To create a Python-based toolbox to simulate commonly occurring artifacts for single voxel gamma-aminobutyric acid (GABA)-edited MRS data. The toolbox was designed to maximize user flexibility and contains artifact, applied, input/output (I/O), and support functions. The artifact functions can produce spurious echoes, eddy currents, nuisance peaks, line broadening, baseline contamination, linear frequency drifts, and frequency and phase shift artifacts. Applied functions combine or apply specific parameter values to produce recognizable effects such as lipid peak and motion contamination. I/O and support functions provide additional functionality to accommodate different kinds of input data (MATLAB FID-A.mat files, NIfTI-MRS files), which vary by domain (time vs. frequency), MRS data type (e.g., edited vs. non-edited) and scale. A frequency and phase correction machine learning model experiment trained on corrupted simulated data and validated on in vivo data is shown to highlight the utility of our toolbox. Data simulated from the toolbox are complementary for research applications, as demonstrated by training a frequency and phase correction deep learning model that is applied to in vivo data containing artifacts. Visual assessment also confirms the resemblance of simulated artifacts compared to artifacts found in in vivo data. Our easy to install Python artifact simulated toolbox SMART_MRS is useful to enhance the diversity and quality of existing simulated edited-MRS data and is complementary to existing MRS simulation software.

Coronary artery calcium (CAC) scoring is an important method for cardiovascular risk assessment. While artificial intelligence (AI) has been applied to automate CAC scoring in calcium scoring computed tomography (CSCT), its application to low-dose computed tomography (LDCT) scans, typically used for lung cancer screening, remains challenging due to the lower image quality and higher noise levels of LDCT. This study presents a diffusion model-based method for converting LDCT to CSCT images with the aim of improving CAC scoring accuracy from LDCT scans. A conditional diffusion model was developed to generate CSCT images from LDCT by modifying the denoising diffusion implicit model (DDIM) sampling process. Two main modifications were introduced: (1) random pointing, a novel sampling technique that enhances the trajectory guidance methodology of DDIM using stochastic Gaussian noise to optimize domain adaptation, and (2) intermediate sampling, an advanced methodology that strategically injects minimal noise into LDCT images prior to sampling to maximize structural preservation. The model was trained on LDCT and CSCT images obtained from the same patients but acquired separately at different time points and patient positions, and validated on 37 test cases. The proposed method showed superior performance compared to widely used image-to-image models (CycleGAN, CUT, DCLGAN, NEGCUT) across several evaluation metrics, including peak signal-to-noise ratio (39.93 ± 0.44), Local Normalized Cross-Correlation (0.97 ± 0.01), structural similarity index (0.97 ± 0.01), and Dice similarity coefficient (0.73 ± 0.10). The modifications to the sampling process reduced the number of iterations from 1000 to 10 while maintaining image quality. Volumetric analysis indicated a stronger correlation between the calcium volumes in the enhanced CSCT images and expert-verified annotations, as compared to the original LDCT images. The proposed method effectively transforms LDCT images to CSCT images while preserving anatomical structures and calcium deposits. The reduction in sampling time and the improved preservation of calcium structures suggest that the method could be applicable for clinical use in cardiovascular risk assessment.

In radiotherapy planning, acquiring both magnetic resonance (MR) and computed tomography (CT) images is crucial for comprehensive evaluation and treatment. However, simultaneous acquisition of MR and CT images is time-consuming, economically expensive, and involves ionizing radiation, which poses health risks to patients. The objective of this study is to generate CT images from radiation-free MR images using a novel quasi-supervised learning framework. In this work, we propose a quasi-supervised framework to explore the underlying relationship between unpaired MR and CT images. Normalized mutual information (NMI) is employed as a similarity metric to evaluate the correspondence between MR and CT scans. To establish optimal pairings, we compute an NMI matrix across the training set and apply the Hungarian algorithm for global matching. The resulting MR-CT pairs, along with their NMI scores, are treated as prior knowledge and integrated into the training process to guide the MR-to-CT image translation model. Experimental results indicate that the proposed method significantly outperforms existing unsupervised image synthesis methods in terms of both image quality and consistency of image features during the MR to CT image conversion process. The generated CT images show a higher degree of accuracy and fidelity to the original MR images, ensuring better preservation of anatomical details and structural integrity. This study proposes a quasi-supervised framework that converts unpaired MR and CT images into structurally consistent pseudo-pairs, providing informative priors to enhance cross-modality image synthesis. This strategy not only improves the accuracy and reliability of MR-CT conversion, but also reduces reliance on costly and scarce paired datasets. The proposed framework offers a practical 1 and scalable solution for real-world medical imaging applications, where paired annotations are often unavailable.

