaneously deblur and supersample prostate specific membrane antigen (PSMA) positron emission tomography (PET) images using neural blind deconvolution. Approach: Blind deconvolution is a method of estimating the hypothetical "deblurred" image along with the blur kernel (related to the point spread function) simultaneously. Traditional \textit{maximum a posteriori} blind deconvolution methods require stringent assumptions and suffer from convergence to a trivial solution. A method of modelling the deblurred image and kernel with independent neural networks, called "neural blind deconvolution" had demonstrated success for deblurring 2D natural images in 2020. In this work, we adapt neural blind deconvolution for PVE correction of PSMA PET images with simultaneous supersampling. We compare this methodology with several interpolation methods, using blind image quality metrics, and test the model's ability to predict kernels by re-running the model after applying artificial "pseudokernels" to deblurred images. The methodology was tested on a retrospective set of 30 prostate patients as well as phantom images containing spherical lesions of various volumes. Results: Neural blind deconvolution led to improvements in image quality over other interpolation methods in terms of blind image quality metrics, recovery coefficients, and visual assessment. Predicted kernels were similar between patients, and the model accurately predicted several artificially-applied pseudokernels. Localization of activity in phantom spheres was improved after deblurring, allowing small lesions to be more accurately defined. Significance: The intrinsically low spatial resolution of PSMA PET leads to PVEs which negatively impact uptake quantification in small regions. The proposed method can be used to mitigate this issue, and can be straightforwardly adapted for other imaging modalities.

physics.med-ph

$^{177}$Lu SPECT Imaging in the Presence of $^{90}$Y: Does $^{90}$Y Degrade Image Quantification? A Simulation Study

This work aims to investigate the accuracy of quantitative SPECT imaging of $^{177}$Lu in the presence of $^{90}$Y, which occurs in dual-isotope radiopharmaceutical therapy (RPT) involving both isotopes. We used the GATE Monte Carlo simulation toolkit to conduct a phantom study, simulating spheres filled with $^{177}$Lu and $^{90}$Y placed in a cylindrical water phantom that was also filled with activity of both radionuclides. We simulated multiple phantom configurations and activity combinations by varying the location of the spheres, the concentrations of $^{177}$Lu and $^{90}$Y in the spheres, and the amount of background activity. We investigated two different scatter window widths to be used with triple energy window (TEW) scatter correction. We also created multiple realizations of each configuration to improve our assessment, leading to a total of 540 simulations. Each configuration was imaged using a simulated Siemens SPECT camera. The projections were reconstructed using the standard 3D OSEM algorithm, and errors associated with $^{177}$Lu activity quantification and contrast-to-noise ratios (CNRs) were determined. In all configurations, the quantification error was within $\pm$6% of the no-$^{90}$Y case, and we found that quantitative accuracy may slightly improve when $^{90}$Y is present because of reduction of errors associated with TEW scatter correction. The CNRs were not significantly impacted by the presence of $^{90}$Y, but they were increased when a wider scatter window width was used for TEW scatter correction. The width of the scatter windows made a small but statistically significant difference of 1-2% on the recovered $^{177}$Lu activity. Based on these results, we can conclude that activity quantification of $^{177}$Lu and lesion detectability is not degraded by the presence of $^{90}$Y.

physics.med-ph

Tensor Radiomics: Paradigm for Systematic Incorporation of Multi-Flavoured Radiomics Features

Radiomics features extract quantitative information from medical images, towards the derivation of biomarkers for clinical tasks, such as diagnosis, prognosis, or treatment response assessment. Different image discretization parameters (e.g. bin number or size), convolutional filters, segmentation perturbation, or multi-modality fusion levels can be used to generate radiomics features and ultimately signatures. Commonly, only one set of parameters is used; resulting in only one value or flavour for a given RF. We propose tensor radiomics (TR) where tensors of features calculated with multiple combinations of parameters (i.e. flavours) are utilized to optimize the construction of radiomics signatures. We present examples of TR as applied to PET/CT, MRI, and CT imaging invoking machine learning or deep learning solutions, and reproducibility analyses: (1) TR via varying bin sizes on CT images of lung cancer and PET-CT images of head & neck cancer (HNC) for overall survival prediction. A hybrid deep neural network, referred to as TR-Net, along with two ML-based flavour fusion methods showed improved accuracy compared to regular rediomics features. (2) TR built from different segmentation perturbations and different bin sizes for classification of late-stage lung cancer response to first-line immunotherapy using CT images. TR improved predicted patient responses. (3) TR via multi-flavour generated radiomics features in MR imaging showed improved reproducibility when compared to many single-flavour features. (4) TR via multiple PET/CT fusions in HNC. Flavours were built from different fusions using methods, such as Laplacian pyramids and wavelet transforms. TR improved overall survival prediction. Our results suggest that the proposed TR paradigm has the potential to improve performance capabilities in different medical imaging tasks.

cs.CV

FlowNet-PET: Unsupervised Learning to Perform Respiratory Motion Correction in PET Imaging

To correct for respiratory motion in PET imaging, an interpretable and unsupervised deep learning technique, FlowNet-PET, was constructed. The network was trained to predict the optical flow between two PET frames from different breathing amplitude ranges. The trained model aligns different retrospectively-gated PET images, providing a final image with similar counting statistics as a non-gated image, but without the blurring effects. FlowNet-PET was applied to anthropomorphic digital phantom data, which provided the possibility to design robust metrics to quantify the corrections. When comparing the predicted optical flows to the ground truths, the median absolute error was found to be smaller than the pixel and slice widths. The improvements were illustrated by comparing against images without motion and computing the intersection over union (IoU) of the tumors as well as the enclosed activity and coefficient of variation (CoV) within the no-motion tumor volume before and after the corrections were applied. The average relative improvements provided by the network were 64%, 89%, and 75% for the IoU, total activity, and CoV, respectively. FlowNet-PET achieved similar results as the conventional retrospective phase binning approach, but only required one sixth of the scan duration. The code and data have been made publicly available (https://github.com/teaghan/FlowNet_PET).

eess.IV

Role of AI in Theranostics: Towards Routine Personalized Radiopharmaceutical Therapies

We highlight emerging uses of artificial intelligence (AI) in the field of theranostics, focusing on its significant potential to enable routine and reliable personalization of radiopharmaceutical therapies (RPTs). Personalized RPTs require patient-individual dosimetry calculations accompanying therapy. Image-based dosimetry needs: 1) quantitative imaging; 2) co-registration and organ/tumor identification on serial and multimodality images; 3) determination of the time-integrated activity; and 4) absorbed dose determination. AI models that facilitate these steps are reviewed. Additionally we discuss the potential to exploit biological information from diagnostic and therapeutic molecular images to derive biomarkers for absorbed dose and outcome prediction, towards personalization of therapies. We try to motivate the nuclear medicine community to expand and align efforts into making routine and reliable personalization of RPTs a reality.

physics.med-ph