Disparity among gender and ethnicity remains an issue across medicine and health science. Only 26%-35% of trainee radiologists are female, despite more than 50% of medical students' being female. Similar gender disparities are evident across the medical imaging professions. Generative artificial intelligence text-to-image production could reinforce or amplify gender biases. <b>Methods:</b> In March 2024, DALL-E 3 was utilized via GPT-4 to generate a series of individual and group images of medical imaging professionals: radiologist, nuclear medicine physician, radiographer, nuclear medicine technologist, medical physicist, radiopharmacist, and medical imaging nurse. Multiple iterations of images were generated using a variety of prompts. Collectively, 120 images were produced for evaluation of 524 characters. All images were independently analyzed by 3 expert reviewers from medical imaging professions for apparent gender and skin tone. <b>Results:</b> Collectively (individual and group images), 57.4% (<i>n</i> = 301) of medical imaging professionals were depicted as male, 42.4% (<i>n</i> = 222) as female, and 91.2% (<i>n</i> = 478) as having a light skin tone. The male gender representation was 65% for radiologists, 62% for nuclear medicine physicians, 52% for radiographers, 56% for nuclear medicine technologists, 62% for medical physicists, 53% for radiopharmacists, and 26% for medical imaging nurses. For all professions, this overrepresents men compared with women. There was no representation of persons with a disability. <b>Conclusion:</b> This evaluation reveals a significant overrepresentation of the male gender associated with generative artificial intelligence text-to-image production using DALL-E 3 across the medical imaging professions. Generated images have a disproportionately high representation of white men, which is not representative of the diversity of the medical imaging professions.

Purpose: Visualization of subcortical gray matter is essential in neuroscience and clinical practice, particularly for disease understanding and surgical planning.While multi-inversion time (multi-TI) T$_1$-weighted (T$_1$-w) magnetic resonance (MR) imaging improves visualization, it is rarely acquired in clinical settings. Approach: We present SyMTIC (Synthetic Multi-TI Contrasts), a deep learning method that generates synthetic multi-TI images using routinely acquired T$_1$-w, T$_2$-weighted (T$_2$-w), and FLAIR images. Our approach combines image translation via deep neural networks with imaging physics to estimate longitudinal relaxation time (T$_1$) and proton density (PD) maps. These maps are then used to compute multi-TI images with arbitrary inversion times. Results: SyMTIC was trained using paired MPRAGE and FGATIR images along with T$_2$-w and FLAIR images. It accurately synthesized multi-TI images from standard clinical inputs, achieving image quality comparable to that from explicitly acquired multi-TI data.The synthetic images, especially for TI values between 400-800 ms, enhanced visualization of subcortical structures and improved segmentation of thalamic nuclei. Conclusion: SyMTIC enables robust generation of high-quality multi-TI images from routine MR contrasts. It generalizes well to varied clinical datasets, including those with missing FLAIR images or unknown parameters, offering a practical solution for improving brain MR image visualization and analysis.

Glioblastoma is among the most aggressive brain tumors in adults, characterized by patient-specific invasion patterns driven by the underlying brain microstructure. In this work, we present a proof-of-concept for a mathematical model of GBL growth, enabling real-time prediction and patient-specific parameter identification from longitudinal neuroimaging data. The framework exploits a diffuse-interface mathematical model to describe the tumor evolution and a reduced-order modeling strategy, relying on proper orthogonal decomposition, trained on synthetic data derived from patient-specific brain anatomies reconstructed from magnetic resonance imaging and diffusion tensor imaging. A neural network surrogate learns the inverse mapping from tumor evolution to model parameters, achieving significant computational speed-up while preserving high accuracy. To ensure robustness and interpretability, we perform both global and local sensitivity analyses, identifying the key biophysical parameters governing tumor dynamics and assessing the stability of the inverse problem solution. These results establish a methodological foundation for future clinical deployment of patient-specific digital twins in neuro-oncology.

Sodium neuroimaging provides unique insights into the cellular and metabolic properties of brain tumors. However, at 3T, sodium neuroimaging MRI's low signal-to-noise ratio (SNR) and resolution discourages routine clinical use. We evaluated the recently developed Anatomically constrained GAN using physics-based synthetic MRI artifacts" (ATHENA) for high-resolution sodium neuroimaging of brain tumors at 3T. We hypothesized the model would improve the image quality while preserving the inherent sodium information. 4,573 proton MRI scans from 1,390 suspected brain tumor patients were used for training. Sodium and proton MRI datasets from Twenty glioma patients were collected for validation. Twenty-four image-guided biopsies from seven patients were available for sodium-proton exchanger (NHE1) expression evaluation on immunohistochemistry. High-resolution synthetic sodium images were generated using the ATHENA model, then compared to native sodium MRI and NHE1 protein expression from image-guided biopsy samples. The ATHENA produced synthetic-sodium MR with significantly improved SNR (native SNR 18.20 ± 7.04; synthetic SNR 23.83 ± 9.33, P = 0.0079). The synthetic-sodium values were consistent with the native measurements (P = 0.2058), with a strong linear correlation within contrast-enhancing areas of the tumor (R² = 0.7565, P = 0.0005), T2-hyperintense (R² = 0.7325, P < 0.0001), and necrotic areas (R² = 0.7678, P < 0.0001). The synthetic-sodium MR and the relative NHE1 expression from image-guided biopsies were better correlated for the synthetic (ρ = 0.3269, P < 0.0001) than the native (ρ = 0.1732, P = 0.0276) with higher sodium signal in samples expressing elevated NHE1 (P < 0.0001). ATHENA generates high-resolution synthetic-sodium MRI at 3T, enabling clinically attainable multinuclear imaging for brain tumors that retain the inherent information from the native sodium. The resulting synthetic sodium significantly correlates with tissue expression, potentially supporting its utility as a non-invasive marker of underlying sodium homeostasis in brain tumors.

Compound figures, which are multi-panel composites containing diverse subfigures, are ubiquitous in biomedical literature, yet large-scale subfigure extraction remains largely unaddressed. Prior work on subfigure extraction has been limited in both dataset size and generalizability, leaving a critical open question: How does high-fidelity image-text alignment via large-scale subfigure extraction impact representation learning in vision-language models? We address this gap by introducing a scalable subfigure extraction pipeline based on transformer-based object detection, trained on a synthetic corpus of 500,000 compound figures, and achieving state-of-the-art performance on both ImageCLEF 2016 and synthetic benchmarks. Using this pipeline, we release OPEN-PMC-18M, a large-scale high quality biomedical vision-language dataset comprising 18 million clinically relevant subfigure-caption pairs spanning radiology, microscopy, and visible light photography. We train and evaluate vision-language models on our curated datasets and show improved performance across retrieval, zero-shot classification, and robustness benchmarks, outperforming existing baselines. We release our dataset, models, and code to support reproducible benchmarks and further study into biomedical vision-language modeling and representation learning.

Multi-modal brain magnetic resonance imaging (MRI) plays a crucial role in clinical diagnostics by providing complementary information across different imaging modalities. However, a common challenge in clinical practice is missing MRI modalities. In this paper, we apply SwinUNETR to the synthesize of missing modalities in brain MRI. SwinUNETR is a novel neural network architecture designed for medical image analysis, integrating the strengths of Swin Transformer and convolutional neural networks (CNNs). The Swin Transformer, a variant of the Vision Transformer (ViT), incorporates hierarchical feature extraction and window-based self-attention mechanisms, enabling it to capture both local and global contextual information effectively. By combining the Swin Transformer with CNNs, SwinUNETR merges global context awareness with detailed spatial resolution. This hybrid approach addresses the challenges posed by the varying modality characteristics and complex brain structures, facilitating the generation of accurate and realistic synthetic images. We evaluate the performance of SwinUNETR on brain MRI datasets and demonstrate its superior capability in generating clinically valuable images. Our results show significant improvements in image quality, anatomical consistency, and diagnostic value.

Deep learning models trained with spatial omics data uncover complex patterns and relationships among cells, genes, and proteins in a high-dimensional space. State-of-the-art in silico spatial multi-cell gene expression methods using histological images of tissue stained with hematoxylin and eosin (H&E) allow us to characterize cellular heterogeneity. We developed a vision transformer (ViT) framework to map histological signatures to spatial single-cell transcriptomic signatures, named SPiRiT. SPiRiT predicts single-cell spatial gene expression using the matched H&E image tiles of human breast cancer and whole mouse pup, evaluated by Xenium (10x Genomics) datasets. Importantly, SPiRiT incorporates rigorous strategies to ensure reproducibility and robustness of predictions and provides trustworthy interpretation through attention-based model explainability. SPiRiT model interpretation revealed the areas, and attention details it uses to predict gene expressions like marker genes in invasive cancer cells. In an apple-to-apple comparison with ST-Net, SPiRiT improved the predictive accuracy by 40%. These gene predictions and expression levels were highly consistent with the tumor region annotation. In summary, SPiRiT highlights the feasibility to infer spatial single-cell gene expression using tissue morphology in multiple-species.